Ecological Therapeutic Opportunities for Oral Diseases.

PubMed

Hoare, Anilei; Marsh, Philip D; Diaz, Patricia I

2017-08-01

The three main oral diseases of humans, that is, caries, periodontal diseases, and oral candidiasis, are associated with microbiome shifts initiated by changes in the oral environment and/or decreased effectiveness of mucosal immune surveillance. In this review, we discuss the role that microbial-based therapies may have in the control of these conditions. Most investigations on the use of microorganisms for management of oral disease have been conducted with probiotic strains with some positive but very discrete clinical outcomes. Other strategies such as whole oral microbiome transplantation or modification of community function by enrichment with health-promoting indigenous oral strains may offer more promise, but research in this field is still in its infancy. Any microbial-based therapeutics for oral conditions, however, are likely to be only one component within a holistic preventive strategy that should also aim at modification of the environmental influences responsible for the initiation and perpetuation of microbiome shifts associated with oral dysbiosis.

Reptiles as Reservoirs of Bacterial Infections: Real Threat or Methodological Bias?

PubMed

Zancolli, Giulia; Mahsberg, Dieter; Sickel, Wiebke; Keller, Alexander

2015-10-01

Bacterial infections secondary to snakebites and human pathogens (e.g., Salmonella) have been linked to the oral microbiota of snakes and pet reptiles. Based on culture-dependent studies, it is speculated that snakes' oral microbiota reflects the fecal flora of their ingested preys. However, cultured-based techniques have been shown to be limited as they fail to identify unculturable microorganisms which represent the vast majority of the microbial diversity. Here, we used culture-independent high-throughput sequencing to identify reptile-associated pathogens and to characterize the oral microbial community of five snakes, one gecko, and two terrapins. Few potential human pathogens were detected at extremely low frequencies. Moreover, bacterial taxa represented in the snake's oral cavity bore little resemblance to their preys' fecal microbiota. Overall, we found distinct, highly diverse microbial communities with consistent, species-specific patterns contrary to previous culture-based studies. Our study does not support the widely held assumption that reptiles' oral cavity acts as pathogen reservoir and provides important insights for future research.

Therapeutic Application of Synbiotics, a Fusion of Probiotics and Prebiotics, and Biogenics as a New Concept for Oral Candida Infections: A Mini Review

PubMed Central

Ohshima, Tomoko; Kojima, Yukako; Seneviratne, Chaminda J.; Maeda, Nobuko

2016-01-01

Candida is a major human fungal pathogen causing infectious conditions predominantly in the elderly and immunocompromised hosts. Although Candida resides as a member of the oral indigenous microbiota in symbiosis, some circumstances may cause microbial imbalance leading to dysbiosis and resultant oral candidiasis. Therefore, oral microbial symbiosis that suppresses the overgrowth of Candida is important for a healthy oral ecosystem. In this regard, probiotics, prebiotics, and synbiotics can be considered a potential therapeutic and preventive strategy against oral candidiasis. Prebiotics have a direct effect on microbial growth as they stimulate the growth of beneficial bacteria and suppress the growth of pathogens. Probiotics render a local protective effect against pathogens and a systemic indirect effect on immunological amelioration. Synbiotics are fusion products of prebiotics and probiotics. This mini review discusses the potential use and associated limitations of probiotics, prebiotics, and synbiotics for the prevention and treatment of oral candidiasis. We will also introduce biogenics, a recent concept derived from the work on probiotics. Biogenics advocates the use of beneficial bioactive substances produced by probiotic bacteria, whose activities are independent from the viability of probiotic bacteria in human bodies. PMID:26834728

The Effect of Fixed Orthodontic Appliances and Fluoride Mouthwash on the Oral Microbiome of Adolescents – A Randomized Controlled Clinical Trial

PubMed Central

Buijs, Mark J.; Elyassi, Yassaman; van der Veen, Monique H.; Crielaard, Wim; ten Cate, Jacob M.; Zaura, Egija

2015-01-01

While the aesthetic effect of orthodontic treatment is clear, the knowledge on how it influences the oral microbiota and the consequential effects on oral health are limited. In this randomized controlled clinical trial we investigated the changes introduced in the oral ecosystem, during and after orthodontic treatment with fixed appliances in combination with or without a fluoride mouthwash, of 10–16.8 year old individuals (N = 91). We followed several clinical parameters in time, in combination with microbiome changes using next-generation sequencing of the bacterial 16S rRNA gene. During the course of our study, the oral microbial community displayed remarkable resilience towards the disturbances it was presented with. The effects of the fluoride mouthwash on the microbial composition were trivial. More pronounced microbial changes were related to gingival health status, orthodontic treatment and time. Periodontal pathogens (e.g. Selenomonas and Porphyromonas) were highest in abundance during the orthodontic treatment, while the health associated Streptococcus, Rothia and Haemophilus gained abundance towards the end and after the orthodontic treatment. Only minor compositional changes remained in the oral microbiome after the end of treatment. We conclude that, provided proper oral hygiene is maintained, changes in the oral microbiome composition resulting from orthodontic treatment are minimal and do not negatively affect oral health. PMID:26332408

The Effect of Fixed Orthodontic Appliances and Fluoride Mouthwash on the Oral Microbiome of Adolescents - A Randomized Controlled Clinical Trial.

PubMed

Koopman, Jessica E; van der Kaaij, Nicoline C W; Buijs, Mark J; Elyassi, Yassaman; van der Veen, Monique H; Crielaard, Wim; Ten Cate, Jacob M; Zaura, Egija

2015-01-01

While the aesthetic effect of orthodontic treatment is clear, the knowledge on how it influences the oral microbiota and the consequential effects on oral health are limited. In this randomized controlled clinical trial we investigated the changes introduced in the oral ecosystem, during and after orthodontic treatment with fixed appliances in combination with or without a fluoride mouthwash, of 10-16.8 year old individuals (N = 91). We followed several clinical parameters in time, in combination with microbiome changes using next-generation sequencing of the bacterial 16S rRNA gene. During the course of our study, the oral microbial community displayed remarkable resilience towards the disturbances it was presented with. The effects of the fluoride mouthwash on the microbial composition were trivial. More pronounced microbial changes were related to gingival health status, orthodontic treatment and time. Periodontal pathogens (e.g. Selenomonas and Porphyromonas) were highest in abundance during the orthodontic treatment, while the health associated Streptococcus, Rothia and Haemophilus gained abundance towards the end and after the orthodontic treatment. Only minor compositional changes remained in the oral microbiome after the end of treatment. We conclude that, provided proper oral hygiene is maintained, changes in the oral microbiome composition resulting from orthodontic treatment are minimal and do not negatively affect oral health.

Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation.

PubMed

Agnello, M; Cen, L; Tran, N C; Shi, W; McLean, J S; He, X

2017-07-01

Dental caries can be described as a dysbiosis of the oral microbial community, in which acidogenic, aciduric, and acid-adapted bacterial species promote a pathogenic environment, leading to demineralization. Alkali generation by oral microbes, specifically via arginine catabolic pathways, is an essential factor in maintaining plaque pH homeostasis. There is evidence that the use of arginine in dentifrices helps protect against caries. The aim of the current study was to investigate the mechanistic and ecological effect of arginine treatment on the oral microbiome and its regulation of pH dynamics, using an in vitro multispecies oral biofilm model that was previously shown to be highly reflective of the in vivo oral microbiome. Pooled saliva from 6 healthy subjects was used to generate overnight biofilms, reflecting early stages of biofilm maturation. First, we investigated the uptake of arginine by the cells of the biofilm as well as the metabolites generated. We next explored the effect of arginine on pH dynamics by pretreating biofilms with 75 mM arginine, followed by the addition of sucrose (15 mM) after 0, 6, 20, or 48 h. pH was measured at each time point and biofilms were collected for 16S sequencing and targeted arginine quantification, and supernatants were prepared for metabolomic analysis. Treatment with only sucrose led to a sustained pH drop from 7 to 4.5, while biofilms treated with sucrose after 6, 20, or 48 h of preincubation with arginine exhibited a recovery to higher pH. Arginine was detected within the cells of the biofilms, indicating active uptake, and arginine catabolites citrulline, ornithine, and putrescine were detected in supernatants, indicating active metabolism. Sequencing analysis revealed a shift in the microbial community structure in arginine-treated biofilms as well as increased species diversity. Overall, we show that arginine improved pH homeostasis through a remodeling of the oral microbial community.

In Vitro Effect of Porphyromonas gingivalis Methionine Gamma Lyase on Biofilm Composition and Oral Inflammatory Response.

PubMed

Stephen, Abish S; Millhouse, Emma; Sherry, Leighann; Aduse-Opoku, Joseph; Culshaw, Shauna; Ramage, Gordon; Bradshaw, David J; Burnett, Gary R; Allaker, Robert P

2016-01-01

Methanethiol (methyl mercaptan) is an important contributor to oral malodour and periodontal tissue destruction. Porphyromonas gingivalis, Prevotella intermedia and Fusobacterium nucleatum are key oral microbial species that produce methanethiol via methionine gamma lyase (mgl) activity. The aim of this study was to compare an mgl knockout strain of P. gingivalis with its wild type using a 10-species biofilm co-culture model with oral keratinocytes and its effect on biofilm composition and inflammatory cytokine production. A P. gingivalis mgl knockout strain was constructed using insertion mutagenesis from wild type W50 with gas chromatographic head space analysis confirming lack of methanethiol production. 10-species biofilms consisting of Streptococcus mitis, Streptococcus oralis, Streptococcus intermedius, Fusobacterium nucleatum ssp polymorphum, Fusobacterium nucleatum ssp vincentii, Veillonella dispar, Actinomyces naeslundii, Prevotella intermedia and Aggregatibacter actinomycetemcomitans with either the wild type or mutant P. gingivalis were grown on Thermanox cover slips and used to stimulate oral keratinocytes (OKF6-TERT2), under anaerobic conditions for 4 and 24 hours. Biofilms were analysed by quantitative PCR with SYBR Green for changes in microbial ecology. Keratinocyte culture supernatants were analysed using a multiplex bead immunoassay for cytokines. Significant population differences were observed between mutant and wild type biofilms; V. dispar proportions increased (p<0.001), whilst A. naeslundii (p<0.01) and Streptococcus spp. (p<0.05) decreased in mutant biofilms. Keratinocytes produced less IL-8, IL-6 and IL-1α when stimulated with the mutant biofilms compared to wild type. Lack of mgl in P. gingivalis has been shown to affect microbial ecology in vitro, giving rise to a markedly different biofilm composition, with a more pro-inflammatory cytokine response from the keratinocytes observed. A possible role for methanethiol in biofilm formation and cytokine response with subsequent effects on oral malodor and periodontitis is suggested.

A Reproducible Oral Microcosm Biofilm Model for Testing Dental Materials

PubMed Central

Rudney, J.D.; Chen, R.; Lenton, P.; Li, J.; Li, Y.; Jones, R.S.; Reilly, C.; Fok, A.S.; Aparicio, C.

2012-01-01

Aims Most studies of biofilm effects on dental materials use single-species biofilms, or consortia. Microcosm biofilms grown directly from saliva or plaque are much more diverse, but difficult to characterize. We used the Human Oral Microbial Identification Microarray (HOMIM) to validate a reproducible oral microcosm model. Methods and Results Saliva and dental plaque were collected from adults and children. Hydroxyapatite and dental composite disks were inoculated with either saliva or plaque, and microcosm biofilms were grown in a CDC biofilm reactor. In later experiments, the reactor was pulsed with sucrose. DNA from inoculums and microcosms were analyzed by HOMIM for 272 species. Microcosms included about 60% of species from the original inoculum. Biofilms grown on hydroxyapatite and composites were extremely similar. Sucrose-pulsing decreased diversity and pH, but increased the abundance of Streptococcus and Veilonella. Biofilms from the same donor, grown at different times, clustered together. Conclusions This model produced reproducible microcosm biofilms that were representative of the oral microbiota. Sucrose induced changes associated with dental caries. Significance and Impact of the Study This is the first use of HOMIM to validate an oral microcosm model that can be used to study the effects of complex biofilms on dental materials. PMID:22925110

The effect of inoculum source and fluid shear force on the development of in vitro oral multispecies biofilms.

PubMed

Fernández, C E; Aspiras, M B; Dodds, M W; González-Cabezas, C; Rickard, A H

2017-03-01

Saliva has been previously used as an inoculum for in vitro oral biofilm studies. However, the microbial community profile of saliva is markedly different from hard- and soft-tissue-associated oral biofilms. Here, we investigated the changes in the biofilm architecture and microbial diversity of in vitro oral biofilms developed from saliva, tongue or plaque-derived inocula under different salivary shear forces. Four inoculum types (saliva, bacteria harvested from the tongue, toothbrush and curette-harvested plaque) were collected and pooled. Biofilms (n ≥ 15) were grown for 20 h in cell-free human saliva flowing at three different shear forces. Stained biofilms were imaged using a confocal laser scanning microscope. Biomass, thickness and roughness were determined by image analysis and bacterial community composition analysed using Ion Torrent. All developed biofilms showed a significant reduction in observed diversity compared with their respective original inoculum. Shear force altered biofilm architecture of saliva and curette-collected plaque and community composition of saliva, tongue and curette-harvested plaque. Different intraoral inocula served as precursors of in vitro oral polymicrobial biofilms which can be influenced by shear. Inoculum selection and shear force are key factors to consider when developing multispecies biofilms within in vitro models. © 2016 The Society for Applied Microbiology.

Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis

PubMed Central

2011-01-01

Background Microbial communities inhabiting human mouth are associated with oral health and disease. Previous studies have indicated the general prevalence of adult gingivitis in China to be high. The aim of this study was to characterize in depth the oral microbiota of Chinese adults with or without gingivitis, by defining the microbial phylogenetic diversity and community-structure using highly paralleled pyrosequencing. Methods Six non-smoking Chinese, three with and three without gingivitis (age range 21-39 years, 4 females and 2 males) were enrolled in the present cross-sectional study. Gingival parameters of inflammation and bleeding on probing were characterized by a clinician using the Mazza Gingival Index (MGI). Plaque (sampled separately from four different oral sites) and salivary samples were obtained from each subject. Sequences and relative abundance of the bacterial 16 S rDNA PCR-amplicons were determined via pyrosequencing that produced 400 bp-long reads. The sequence data were analyzed via a computational pipeline customized for human oral microbiome analyses. Furthermore, the relative abundances of selected microbial groups were validated using quantitative PCR. Results The oral microbiomes from gingivitis and healthy subjects could be distinguished based on the distinct community structures of plaque microbiomes, but not the salivary microbiomes. Contributions of community members to community structure divergence were statistically accessed at the phylum, genus and species-like levels. Eight predominant taxa were found associated with gingivitis: TM7, Leptotrichia, Selenomonas, Streptococcus, Veillonella, Prevotella, Lautropia, and Haemophilus. Furthermore, 98 species-level OTUs were identified to be gingivitis-associated, which provided microbial features of gingivitis at a species resolution. Finally, for the two selected genera Streptococcus and Fusobacterium, Real-Time PCR based quantification of relative bacterial abundance validated the pyrosequencing-based results. Conclusions This methods study suggests that oral samples from this patient population of gingivitis can be characterized via plaque microbiome by pyrosequencing the 16 S rDNA genes. Further studies that characterize serial samples from subjects (longitudinal study design) with a larger population size may provide insight into the temporal and ecological features of oral microbial communities in clinically-defined states of gingivitis. PMID:22152152

The Oral Microbiome Bank of China.

PubMed

Xian, Peng; Xuedong, Zhou; Xin, Xu; Yuqing, Li; Yan, Li; Jiyao, Li; Xiaoquan, Su; Shi, Huang; Jian, Xu; Ga, Liao

2018-05-03

The human microbiome project (HMP) promoted further understanding of human oral microbes. However, research on the human oral microbiota has not made as much progress as research on the gut microbiota. Currently, the causal relationship between the oral microbiota and oral diseases remains unclear, and little is known about the link between the oral microbiota and human systemic diseases. To further understand the contribution of the oral microbiota in oral diseases and systemic diseases, a Human Oral Microbiome Database (HOMD) was established in the US. The HOMD includes 619 taxa in 13 phyla, and most of the microorganisms are from American populations. Due to individual differences in the microbiome, the HOMD does not reflect the Chinese oral microbial status. Herein, we established a new oral microbiome database-the Oral Microbiome Bank of China (OMBC, http://www.sklod.org/ombc ). Currently, the OMBC includes information on 289 bacterial strains and 720 clinical samples from the Chinese population, along with lab and clinical information. The OMBC is the first curated description of a Chinese-associated microbiome; it provides tools for use in investigating the role of the oral microbiome in health and diseases, and will give the community abundant data and strain information for future oral microbial studies.

Association of Colonization with Streptococcus mutans Genotypes from Mothers and Early Childhood Caries

PubMed Central

Childers, Noel K.; Momeni, Stephanie S.; Whiddon, Jennifer; Cheon, Kyounga; Cutter, Gary R.; Wiener, Howard W.; Ghazal, Tariq S.; Ruby, John D.; Moser, Stephen A.

2016-01-01

Purpose This study evaluated Streptococcus mutans (Sm) genotypes (GT) between mother and child (M-C) in a high caries risk cohort to explore the association with early childhood caries (ECC). Methods Sixty-nine infants (~1 year-old) had periodic oral examination (dmfs) and collection of microbial samples from dental plaque, saliva and oral other surfaces. Their mothers had an examination and plaque collected. Sm isolates were genotyped using repetitive extragenic palindromic-PCR (rep-PCR). Statistical analyses were conducted for associations of Sm in M-C dyads with caries outcomes. Results Twenty-seven Sm genotypes (GT) from 3,414 isolates were identified. M-C were categorized as GT Match (N=40) or no-Match (N=29). When modeling the severity of ECC at 36-months (~4 years old), the estimated dmfs in the Match group was 2.61 times that in the no-Match group (P=.014). Conclusions Colonization of children with Sm GT that matched with mothers was shown to be highly associated with ECC. Although the data suggest vertical transmission of Sm in 40 of 69 children that shared GT with their mother, it is possible that other individuals transmitted the Sm. Nonetheless, these findings support the importance of the mother's oral microbial status as a contributing influence to their children's oral health. PMID:28390463

[Modern hygiene products impact on oral microbial, pH and mineral balance].

PubMed

Gromova, S N; Rumiantsev, V A

2012-01-01

Several toothpastes are compared in the study: "Zhemchuzhnaya-complex protection" containing as abrasive substance finely dispersed dicalcium phosphate phosphathydrate, "Noviy zhemchug ftor" and "Zhemchug svezhaya myata" with calcium carbonate. "Zhemchuzhnaya-complex protection" and "Noviy zhemchug ftor" both contain sodium monophosphate as active substance. Impact of these toothpastes on oral microbial, pH and mineral balance was assessed in the study.

Oral Health and the Oral Microbiome in Pancreatic Cancer: An Overview of Epidemiological Studies.

PubMed

Bracci, Paige M

The aim was to provide a cohesive overview of epidemiological studies of periodontal disease, oral microbiome profiles, and pancreatic cancer risk. A PubMed search of articles published in English through July 2017 with additional review of bibliographies of identified articles. Risk estimates for periodontal disease associated with pancreatic cancer consistently ranged from 1.5 to 2, aligning with a meta-analysis summary relative risk of 1.74. Analyses of antibodies to pathogenic and/or commensal oral bacteria in prediagnostic blood provided evidence that some oral bacteria and oral microbial diversity may be related to pancreatic cancer. Overall, the data present a plausible but complex relationship among pancreatic cancer, the oral microbiome, periodontal disease, and other risk factors that might be explained by systemic effects on immune and inflammatory processes. Larger comprehensive studies that examine serially collected epidemiological/clinical data and blood, tissue, and various microbial samples are needed to definitively determine how and whether oral health-related factors contribute to pancreatic cancer risk.

Differences in carbon source usage by dental plaque in children with and without early childhood caries

PubMed Central

Zhao, Yan; Zhong, Wen-Jie; Xun, Zhe; Zhang, Qian; Song, Ye-Qing; Liu, Yun-Song; Chen, Feng

2017-01-01

Early childhood caries (ECC) is a considerable pediatric and public health problem worldwide. Preceding studies have focused primarily on bacterial diversity at the taxonomic level. Although these studies have provided significant information regarding the connection between dental caries and oral microbiomes, further comprehension of this microbial community’s ecological relevance is limited. This study identified the carbon source metabolic differences in dental plaque between children with and without ECC. We compared the microbial community functional diversity in 18 caries-free subjects with 18 severe ECC patients based on sole carbon source usage using a Biolog assay. The anaerobic microbial community in the ECC patients displayed greater metabolic activity than that of the control group. Specific carbon source metabolism differed significantly between the two groups. Subjects from the two groups were well distinguished by cluster and principal component analyses based on discriminative carbon sources. Our results implied that the microbial functional diversity between the ECC patients and healthy subjects differed significantly. In addition, the Biolog assay furthered our understanding of oral microbiomes as a composite of functional abilities, thus enabling us to identify the ecologically relevant functional differences among oral microbial communities.

Exploring the Association between Alzheimer's Disease, Oral Health, Microbial Endocrinology and Nutrition.

PubMed

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J; Crean, StJohn; Singhrao, Sim K

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer's disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis , a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host's inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual's diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD.

Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition

PubMed Central

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J.; Crean, StJohn; Singhrao, Sim K.

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer’s disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis, a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host’s inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual’s diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD. PMID:29249963

Impact of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization method.

PubMed

do Nascimento, Cássio; dos Santos, Janine Navarro; Pedrazzi, Vinícius; Pita, Murillo Sucena; Monesi, Nadia; Ribeiro, Ricardo Faria; de Albuquerque, Rubens Ferreira

2014-01-01

Molecular diagnosis methods have been largely used in epidemiological or clinical studies to detect and quantify microbial species that may colonize the oral cavity in healthy or disease. The preservation of genetic material from samples remains the major challenge to ensure the feasibility of these methodologies. Long-term storage may compromise the final result. The aim of this study was to evaluate the effect of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization. Saliva and supragingival biofilm were taken from 10 healthy subjects, aliquoted (n=364) and processed according to proposed protocols: immediate processing and processed after 2 or 4 weeks, and 6 or 12 months of storage at 4°C, -20°C and -80°C. Either total or individual microbial counts were recorded in lower values for samples processed after 12 months of storage, irrespective of temperatures tested. Samples stored up to 6 months at cold temperatures showed similar counts to those immediately processed. The microbial incidence was also significantly reduced in samples stored during 12 months in all temperatures. Temperature and time of oral samples storage have relevant impact in the detection and quantification of bacterial and fungal species by Checkerboard DNA-DNA hybridization method. Samples should be processed immediately after collection or up to 6 months if conserved at cold temperatures to avoid false-negative results. Copyright © 2013 Elsevier Ltd. All rights reserved.

OC28 - Effect of mode of delivery on early oral colonization and childhood dental caries: a systematic review.

PubMed

Antão, Celeste; Teixeira, Cristina; Gomes, Maria José

2016-05-09

Theme: Multidisciplinary team working. Oral colonization starts at birth by vertical transmission. To determine whether mode of delivery influences the oral colonization of infants and contributes to the risk of childhood dental caries. A systematic review was conducted in the electronic database Web of Science for articles published from January 1995 to December 2015 by using a set of keywords. From 2,644 citations identified through electronic search, ten studies met the inclusion criteria. According to the studies mode of delivery influences oral microbial density, oral microbial profile and the timing of oral colonization by cariogenic microbiota. However, there are no consistent results concerning either the prevalence of children harboring cariogenic microbiota or the prevalence of early childhood caries by mode of delivery. Mode of delivery influences early oral colonization. However, it seems that other determinants rather than mode of delivery could be major contributors to the development of early childhood caries.

Oral tolerance in neonates: from basics to potential prevention of allergic disease.

PubMed

Verhasselt, V

2010-07-01

Oral tolerance refers to the observation that prior feeding of an antigen induces local and systemic immune tolerance to that antigen. Physiologically, this process is probably of central importance for preventing inflammatory responses to the numerous dietary and microbial antigens present in the gut. Defective oral tolerance can lead to gut inflammatory disease, food allergies, and celiac disease. In the last two cases, the diseases develop early in life, stressing the necessity of understanding how oral tolerance is set up in neonates. This article reviews the parameters that have been outlined in adult animal models as necessary for tolerance induction and assesses whether these factors operate in neonates. In addition, we highlight the factors that are specific for this period of life and discuss how they could have an impact on oral tolerance. We pay particular attention to maternal influence on early oral tolerance induction through breast-feeding and outline the major parameters that could be modified to optimize tolerance induction in early life and possibly prevent allergic diseases.

Antimicrobial Barrier of an in vitro Oral Epithelial Model

PubMed Central

Kimball, Janet R.; Nittayananta, Wipawee; Klausner, Mitchell; Chung, Whasun O.; Dale, Beverly A.

2008-01-01

Objective Oral epithelia function as a microbial barrier and are actively involved in recognizing and responding to bacteria. Our goal was to examine a tissue engineered model of buccal epithelium for its response to oral bacteria and proinflammatory cytokines and compare the tissue responses with those of a submerged monolayer cell culture. Design The tissue model was characterized for keratin and β-defensin expression. Altered expression of β-defensins was evaluated by RT-PCR after exposure of the apical surface to oral bacteria and after exposure to TNF-α in the medium. These were compared to the response in traditional submerged oral epithelial cell culture. Results The buccal model showed expression of differentiation specific keratin 13, hBD1 and hBD3 in the upper half of the tissue; hBD2 was not detected. hBD1 mRNA was constitutively expressed, while hBD2 mRNA increased 2-fold after exposure of the apical surface to three oral bacteria tested and hBD3 mRNA increased in response to the non-pathogenic bacteria tested. In contrast, hBD2 mRNA increased 3–600 fold in response to bacteria in submerged cell culture. HBD2 mRNA increased over 100 fold in response to TNF-α in the tissue model and 50 fold in submerged cell culture. Thus, the tissue model is capable of upregulating hBD2, however, the minimal response to bacteria suggests that the tissue has an effective antimicrobial barrier due to its morphology, differentiation, and defensin expression. Conclusions The oral mucosal model is differentiated, expresses hBD1 and hBD3, and has an intact surface with a functional antimicrobial barrier. PMID:16815238

Oral microbial community typing of caries and pigment in primary dentition.

PubMed

Li, Yanhui; Zou, Cheng-Gang; Fu, Yu; Li, Yanhong; Zhou, Qing; Liu, Bo; Zhang, Zhigang; Liu, Juan

2016-08-05

Black extrinsic discoloration in primary dentition is a common clinical and aesthetic problem that can co-occur with dental caries, the most common oral diseases in childhood. Although the role of bacteria in the formation of pigment and caries in primary dentition is important, their basic features still remain a further mystery. Using targeted sequencing of the V1-V3 hypervariable regions of bacterial 16S ribosomal RNA (rRNA) genes, we obtained a dataset consisting of 831,381 sequences from 111 saliva samples and 110 supragingival plaque samples from 40 patients with pigment (black extrinsic stain), 20 with caries (obvious decay), and 25 with both pigment and caries and from 26 healthy individuals. We applied a Dirichlet multinomial mixture (DMM)-based community typing approach to investigate oral microbial community types. Our results revealed significant structural segregation of microbial communities, as indicated by the identification of two plaque community types (A and B) and three saliva community types (C-E). We found that the independent occurrence of the two plaque community types, A and B, was potentially associated with our oral diseases of interest. For type A, three co-occurring bacterial genus pairs could separately play a potential role in the formation of pigment (Leptotrichia and Fusobacterium), caries (unclassified Gemellales and Granulicatella), and mixed caries and pigment (Streptococcus and Mogibacterium). For type B, three co-occurring bacterial genera (unclassified Clostridiaceae, Peptostreptococcus, and Clostridium) were related to mixed pigment and caries. Three dominant bacterial genera (Selenomonas, Gemella, and Streptobacillus) were linked to the presence of caries. Our study demonstrates that plaque-associated oral microbial communities could majorly contribute to the formation of pigment and caries in primary dentition and suggests potential clinical applications of monitoring oral microbiota as an indicator for disease diagnosis and prognosis.

Microbial profiling of dental plaque from mechanically ventilated patients

PubMed Central

Twigg, Joshua A.; Lewis, Michael A. O.; Wise, Matt P.; Marchesi, Julian R.; Smith, Ann; Wilson, Melanie J.; Williams, David W.

2016-01-01

Micro-organisms isolated from the oral cavity may translocate to the lower airways during mechanical ventilation (MV) leading to ventilator-associated pneumonia (VAP). Changes within the dental plaque microbiome during MV have been documented previously, primarily using culture-based techniques. The aim of this study was to use community profiling by high throughput sequencing to comprehensively analyse suggested microbial changes within dental plaque during MV. Bacterial 16S rDNA gene sequences were obtained from 38 samples of dental plaque sampled from 13 mechanically ventilated patients and sequenced using the Illumina platform. Sequences were processed using Mothur, applying a 97 % gene similarity cut-off for bacterial species level identifications. A significant ‘microbial shift’ occurred in the microbial community of dental plaque during MV for nine out of 13 patients. Following extubation, or removal of the endotracheal tube that facilitates ventilation, sampling revealed a decrease in the relative abundance of potential respiratory pathogens and a compositional change towards a more predominantly (in terms of abundance) oral microbiota including Prevotella spp., and streptococci. The results highlight the need to better understand microbial shifts in the oral microbiome in the development of strategies to reduce VAP, and may have implications for the development of other forms of pneumonia such as community-acquired infection. PMID:26690690

Microbial profiling of dental plaque from mechanically ventilated patients.

PubMed

Sands, Kirsty M; Twigg, Joshua A; Lewis, Michael A O; Wise, Matt P; Marchesi, Julian R; Smith, Ann; Wilson, Melanie J; Williams, David W

2016-02-01

Micro-organisms isolated from the oral cavity may translocate to the lower airways during mechanical ventilation (MV) leading to ventilator-associated pneumonia (VAP). Changes within the dental plaque microbiome during MV have been documented previously, primarily using culture-based techniques. The aim of this study was to use community profiling by high throughput sequencing to comprehensively analyse suggested microbial changes within dental plaque during MV. Bacterial 16S rDNA gene sequences were obtained from 38 samples of dental plaque sampled from 13 mechanically ventilated patients and sequenced using the Illumina platform. Sequences were processed using Mothur, applying a 97% gene similarity cut-off for bacterial species level identifications. A significant 'microbial shift' occurred in the microbial community of dental plaque during MV for nine out of 13 patients. Following extubation, or removal of the endotracheal tube that facilitates ventilation, sampling revealed a decrease in the relative abundance of potential respiratory pathogens and a compositional change towards a more predominantly (in terms of abundance) oral microbiota including Prevotella spp., and streptococci. The results highlight the need to better understand microbial shifts in the oral microbiome in the development of strategies to reduce VAP, and may have implications for the development of other forms of pneumonia such as community-acquired infection.

Association Between Early Childhood Caries and Colonization with Streptococcus mutans Genotypes From Mothers.

PubMed

Childers, Noel K; Momeni, Stephanie S; Whiddon, Jennifer; Cheon, Kyounga; Cutter, Gary R; Wiener, Howard W; Ghazal, Tariq S; Ruby, John D; Moser, Stephen A

2017-03-15

The purpose of this study was to evaluate Streptococcus mutans genotypes (GT) between mother and child (M-C) in a high caries risk cohort to explore the association with early childhood caries (ECC). Sixty-nine infants (each approximately one year old) had periodic oral examinations (dmfs) and microbial samples collected from dental plaque, saliva, and other oral surfaces. Their mothers had an examination and plaque collected. S mutans isolates were genotyped using repetitive extragenic palindromic-PCR (rep-PCR). Statistical analyses were conducted for associations of S mutans in M-C dyads with caries outcomes. Twenty-seven S mutans genotypes (GT) from 3,414 isolates were identified. M-C were categorized as GT match (n equals 40) or no-match (n equals 29). When modeling the severity of ECC at 36 months (approximately four years old), the estimated dmfs in the match group was 2.61 times that of the no-match group (P=.014). Colonization of children with Streptococcus mutans genotypes that matched with mothers was shown to be highly associated with early childhood caries. Although the data suggest vertical transmission of S mutans in 40 of 69 children that shared GT with their mother, it is possible that other individuals transmitted the S mutans. Nonetheless, these findings support the importance of the mother's oral microbial status as a contributing influence to their children's oral health.

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

PubMed Central

Kirk, Michelle R.; Jonker, Arjan; McCulloch, Alan

2015-01-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. PMID:26276109

Re-discovering periodontal butyric acid: New insights on an old metabolite.

PubMed

Cueno, Marni E; Ochiai, Kuniyasu

2016-05-01

The oral microbiome is composed of detrimental and beneficial microbial communities producing several microbial factors that could contribute to the development of the oral microbiome and, likewise, may lead to the development of host diseases. Metabolites, like short-chain fatty acids, are commonly produced by the oral microbiome and serve various functions. Among the periodontal short-chain fatty acids, butyric acid is mainly produced by periodontopathic bacteria and, attributable to the butyrate paradox, is postulated to exhibit a dual function depending on butyric acid concentration. A better understanding of the interconnecting networks that would influence butyric acid function in the oral cavity may shed a new light on the current existing knowledge and view regarding butyric acid. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of Periodontal Pathogens on the Metatranscriptome of a Healthy Multispecies Biofilm Model

PubMed Central

Duran-Pinedo, Ana

2012-01-01

Oral bacterial biofilms are highly complex microbial communities with up to 700 different bacterial taxa. We report here the use of metatranscriptomic analysis to study patterns of community gene expression in a multispecies biofilm model composed of species found in healthy oral biofilms (Actinomyces naeslundii, Lactobacillus casei, Streptococcus mitis, Veillonella parvula, and Fusobacterium nucleatum) and the same biofilm plus the periodontopathogens Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans. The presence of the periodontopathogens altered patterns in gene expression, and data indicate that transcription of protein-encoding genes and small noncoding RNAs is stimulated. In the healthy biofilm hypothetical proteins, transporters and transcriptional regulators were upregulated while chaperones and cell division proteins were downregulated. However, when the pathogens were present, chaperones were highly upregulated, probably due to increased levels of stress. We also observed a significant upregulation of ABC transport systems and putative transposases. Changes in Clusters of Orthologous Groups functional categories as well as gene set enrichment analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that in the absence of pathogens, only sets of proteins related to transport and secondary metabolism were upregulated, while in the presence of pathogens, proteins related to growth and division as well as a large portion of transcription factors were upregulated. Finally, we identified several small noncoding RNAs whose predicted targets were genes differentially expressed in the open reading frame libraries. These results show the importance of pathogens controlling gene expression of a healthy oral community and the usefulness of metatranscriptomic techniques to study gene expression profiles in complex microbial community models. PMID:22328675

Emerging role of bacteria in oral carcinogenesis: a review with special reference to perio-pathogenic bacteria.

PubMed

Perera, Manosha; Al-Hebshi, Nezar Noor; Speicher, David J; Perera, Irosha; Johnson, Newell W

2016-01-01

Oral cancer, primarily oral squamous cell carcinoma (OSCC), continues to be a major global health problem with high incidence and low survival rates. While the major risk factors for this malignancy, mostly lifestyle related, have been identified, around 15% of oral cancer cases remain unexplained. In light of evidence implicating bacteria in the aetiology of some cancer types, several epidemiological studies have been conducted in the last decade, employing methodologies ranging from traditional culture techniques to 16S rRNA metagenomics, to assess the possible role of bacteria in OSCC. While these studies have demonstrated differences in microbial composition between cancerous and healthy tissues, they have failed to agree on specific bacteria or patterns of oral microbial dysbiosis to implicate in OSCC. On the contrary, some oral taxa, particularly Porphyromonas gingivalis and Fusobacterium nucleatum, show strong oral carcinogenic potential in vitro and in animal studies. Bacteria are thought to contribute to oral carcinogenesis via inhibition of apoptosis, activation of cell proliferation, promotion of cellular invasion, induction of chronic inflammation, and production of carcinogens. This narrative review provides a critical analysis of and an update on the association between bacteria and oral carcinogenesis and the possible mechanisms underlying it.

Oral and dental infections with anaerobic bacteria: clinical features, predominant pathogens, and treatment.

PubMed

Tanner, A; Stillman, N

1993-06-01

Microbial populations colonizing the teeth are a major source of pathogens responsible for oral and dental infections, including periodontal diseases, gingivitis, pericoronitis, endodontitis, peri-implantitis, and postextraction infections. Each entity has distinct clinical and microbial features. Bacterial species associated with oral infections include Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Bacteroides forsythus, Campylobacter rectus, Eubacterium species, Fusobacterium nucleatum, Eikenella corrodens, and Peptostreptococcus micros. Treponema pallidum-related spirochetes have been associated with acute necrotizing ulcerative gingivitis. Porphyromonas endodontalis appears to be specifically related to endodontic infections. Oral infections in medically compromised patients, including those with AIDS, are associated with similar species and are usually complicated by superinfection with enteric and Candida species. Isolation of species causing oral infections requires the collection of appropriate samples and the use of strictly anaerobic techniques. Rapid selective culture, immunofluorescence, and DNA probe methods have been developed for the identification of these oral species. The varied measures required in the management of oral and dental infections may include antimicrobial therapy. Accurate microbiological diagnosis, including antibiotic susceptibility testing, is indicated for cases that do not respond to therapy.

Oral Microbial Profile Discriminates Breastfed from Formula-Fed Infants

PubMed Central

Holgerson, Pernilla Lif; Vestman, Nelly Romani; Claesson, Rolf; Öhman, Carina; Domellöf, Magnus; Tanner, Anne CR; Hernell, Olle; Johansson, Ingegerd

2012-01-01

Objectives Little is known about the impact of diet on the oral microbiota of infants although diet is known to affect the gut microbiota. The aims of the present study were to compare the oral microbiota in breastfed and formula-fed infants, and investigate growth inhibition of streptococci by infant-isolated lactobacilli. Subjects and Methods 207 mothers consented to participation of their three-month old infants. 146 (70.5%) infants were exclusively and 38 (18.4%) partially breastfed, and 23 (11.1%) were exclusively formula-fed. Saliva from all infants was cultured for Lactobacillus species, with isolate identifications from 21 infants. Lactobacillus isolates were tested for their ability to supress Streptococcus mutans and Streptococcus sanguinis. Oral swabs from 73 infants were analysed by the Human Oral Microbe Identification Microarray (HOMIM) and by q-PCR for Lactobacilius gasseri. Results Lactobacilli were cultured from 27.8% of exclusively and partially breastfed infants, but not from formula-fed infants. The prevalence of 14 HOMIM detected taxa, and total salivary lactobacilli counts differed by feeding method. Multivariate modelling of HOMIM detected bacteria and possible confounders clustered samples from breastfed infants separately from formula-fed infants. The microbiota of breastfed infants differed based on vaginal or C-section delivery. Isolates of Lactobacillus plantarum, L. gasseri and Lactobacillus vaginalis inhibited growth of the cariogenic S. mutans and the commensal S. sanguinis: L. plantarum > L. gasseri > L. vaginalis. Conclusion The microbiota of the mouth differs between breastfed and formula-fed three-month-old infants. Possible mechanisms for microbial differences observed include species suppression by lactobacilli indigenous to breast milk. PMID:22955450

Effect of Antimicrobial Peptide KSL-W on Human Gingival Tissue and C. albicans Growth, Transition and Secreted Aspartyl Proteinase (SAPS) 2, 4, 5 and 6 Expressions

DTIC Science & Technology

2016-07-01

broad range of antibacterial activity and could play a role in preventing microbial infections(Decanis et al., 2009), (Zaslof, 2002). These antimicrobial...range of antibacterial activity and could play a role in preventing microbial infections(Decanis et al., 2009),(Zaslof, 2002). These antimicrobial...KSL- W (KKVVFWVKFK)(Na et al., 2007), which possess a broad range of antibacterial activity . It killed selected strains of non-oral and oral

Communication among Oral Bacteria

PubMed Central

Kolenbrander, Paul E.; Andersen, Roxanna N.; Blehert, David S.; Egland, Paul G.; Foster, Jamie S.; Palmer, Robert J.

2002-01-01

Human oral bacteria interact with their environment by attaching to surfaces and establishing mixed-species communities. As each bacterial cell attaches, it forms a new surface to which other cells can adhere. Adherence and community development are spatiotemporal; such order requires communication. The discovery of soluble signals, such as autoinducer-2, that may be exchanged within multispecies communities to convey information between organisms has emerged as a new research direction. Direct-contact signals, such as adhesins and receptors, that elicit changes in gene expression after cell-cell contact and biofilm growth are also an active research area. Considering that the majority of oral bacteria are organized in dense three-dimensional biofilms on teeth, confocal microscopy and fluorescently labeled probes provide valuable approaches for investigating the architecture of these organized communities in situ. Oral biofilms are readily accessible to microbiologists and are excellent model systems for studies of microbial communication. One attractive model system is a saliva-coated flowcell with oral bacterial biofilms growing on saliva as the sole nutrient source; an intergeneric mutualism is discussed. Several oral bacterial species are amenable to genetic manipulation for molecular characterization of communication both among bacteria and between bacteria and the host. A successful search for genes critical for mixed-species community organization will be accomplished only when it is conducted with mixed-species communities. PMID:12209001

The Application of Magnetic Bead Selection to Investigate Interactions between the Oral Microbiota and Salivary Immunoglobulins.

PubMed

Madhwani, Tejal; McBain, Andrew J

2016-01-01

The effect of humoral immunity on the composition of the oral microbiota is less intensively investigated than hygiene and diet, in part due to a lack of simple and robust systems for investigating interactions between salivary immunoglobulins and oral bacteria. Here we report the application of an ex situ method to investigate the specificity of salivary immunoglobulins for salivary bacteria. Saliva collected from six volunteers was separated into immunoglobulin and microbial fractions, and the microbial fractions were then directly exposed to salivary immunoglobulins of "self" and "non-self" origin. Antibody-selected bacteria were separated from their congeners using a magnetic bead system, selective for IgA or IgG isotypes. The positively selected fractions were then characterized using gel-based eubacterial-specific DNA profiling. The eubacterial profiles of positively selected fractions diverged significantly from profiles of whole salivary consortia based on volunteer (P≤ 0.001%) and immunoglobulin origin (P≤ 0.001%), but not immunoglobulin isotype (P = 0.2). DNA profiles of separated microbial fractions were significantly (p≤ 0.05) less diverse than whole salivary consortia and included oral and environmental bacteria. Consortia selected using self immunoglobulins were generally less diverse than those selected with immunoglobulins of non-self origin. Magnetic bead separation facilitated the testing of interactions between salivary antibodies and oral bacteria, showing that these interactions are specific and may reflect differences in recognition by self and non-self immunoglobulins. Further development of this system could improve understanding of the relationship between the oral microbiota and the host immune system and of mechanisms underlying the compositional stability of the oral microbiota.

Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen.

PubMed

Kittelmann, Sandra; Kirk, Michelle R; Jonker, Arjan; McCulloch, Alan; Janssen, Peter H

2015-11-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Distinct Ecological Niche of Anal, Oral, and Cervical Mucosal Microbiomes in Adolescent Women.

PubMed

Smith, Benjamin C; Zolnik, Christine P; Usyk, Mykhaylo; Chen, Zigui; Kaiser, Katherine; Nucci-Sack, Anne; Peake, Ken; Diaz, Angela; Viswanathan, Shankar; Strickler, Howard D; Schlecht, Nicolas F; Burk, Robert D

2016-09-01

Human body sites represent ecological niches for microorganisms, each providing variations in microbial exposure, nutrient availability, microbial competition, and host immunological responses. In this study, we investigated the oral, anal, and cervical microbiomes from the same 20 sexually active adolescent females, using culture-independent, next-generation sequencing. DNA from each sample was amplified for the bacterial 16S rRNA gene and sequenced on an Illumina platform using paired-end reads. Across the three anatomical niches, we found significant differences in bacterial community composition and diversity. Overall anal samples were dominated with Prevotella and Bacteriodes , oral samples with Streptococcus and Prevotella , and cervical samples with Lactobacillus . The microbiomes of a few cervical samples clustered with anal samples in weighted principal coordinate analyses, due in part to a higher proportion of Prevotella in those samples. Additionally, cervical samples had the lowest alpha diversity. Our results demonstrate the occurrence of distinct microbial communities across body sites within the same individual.

Emerging role of bacteria in oral carcinogenesis: a review with special reference to perio-pathogenic bacteria

PubMed Central

Perera, Manosha; Al-hebshi, Nezar Noor; Speicher, David J.; Perera, Irosha; Johnson, Newell W.

2016-01-01

Oral cancer, primarily oral squamous cell carcinoma (OSCC), continues to be a major global health problem with high incidence and low survival rates. While the major risk factors for this malignancy, mostly lifestyle related, have been identified, around 15% of oral cancer cases remain unexplained. In light of evidence implicating bacteria in the aetiology of some cancer types, several epidemiological studies have been conducted in the last decade, employing methodologies ranging from traditional culture techniques to 16S rRNA metagenomics, to assess the possible role of bacteria in OSCC. While these studies have demonstrated differences in microbial composition between cancerous and healthy tissues, they have failed to agree on specific bacteria or patterns of oral microbial dysbiosis to implicate in OSCC. On the contrary, some oral taxa, particularly Porphyromonas gingivalis and Fusobacterium nucleatum, show strong oral carcinogenic potential in vitro and in animal studies. Bacteria are thought to contribute to oral carcinogenesis via inhibition of apoptosis, activation of cell proliferation, promotion of cellular invasion, induction of chronic inflammation, and production of carcinogens. This narrative review provides a critical analysis of and an update on the association between bacteria and oral carcinogenesis and the possible mechanisms underlying it. PMID:27677454

A Pilot Study on Integrating Videography and Environmental Microbial Sampling to Model Fecal Bacterial Exposures in Peri-Urban Tanzania.

PubMed

Julian, Timothy R; Pickering, Amy J

2015-01-01

Diarrheal diseases are a leading cause of under-five mortality and morbidity in sub-Saharan Africa. Quantitative exposure modeling provides opportunities to investigate the relative importance of fecal-oral transmission routes (e.g. hands, water, food) responsible for diarrheal disease. Modeling, however, requires accurate descriptions of individuals' interactions with the environment (i.e., activity data). Such activity data are largely lacking for people in low-income settings. In the present study, we collected activity data and microbiological sampling data to develop a quantitative microbial exposure model for two female caretakers in peri-urban Tanzania. Activity data were combined with microbiological data of contacted surfaces and fomites (e.g. broom handle, soil, clothing) to develop example exposure profiles describing second-by-second estimates of fecal indicator bacteria (E. coli and enterococci) concentrations on the caretaker's hands. The study demonstrates the application and utility of video activity data to quantify exposure factors for people in low-income countries and apply these factors to understand fecal contamination exposure pathways. This study provides both a methodological approach for the design and implementation of larger studies, and preliminary data suggesting contacts with dirt and sand may be important mechanisms of hand contamination. Increasing the scale of activity data collection and modeling to investigate individual-level exposure profiles within target populations for specific exposure scenarios would provide opportunities to identify the relative importance of fecal-oral disease transmission routes.

Interactions between Lactobacillus rhamnosus GG and oral micro-organisms in an in vitro biofilm model.

PubMed

Jiang, Qingru; Stamatova, Iva; Kainulainen, Veera; Korpela, Riitta; Meurman, Jukka H

2016-07-12

Probiotics have shown favourable properties in maintaining oral health. By interacting with oral microbial communities, these species could contribute to healthier microbial equilibrium. This study aimed to investigate in vitro the ability of probiotic Lactobacillus rhamnosus GG (L.GG) to integrate in oral biofilm and affect its species composition. Five oral strains, Streptococcus mutans, Streptococcus sanguinis, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum and Candida albicans were involved. The group setup included 6 mono-species groups, 3 dual-species groups (L.GG + S. mutans/S. sanguinis/C. albicans), and 4 multi-species groups (4/5 species and 4/5 species + L.GG, 4 species were all the tested strains except S. mutans). Cell suspensions of six strains were pooled according to the group setup. Biofilms were grown on saliva-coated hydroxyapatite (HA) discs at 37 °C in anaerobic conditions for 64.5 h. Biofilm medium was added and refreshed at 0, 16.5, and 40.5 h. The pH of spent media was measured. Viable cells of the 16.5 h and 64.5 h biofilms were counted. 64.5 h biofilms were stained and scanned with confocal laser scanning microscopy. Our results showed that L.GG and S. mutans demonstrated stronger adhesion ability than the other strains to saliva-coated HA discs. L.GG, C. albicans, S. mutans and F. nucleatum, with poor ability to grow in mono-species biofilms demonstrated better abilities of adhesion and reproduction in dual- and/or multi-species biofilms. L.GG slightly suppressed the growth of C. albicans in all groups, markedly weakened the growth of S. sanguinis and F. nucleatum in 4sp + L.GG group, and slightly reduced the adhesion of S. mutans in L.GG+ S. mutans group. To conclude, in this in vitro model L.GG successfully integrated in all oral biofilms, and reduced the counts of S. sanguinis and C. albicans and lowered the biofilm-forming ability of F. nucleatum, but only slightly reduced the adhesion of S. mutans. C. albicans significantly promoted the growth of L.GG.

Host Immune Selection of Rumen Bacteria through Salivary Secretory IgA

PubMed Central

Fouhse, Janelle M.; Smiegielski, Luke; Tuplin, Melanie; Guan, Le Luo; Willing, Benjamin P.

2017-01-01

The rumen microbiome is integral to efficient production in cattle and shows strong host specificity, yet little is known about what host factors shape rumen microbial composition. Secretory immunoglobulin A (SIgA) is produced in large amounts in the saliva, can coat both commensal and pathogenic microbes within the gut, and presents a plausible mechanism of host specificity. However, the role salivary SIgA plays in commensal bacteria selection in ruminants remains elusive. The main objectives of this study were to develop an immuno-affinity benchtop method to isolate SIgA-tagged microbiota and to determine if salivary SIgA preferentially binds selected bacteria. We hypothesized that SIgA-tagged bacteria would differ from total bacteria, thus supporting a potential host-derived mechanism in commensal bacterial selection. Whole rumen (n = 9) and oral secretion samples (n = 10) were incubated with magnetic beads conjugated with anti-secretory IgA antibodies to enrich SIgA-tagged microbiota. Microbial DNA from the oral secretion, whole rumen, SIgA-tagged oral secretion, and SIgA-tagged rumen was isolated for amplicon sequencing of V1–V3 region of 16S rDNA genes. Whole rumen and oral secretion had distinctive (P < 0.05) bacterial compositions indicated by the non-parametric multidimensional scaling plot using Euclidean distance metrics. The SIgA-tagged microbiota from rumen and oral secretion had similar abundance of Bacteroidetes, Actinobacteria, Fibrobacter, candidate phyla TM7, and Tenericutes and are clustered tightly. Composition of SIgA-tagged oral secretion microbiota was more similar to whole rumen microbiota than whole oral secretion due to enrichment of rumen bacteria (Lachnospiraceae) and depletion of oral taxa (Streptococcus, Rothia, Neisseriaceae, and Lactobacillales). In conclusion, SIgA-tagged oral secretion microbiota had an increased resemblance to whole rumen microbiota, suggesting salivary SIgA-coating may be one host-derived mechanism impacting commensal colonization. Further studies, to explore the variations in antibody affinity between different animals as a driver of microbial composition are warranted. PMID:28553275

Use of Probiotics and Oral Health.

PubMed

Allaker, Robert P; Stephen, Abish S

2017-01-01

The purpose of this study is to critically assess recent studies concerning the use of probiotics to control periodontal diseases, dental caries and halitosis (oral malodour). Clinical studies have shown that probiotics when allied to conventional periodontal treatment can ameliorate microbial dysbiosis and produce significant improvement in clinical indicators of disease. However, this effect is often not maintained by the host after the end of probiotic use. Current probiotics also show limited effects in treating caries and halitosis. Novel approaches based up on replacement therapy and using highly abundant health-associated oral species, including nitrate-reducing bacteria, have been proposed to improve persistence of probiotic strains and maintain oral health benefits. Probiotics have potential in the management of multifactorial diseases such as the periodontal diseases and caries, by more effectively addressing the host-microbial interface to restore homeostasis that may not be achieved with conventional treatments.

A molecular survey of S. mutans and P. gingivalis oral microbial burden in human saliva using Relative Endpoint Polymerase Chain Reaction (RE-PCR) within the population of a Nevada dental school revealed disparities among minorities

PubMed Central

2012-01-01

Background The University of Nevada, Las Vegas School of Dental Medicine recently opened an orthodontic treatment clinic to address the needs of the racially and ethnically diverse population of Southern Nevada, primarily focusing on the treatment and care of low-income and minority patients. Although orthodontic treatment and therapy has been shown to induce changes in the oral cavity, much of this evidence was collected from traditional White, teenage orthodontic clinic populations. The primary goal of this study was to describe the microbial burden of the cariogenic and periodontal pathogens, Streptococcus mutans and Porphyromonas gingivalis within the UNLV-SDM patient population. Methods Representative saliva samples were collected from healthy adult patients for DNA isolation. Relative endpoint polymerase chain reaction (RE-PCR) was performed to ascertain the presence and relative microbial burden of these oral pathogens. Results Nearly one quarter (13/56) or 23.3% of these patients had elevated levels of S. mutans, while (10/56) and 17.8% of these samples were found to have elevated levels of P. gingivalis, - with (90%) of P. gingivalis-positive samples from minority patients (X2 = 17.921, d.f. = 1; p < 0.0001). Conclusions These findings of elevated P. gingivalis levels, primarily among minority patients, may suggest underlying oral health practices contributing to adverse oral health conditions within this population. Oral health knowledge and practices among minority patients may be strongly influenced by other factors, including education and socioeconomic status, suggesting additional research may be needed to accurately determine the most appropriate standards for care and oral health education within this patient population. PMID:22925755

The Application of Magnetic Bead Selection to Investigate Interactions between the Oral Microbiota and Salivary Immunoglobulins

PubMed Central

Madhwani, Tejal

2016-01-01

The effect of humoral immunity on the composition of the oral microbiota is less intensively investigated than hygiene and diet, in part due to a lack of simple and robust systems for investigating interactions between salivary immunoglobulins and oral bacteria. Here we report the application of an ex situ method to investigate the specificity of salivary immunoglobulins for salivary bacteria. Saliva collected from six volunteers was separated into immunoglobulin and microbial fractions, and the microbial fractions were then directly exposed to salivary immunoglobulins of “self” and “non-self” origin. Antibody-selected bacteria were separated from their congeners using a magnetic bead system, selective for IgA or IgG isotypes. The positively selected fractions were then characterized using gel-based eubacterial-specific DNA profiling. The eubacterial profiles of positively selected fractions diverged significantly from profiles of whole salivary consortia based on volunteer (P≤ 0.001%) and immunoglobulin origin (P≤ 0.001%), but not immunoglobulin isotype (P = 0.2). DNA profiles of separated microbial fractions were significantly (p≤ 0.05) less diverse than whole salivary consortia and included oral and environmental bacteria. Consortia selected using self immunoglobulins were generally less diverse than those selected with immunoglobulins of non-self origin. Magnetic bead separation facilitated the testing of interactions between salivary antibodies and oral bacteria, showing that these interactions are specific and may reflect differences in recognition by self and non-self immunoglobulins. Further development of this system could improve understanding of the relationship between the oral microbiota and the host immune system and of mechanisms underlying the compositional stability of the oral microbiota. PMID:27483159

Effect of an oxygenating agent on oral bacteria in vitro and on dental plaque composition in healthy young adults.

PubMed

Fernandez y Mostajo, Mercedes; van der Reijden, Wil A; Buijs, Mark J; Beertsen, Wouter; Van der Weijden, Fridus; Crielaard, Wim; Zaura, Egija

2014-01-01

Oral bacteria live in symbiosis with the host. Therefore, when mouthwashes are indicated, selective inhibition of taxa contributing to disease is preferred instead of broad-spectrum antimicrobials. The potential selectivity of an oxygenating mouthwash, Ardox-X® (AX), has not been assessed. The aim of this study was to determine the antimicrobial potential of AX and the effects of a twice-daily oral rinse on dental plaque composition. In vitro, 16 oral bacterial strains were tested using agar diffusion susceptibility, minimum inhibitory and minimum bactericidal concentration tests. A pilot clinical study was performed with 25 healthy volunteers. Clinical assessments and microbiological sampling of supragingival plaque were performed at 1 month before the experiment (Pre-exp), at the start of the experiment (Baseline) and after the one-week experimental period (Post-exp). During the experiment individuals used AX mouthwash twice daily in absence of other oral hygiene measures. The microbiological composition of plaque was assessed by 16S rRNA gene amplicon sequencing. AX showed high inter-species variation in microbial growth inhibition. The tested Prevotella strains and Fusobacterium nucleatum showed the highest sensitivity, while streptococci and Lactobacillus acidophilus were most resistant to AX. Plaque scores at Pre-exp and Baseline visits did not differ significantly (p = 0.193), nor did the microbial composition of plaque. During a period of 7-days non-brushing but twice daily rinsing plaque scores increased from 2.21 (0.31) at Baseline to 2.43 (0.39) Post-exp. A significant microbial shift in composition was observed: genus Streptococcus and Veillonella increased while Corynebacterium, Haemophilus, Leptotrichia, Cardiobacterium and Capnocytophaga decreased (p ≤ 0.001). AX has the potential for selective inhibition of oral bacteria. The shift in oral microbiome after 1 week of rinsing deserves further research.

Oral microbial profile discriminates breast-fed from formula-fed infants.

PubMed

Holgerson, Pernilla L; Vestman, Nelly R; Claesson, Rolf; Ohman, Carina; Domellöf, Magnus; Tanner, Anne C R; Hernell, Olle; Johansson, Ingegerd

2013-02-01

Little is known about the effect of diet on the oral microbiota of infants, although diet is known to affect the gut microbiota. The aims of the present study were to compare the oral microbiota in breast-fed and formula-fed infants, and investigate growth inhibition of streptococci by infant-isolated lactobacilli. A total of 207 mothers consented to participation of their 3-month-old infants. A total of 146 (70.5%) infants were exclusively and 38 (18.4%) partially breast-fed, and 23 (11.1%) were exclusively formula-fed. Saliva from all of their infants was cultured for Lactobacillus species, with isolate identifications from 21 infants. Lactobacillus isolates were tested for their ability to suppress Streptococcus mutans and S sanguinis. Oral swabs from 73 infants were analysed by the Human Oral Microbe Identification Microarray (HOMIM) and by quantitative polymerase chain reaction for Lactobacillus gasseri. Lactobacilli were cultured from 27.8% of exclusively and partially breast-fed infants, but not from formula-fed infants. The prevalence of 14 HOMIM-detected taxa, and total salivary lactobacilli counts differed by feeding method. Multivariate modelling of HOMIM-detected bacteria and possible confounders clustered samples from breast-fed infants separately from formula-fed infants. The microbiota of breast-fed infants differed based on vaginal or C-section delivery. Isolates of L plantarum, L gasseri, and L vaginalis inhibited growth of the cariogenic S mutans and the commensal S sanguinis: L plantarum >L gasseri >L vaginalis. The microbiota of the mouth differs between 3-month-old breast-fed and formula-fed infants. Possible mechanisms for microbial differences observed include species suppression by lactobacilli indigenous to breast milk.

Stability and resilience of oral microcosms toward acidification and Candida outgrowth by arginine supplementation.

PubMed

Koopman, Jessica E; Röling, Wilfred F M; Buijs, Mark J; Sissons, Christopher H; ten Cate, Jacob M; Keijser, Bart J F; Crielaard, Wim; Zaura, Egija

2015-02-01

Dysbiosis induced by low pH in the oral ecosystem can lead to caries, a prevalent bacterial disease in humans. The amino acid arginine is one of the pH-elevating agents in the oral cavity. To obtain insights into the effect of arginine on oral microbial ecology, a multi-plaque "artificial mouth" (MAM) biofilm model was inoculated with saliva from a healthy volunteer and microcosms were grown for 4 weeks with 1.6 % (w/v) arginine supplement (Arginine) or without (Control), samples were taken at several time-points. A cariogenic environment was mimicked by sucrose pulsing. The bacterial composition was determined by 16S rRNA gene amplicon sequencing, the presence and amount of Candida and arginine deiminase system genes arcA and sagP by qPCR. Additionally, ammonium and short-chain fatty acid concentrations were determined. The Arginine microcosms were dominated by Streptococcus, Veillonella, and Neisseria and remained stable in time, while the composition of the Control microcosms diverged significantly in time, partially due to the presence of Megasphaera. The percentage of Candida increased 100-fold in the Control microcosms compared to the Arginine microcosms. The pH-raising effect of arginine was confirmed by the pH and ammonium results. The abundances of sagP and arcA were highest in the Arginine microcosms, while the concentration of butyrate was higher in the Control microcosms. We demonstrate that supplementation with arginine serves a health-promoting function; it enhances microcosm resilience toward acidification and suppresses outgrowth of the opportunistic pathogen Candida. Arginine facilitates stability of oral microbial communities and prevents them from becoming cariogenic.

Oral Health in a Sample of Pregnant Women from Northern Appalachia (2011–2015)

PubMed Central

Neiswanger, Katherine; McNeil, Daniel W.; Foxman, Betsy; Govil, Manika; Cooper, Margaret E.; Weyant, Robert J.; Shaffer, John R.; Crout, Richard J.; Simhan, Hyagriv N.; Beach, Scott R.; Chapman, Stella; Zovko, Jayme G.; Brown, Linda J.; Strotmeyer, Stephen J.; Maurer, Jennifer L.; Marazita, Mary L.

2015-01-01

Background. Chronic poor oral health has a high prevalence in Appalachia, a large region in the eastern USA. The Center for Oral Health Research in Appalachia (COHRA) has been enrolling pregnant women and their babies since 2011 in the COHRA2 study of genetic, microbial, and environmental factors involved in oral health in Northern Appalachia. Methods. The COHRA2 protocol is presented in detail, including inclusion criteria (healthy, adult, pregnant, US Caucasian, English speaking, and nonimmunocompromised women), recruiting (two sites: Pittsburgh, Pennsylvania, and West Virginia, USA), assessments (demographic, medical, dental, psychosocial/behavioral, and oral microbial samples and DNA), timelines (longitudinal from pregnancy to young childhood), quality control, and retention rates. Results. Preliminary oral health and demographic data are presented in 727 pregnant women, half from the greater Pittsburgh region and half from West Virginia. Despite similar tooth brushing and flossing habits, COHRA2 women in West Virginia have significantly worse oral health than the Pittsburgh sample. Women from Pittsburgh are older and more educated and have less unemployment than the West Virginia sample. Conclusions. We observed different prevalence of oral health and demographic variables between pregnant women from West Virginia (primarily rural) and Pittsburgh (primarily urban). These observations suggest site-specific differences within Northern Appalachia that warrant future studies. PMID:26089906

Biofilm on the tracheoesophageal voice prosthesis: considerations for oral decontamination.

PubMed

Somogyi-Ganss, Eszter; Chambers, Mark S; Lewin, Jan S; Tarrand, Jeffrey J; Hutcheson, Katherine A

2017-01-01

The tracheoesophageal puncture (TEP) restores verbal communication after total laryngectomy using a one-way valved voice prosthesis (VP). Microbial colonization can shorten VP device life. Our aims were to investigate patterns of prosthetic and oral colonization, and record changes in VP device life after targeted decontamination. We conducted a retrospective review of TEP clinic patients who underwent microbial analysis of the VP between 01/2003 and 07/2013. Two subgroups were analyzed: (1) patients with microbial analysis of the VP and the mouth were analyzed to identify patterns of common contamination, and (2) patients who were prescribed targeted oral decontamination on the basis of the microbial analysis of the VP were analyzed to evaluate effects on device life. Among 42 patients, 3 patients had only fungal, 5 only bacterial, and 33 had polyspecies fungal and bacterial colonization. In the TEP-oral microflora subgroup (n = 15), 7 had common microorganisms in the mouth and on the VP. Among the decontamination subgroup (n = 23), 6 patients received broad spectrum rinse, 16 antifungal agents and 13 antibiotics, or a combination thereof. After targeted decontamination, the median device life of prostheses improved from 7.89 to 10.82 weeks (p = 0.260). The majority of patients with a suboptimal VP device life in this pilot had polyspecies bacterial and fungal colonization. VPs rarely had fungal contamination alone (3 %), and non-albicans fungal species were more common than expected. For these reasons, we are exploring the use of targeted decontamination regimens that were associated with 1.4-fold improvement in VP duration.

Oral Microbiome Metabolism: From "Who Are They?" to "What Are They Doing?".

PubMed

Takahashi, N

2015-12-01

Recent advances in molecular biology have facilitated analyses of the oral microbiome ("Who are they?"); however, its functions (e.g., metabolic activities) are poorly understood ("What are they doing?"). This review aims to summarize our current understanding of the metabolism of the oral microbiome. Saccharolytic bacteria-including Streptococcus, Actinomyces, and Lactobacillus species-degrade carbohydrates into organic acids via the Embden-Meyerhof-Parnas pathway and several of its branch pathways, resulting in dental caries, while alkalization and acid neutralization via the arginine deiminase system, urease, and so on, counteract acidification. Proteolytic/amino acid-degrading bacteria, including Prevotella and Porphyromonas species, break down proteins and peptides into amino acids and degrade them further via specific pathways to produce short-chain fatty acids, ammonia, sulfur compounds, and indole/skatole, which act as virulent and modifying factors in periodontitis and oral malodor. Furthermore, it is suggested that ethanol-derived acetaldehyde can cause oral cancer, while nitrate-derived nitrite can aid caries prevention and systemic health. Microbial metabolic activity is influenced by the oral environment; however, it can also modify the oral environment, enhance the pathogenicity of bacteria, and induce microbial selection to create more pathogenic microbiome. Taking a metabolomic approach to analyzing the oral microbiome is crucial to improving our understanding of the functions of the oral microbiome. © International & American Associations for Dental Research 2015.

Oral health and care in the intensive care unit: state of the science.

PubMed

Munro, Cindy L; Grap, Mary Jo

2004-01-01

Oral health is influenced by oral microbial flora, which are concentrated in dental plaque. Dental plaque provides a microhabitat for organisms and an opportunity for adherence of the organisms to either the tooth surface or other microorganisms. In critically ill patients, potential pathogens can be cultured from the oral cavity. These microorganisms in the mouth can translocate and colonize the lung, resulting in ventilator-associated pneumonia. The importance of oral care in the intensive care unit has been noted in the literature, but little research is available on mechanical or pharmacological approaches to reducing oral microbial flora via oral care in critically ill adults. Most research in oral care has been directed toward patients' comfort; the microbiological and physiological effects of tooth brushing in the intensive care unit have not been reported. Although 2 studies indicated reductions in rates of ventilator-associated pneumonia in cardiac surgery patients who received chlorhexidine before intubation and postoperatively, the effects of chlorhexidine in reducing ventilator-associated pneumonia in other populations of critically ill patients or its effect when treatment with the agent initiated after intubation have not been reported. In addition, no evaluation of the effectiveness of pharmacological and mechanical interventions relative to each other or in combination has been published. Additional studies are needed to develop and test best practices for oral care in critically ill patients.

Effect of Fixed Orthodontic Treatment on Salivary Flow, pH and Microbial Count.

PubMed

Arab, Sepideh; Nouhzadeh Malekshah, Sepideh; Abouei Mehrizi, Ehsan; Ebrahimi Khanghah, Anita; Naseh, Roya; Imani, Mohammad Moslem

2016-01-01

The present study was designed to evaluate the changes in saliva properties and oral microbial flora in patients undergoing fixed orthodontic treatment. Two important saliva properties namely the salivary flow rate and pH as well as oral microbial flora were assessed in 30 orthodontic patients before starting fixed orthodontic treatment and after six, 12 and 18 weeks of treatment. Selective media, Sabouraud dextrose agar, Mitis salivarius agar and Rogosa agar were used for isolation of Candida albicans, Streptococcus mutans and Lactobacillus acidophilus, respectively. Statistical analysis was performed using Friedman and Dunn's tests. P< 0.05 was considered statistically significant. After six, 12 and 18 weeks of commencing fixed orthodontic treatment, the total colony counts of Candida albicans, Streptococcus mutans and Lactobacillus acidophilus showed a significant increase. The saliva pH decreased during the orthodontic treatment (P< 0.05) while the salivary flow did not change significantly. Fixed orthodontic treatment causes major changes in the saliva properties. The changes in oral microflora and saliva properties show the importance of caries preventive measures during orthodontic treatment.

Cohabiting family members share microbiota with one another and with their dogs.

PubMed

Song, Se Jin; Lauber, Christian; Costello, Elizabeth K; Lozupone, Catherine A; Humphrey, Gregory; Berg-Lyons, Donna; Caporaso, J Gregory; Knights, Dan; Clemente, Jose C; Nakielny, Sara; Gordon, Jeffrey I; Fierer, Noah; Knight, Rob

2013-04-16

Human-associated microbial communities vary across individuals: possible contributing factors include (genetic) relatedness, diet, and age. However, our surroundings, including individuals with whom we interact, also likely shape our microbial communities. To quantify this microbial exchange, we surveyed fecal, oral, and skin microbiota from 60 families (spousal units with children, dogs, both, or neither). Household members, particularly couples, shared more of their microbiota than individuals from different households, with stronger effects of co-habitation on skin than oral or fecal microbiota. Dog ownership significantly increased the shared skin microbiota in cohabiting adults, and dog-owning adults shared more 'skin' microbiota with their own dogs than with other dogs. Although the degree to which these shared microbes have a true niche on the human body, vs transient detection after direct contact, is unknown, these results suggest that direct and frequent contact with our cohabitants may significantly shape the composition of our microbial communities. DOI:http://dx.doi.org/10.7554/eLife.00458.001.

Cohabiting family members share microbiota with one another and with their dogs

PubMed Central

Song, Se Jin; Lauber, Christian; Costello, Elizabeth K; Lozupone, Catherine A; Humphrey, Gregory; Berg-Lyons, Donna; Caporaso, J Gregory; Knights, Dan; Clemente, Jose C; Nakielny, Sara; Gordon, Jeffrey I; Fierer, Noah; Knight, Rob

2013-01-01

Human-associated microbial communities vary across individuals: possible contributing factors include (genetic) relatedness, diet, and age. However, our surroundings, including individuals with whom we interact, also likely shape our microbial communities. To quantify this microbial exchange, we surveyed fecal, oral, and skin microbiota from 60 families (spousal units with children, dogs, both, or neither). Household members, particularly couples, shared more of their microbiota than individuals from different households, with stronger effects of co-habitation on skin than oral or fecal microbiota. Dog ownership significantly increased the shared skin microbiota in cohabiting adults, and dog-owning adults shared more ‘skin’ microbiota with their own dogs than with other dogs. Although the degree to which these shared microbes have a true niche on the human body, vs transient detection after direct contact, is unknown, these results suggest that direct and frequent contact with our cohabitants may significantly shape the composition of our microbial communities. DOI: http://dx.doi.org/10.7554/eLife.00458.001 PMID:23599893

[New approaches to oral cavity opportunistic microbiota study].

PubMed

Tets, G V; Vikina, D S; Vecherkovskaia, M F; Domorad, A A; Kharlamova, V V; Tets, V V

2013-01-01

Identification of some bacteria of the oral microbiota in humans including opportunistic pathogens capable of causing infections of various locations is a challenging problem for dentistry. Lack of knowledge on oral microbiota is the result of the absence of appropriate culture technique for isolation of pure cultures of those bacteria. The paper presents the study on mixed oral microbial biofilms with isolation and identification of insufficiently explored or still unknown aerobic opportunistic bacteria.

Towards understanding oral health.

PubMed

Zaura, Egija; ten Cate, Jacob M

2015-01-01

During the last century, dental research has focused on unraveling the mechanisms behind various oral pathologies, while oral health was typically described as the mere absence of oral diseases. The term 'oral microbial homeostasis' is used to describe the capacity of the oral ecosystem to maintain microbial community stability in health. However, the oral ecosystem itself is not stable: throughout life an individual undergoes multiple physiological changes while progressing through infancy, childhood, adolescence, adulthood and old age. Recent discussions on the definition of general health have led to the proposal that health is the ability of the individual to adapt to physiological changes, a condition known as allostasis. In this paper the allostasis principle is applied to the oral ecosystem. The multidimensionality of the host factors contributing to allostasis in the oral cavity is illustrated with an example on changes occurring in puberty. The complex phenomenon of oral health and the processes that prevent the ecosystem from collapsing during allostatic changes in the entire body are far from being understood. As yet individual components (e.g. hard tissues, microbiome, saliva, host response) have been investigated, while only by consolidating these and assessing their multidimensional interactions should we be able to obtain a comprehensive understanding of the ecosystem, which in turn could serve to develop rational schemes to maintain health. Adapting such a 'system approach' comes with major practical challenges for the entire research field and will require vast resources and large-scale multidisciplinary collaborations. 2015 S. Karger AG, Basel

Genetic profiling of the oral microbiota associated with severe early-childhood caries.

PubMed

Li, Y; Ge, Y; Saxena, D; Caufield, P W

2007-01-01

The determination of the composition of the microbial community in the oral cavity is usually based on cultivation methods; however, nearly half of the bacteria in the saliva and the dental plaque are not cultivable. In this study, we evaluated the difference in oral microbial diversity between children with severe early-childhood caries (S-ECC) and caries-free (CF) controls by means of a cultivation-independent approach called denaturing gradient gel electrophoresis (DGGE). Pooled dental plaque samples were collected from 20 children aged 2 to 8 years. Total microbial genomic DNA was isolated from those subjects, and a portion of the 16S rRNA gene locus was PCR amplified by using universal primers. We observed that the mean species richness of the bacterial population was greater in the CF children (n = 12) (42 +/- 3.7) than in the S-ECC children (n = 8) (35 +/- 4.3); the difference was statistically significant (P = 0.005). The overall diversity of plaque samples as measured by the Shannon index was 3.5 for the S-ECC group and 3.7 for the CF group (P = 0.004). Differences in DGGE profiles were distinguished on the basis of a cluster analysis. Sequence analysis of excised DGGE bands consisted of 2.7 phylotypes, on average. After adjusting for the number of observed bands, we estimated that the S-ECC group exhibited 94.5 total phylotypes and that the CF group exhibited 113.4. These results suggest that the microbial diversity and complexity of the microbial biota in dental plaque are significantly less in S-ECC children than in CF children.

Temporal Variability of Oral Microbiota over 10 Months and the Implications for Future Epidemiologic Studies.

PubMed

Vogtmann, Emily; Hua, Xing; Zhou, Liang; Wan, Yunhu; Suman, Shalabh; Zhu, Bin; Dagnall, Casey L; Hutchinson, Amy; Jones, Kristine; Hicks, Belynda D; Sinha, Rashmi; Shi, Jianxin; Abnet, Christian C

2018-05-01

Background: Few studies have prospectively evaluated the association between oral microbiota and health outcomes. Precise estimates of the intrasubject microbial metric stability will allow better study planning. Therefore, we conducted a study to evaluate the temporal variability of oral microbiota. Methods: Forty individuals provided six oral samples using the OMNIgene ORAL kit and Scope mouthwash oral rinses approximately every two months over 10 months. DNA was extracted using the QIAsymphony and the V4 region of the 16S rRNA gene was amplified and sequenced using the MiSeq. To estimate temporal variation, we calculated intraclass correlation coefficients (ICCs) for a variety of metrics and examined stability after clustering samples into distinct community types using Dirichlet multinomial models (DMMs). Results: The ICCs for the alpha diversity measures were high, including for number of observed bacterial species [0.74; 95% confidence interval (CI): 0.65-0.82 and 0.79; 95% CI: 0.75-0.94] from OMNIgene ORAL and Scope mouthwash, respectively. The ICCs for the relative abundance of the top four phyla and beta diversity matrices were lower. Three clusters provided the best model fit for the DMM from the OMNIgene ORAL samples, and the probability of remaining in a specific cluster was high (59.5%-80.7%). Conclusions: The oral microbiota appears to be stable over time for multiple metrics, but some measures, particularly relative abundance, were less stable. Impact: We used this information to calculate stability-adjusted power calculations that will inform future field study protocols and experimental analytic designs. Cancer Epidemiol Biomarkers Prev; 27(5); 594-600. ©2018 AACR . ©2018 American Association for Cancer Research.

The microbiome of the oral mucosa in irritable bowel syndrome

PubMed Central

Fourie, Nicolaas H.; Wang, Dan; Abey, Sarah K.; Sherwin, LeeAnne B.; Joseph, Paule V.; Rahim-Williams, Bridgett; Ferguson, Eric G.; Henderson, Wendy A.

2016-01-01

abstract Irritable bowel syndrome (IBS) is a poorly understood disorder characterized by persistent symptoms, including visceral pain. Studies have demonstrated oral microbiome differences in inflammatory bowel diseases suggesting the potential of the oral microbiome in the study of non-oral conditions. In this exploratory study we examine whether differences exist in the oral microbiome of IBS participants and healthy controls, and whether the oral microbiome relates to symptom severity. The oral buccal mucosal microbiome of 38 participants was characterized using PhyloChip microarrays. The severity of visceral pain was assessed by orally administering a gastrointestinal test solution. Participants self-reported their induced visceral pain. Pain severity was highest in IBS participants (P = 0.0002), particularly IBS-overweight participants (P = 0.02), and was robustly correlated to the abundance of 60 OTUs, 4 genera, 5 families and 4 orders of bacteria (r2 > 0.4, P < 0.001). IBS-overweight participants showed decreased richness in the phylum Bacteroidetes (P = 0.007) and the genus Bacillus (P = 0.008). Analysis of β-diversity found significant separation of the IBS-overweight group (P < 0.05). Our oral microbial results are concordant with described fecal and colonic microbiome-IBS and -weight associations. Having IBS and being overweight, rather than IBS-subtypes, was the most important factor in describing the severity of visceral pain and variation in the microbiome. Pain severity was strongly correlated to the abundance of many taxa, suggesting the potential of the oral microbiome in diagnosis and patient phenotyping. The oral microbiome has potential as a source of microbial information in IBS. PMID:26963804

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome.

PubMed

Warinner, Christina; Speller, Camilla; Collins, Matthew J

2015-01-19

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.

Metagenomic and metatranscriptomic analysis of saliva reveals disease-associated microbiota in patients with periodontitis and dental caries.

PubMed

Belstrøm, Daniel; Constancias, Florentin; Liu, Yang; Yang, Liang; Drautz-Moses, Daniela I; Schuster, Stephan C; Kohli, Gurjeet Singh; Jakobsen, Tim Holm; Holmstrup, Palle; Givskov, Michael

2017-01-01

The taxonomic composition of the salivary microbiota has been reported to differentiate between oral health and disease. However, information on bacterial activity and gene expression of the salivary microbiota is limited. The purpose of this study was to perform metagenomic and metatranscriptomic characterization of the salivary microbiota and test the hypothesis that salivary microbial presence and activity could be an indicator of the oral health status. Stimulated saliva samples were collected from 30 individuals (periodontitis: n  = 10, dental caries: n  = 10, oral health: n  = 10). Salivary microbiota was characterized using metagenomics and metatranscriptomics in order to compare community composition and the gene expression between the three groups. Streptococcus was the predominant bacterial genus constituting approx. 25 and 50% of all DNA and RNA reads, respectively. A significant disease-associated higher relative abundance of traditional periodontal pathogens such as Porphyromonas gingivalis and Filifactor alocis and salivary microbial activity of F . alocis was associated with periodontitis. Significantly higher relative abundance of caries-associated bacteria such as Streptococcus mutans and Lactobacillus fermentum was identified in saliva from patients with dental caries. Multiple genes involved in carbohydrate metabolism were significantly more expressed in healthy controls compared to periodontitis patients. Using metagenomics and metatranscriptomics we show that relative abundance of specific oral bacterial species and bacterial gene expression in saliva associates with periodontitis and dental caries. Further longitudinal studies are warranted to evaluate if screening of salivary microbial activity of specific oral bacterial species and metabolic gene expression can identify periodontitis and dental caries at preclinical stages.

Effect of an oxygenating agent on oral bacteria in vitro and on dental plaque composition in healthy young adults

PubMed Central

Fernandez y Mostajo, Mercedes; van der Reijden, Wil A.; Buijs, Mark J.; Beertsen, Wouter; van der Weijden, Fridus; Crielaard, Wim; Zaura, Egija

2014-01-01

Oral bacteria live in symbiosis with the host. Therefore, when mouthwashes are indicated, selective inhibition of taxa contributing to disease is preferred instead of broad-spectrum antimicrobials. The potential selectivity of an oxygenating mouthwash, Ardox-X® (AX), has not been assessed. The aim of this study was to determine the antimicrobial potential of AX and the effects of a twice-daily oral rinse on dental plaque composition. Material and methods: In vitro, 16 oral bacterial strains were tested using agar diffusion susceptibility, minimum inhibitory and minimum bactericidal concentration tests. A pilot clinical study was performed with 25 healthy volunteers. Clinical assessments and microbiological sampling of supragingival plaque were performed at 1 month before the experiment (Pre-exp), at the start of the experiment (Baseline) and after the one-week experimental period (Post-exp). During the experiment individuals used AX mouthwash twice daily in absence of other oral hygiene measures. The microbiological composition of plaque was assessed by 16S rRNA gene amplicon sequencing. Results: AX showed high inter-species variation in microbial growth inhibition. The tested Prevotella strains and Fusobacterium nucleatum showed the highest sensitivity, while streptococci and Lactobacillus acidophilus were most resistant to AX. Plaque scores at Pre-exp and Baseline visits did not differ significantly (p = 0.193), nor did the microbial composition of plaque. During a period of 7-days non-brushing but twice daily rinsing plaque scores increased from 2.21 (0.31) at Baseline to 2.43 (0.39) Post-exp. A significant microbial shift in composition was observed: genus Streptococcus and Veillonella increased while Corynebacterium, Haemophilus, Leptotrichia, Cardiobacterium and Capnocytophaga decreased (p ≤ 0.001). Conclusion: AX has the potential for selective inhibition of oral bacteria. The shift in oral microbiome after 1 week of rinsing deserves further research. PMID:25101249

In vitro antimicrobial activity of Caesalpinia ferrea Martius fruits against oral pathogens.

PubMed

Sampaio, Fábio C; Pereira, Maria do Socorro V; Dias, Celidarque S; Costa, Vicente Carlos O; Conde, Nikeila C O; Buzalaf, Marília A R

2009-07-15

In the Amazon region of Brazil, the fruits of Caesalpinia ferrea Martius (Brazilian ironwood) are widely used as an antimicrobial and healing medicine in many situations including oral infections. This study aimed to evaluate the antimicrobial activity of Caesalpinia ferrea Martius fruit extract against oral pathogens. Polyphenols estimation and spectral analysis ((1)H NMR) of the methanol extract were carried out. The microorganisms Candida albicans, Streptococcus mutans, Streptococcus salivarius, Streptococcus oralis and Lactobacillus casei were tested using the microdilution method for planktonic cells (MIC) and a multispecies biofilm model. Chlorhexidine was used as positive control. Polyphenols in the extract were estimated at 7.3% and (1)H NMR analysis revealed hydroxy phenols and methoxilated compounds. MIC values for Candida albicans, Streptococcus mutans, Streptococcus salivarius, Streptococcus oralis and Lactobacillus casei were 25.0, 40.0, 66.0, 100.0, 66.0 microg/mL, respectively. For the biofilm assay, chlorhexidine and plant extract showed no growth at 10(-4) and 10(-5) microbial dilution, respectively. At 10(-4) and 10(-5) the growth values (mean+/-SD) of the negative controls (DMSO and saline solution) for Streptococcus mutans, Streptococcus sp. and Candida albicans were 8.1+/-0.7, 7.0+/-0.6 and 5.9+/-0.9 x 10(6)CFU, respectively. Caesalpinia ferrea fruit extract can inhibit in vitro growth of oral pathogens in planktonic and biofilm models supporting its use for oral infections.

Protective and destructive immunity in the periodontium: Part 1--innate and humoral immunity and the periodontium.

PubMed

Teng, Y-T A

2006-03-01

Based on the results of recent research in the field, the present paper will discuss the protective and destructive aspects of the innate vs. adaptive (humoral and cell-mediated) immunity associated with the bacterial virulent factors or antigenic determinants during periodontal pathogenesis. Attention will be focused on: (i) the Toll-like receptors (TLR), the innate immune repertoire for recognizing the unique molecular patterns of microbial components that trigger innate and adaptive immunity for effective host defenses, in some general non-oral vs. periodontal microbial infections; (ii) T-cell-mediated immunity, Th-cytokines, and osteoclastogenesis in periodontal disease progression; and (iii) some molecular techniques developed and used to identify critical microbial virulence factors or antigens associated with host immunity (using Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis as the model species). Therefore, further understanding of the molecular interactions and mechanisms associated with the host's innate and adaptive immune responses will facilitate the development of new and innovative therapeutics for future periodontal treatments.

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients.

PubMed

Marino, Poala J; Wise, Matt P; Smith, Ann; Marchesi, Julian R; Riggio, Marcello P; Lewis, Michael A O; Williams, David W

2017-06-01

Mechanically ventilated patients are at risk for developing ventilator-associated pneumonia, and it has been reported that dental plaque provides a reservoir of respiratory pathogens that may aspirate to the lungs and endotracheal tube (ETT) biofilms. For the first time, metataxonomics was used to simultaneously characterize the microbiome of dental plaque, ETTs, and non-directed bronchial lavages (NBLs) in mechanically ventilated patients to determine similarities in respective microbial communities and therefore likely associations. Bacterial 16S rRNA gene sequences from 34 samples of dental plaque, NBLs, and ETTs from 12 adult mechanically ventilated patients were analyzed. No significant differences in the microbial communities of these samples were evident. Detected bacteria were primarily oral species (e.g., Fusobacterium nucleatum, Streptococcus salivarius, Prevotella melaninogenica) with respiratory pathogens (Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcuspneumoniae, and Haemophilus influenzae) also in high abundance. The high similarity between the microbiomes of dental plaque, NBLs, and ETTs suggests that the oral cavity is indeed an important site involved in microbial aspiration to the lower airway and ETT. As such, maintenance of good oral hygiene is likely to be highly important in limiting aspiration of bacteria in this vulnerable patient group. Copyright © 2017 Elsevier Inc. All rights reserved.

Dynamics of oral microbial community profiling during severe early childhood caries development monitored by PCR-DGGE.

PubMed

Tao, Ye; Zhou, Yan; Ouyang, Yong; Lin, HuanCai

2013-09-01

To monitor the longitudinal changes in oral microbial diversity of children with severe early childhood caries (S-ECC) compared to caries free (CF) controls. Dental plaque samples of 12 children in each group at 8, 14, 20, 26 and 32 months of age were analysed. Total microbial genomic DNA was isolated from each sample, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses were carried out. The number of bands was significantly higher in the CF group (18.17±4.91 bands) than in the S-ECC group (14.54±5.56 bands) at 32 months of age (P<0.05). A total of 21 genera were identified in all subjects, and there were no significant differences between the two groups at genus level. DGGE profiles showed that most of the clusters were constructed from one individual over time in the both groups. The onset of S-ECC is accompanied by a decrease in microbial diversity. The overall composition of the microbiota is highly similar within an individual over time. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Review of Evidence for a Therapeutic Application of Traditional Japanese Kampo Medicine for Oral Diseases/Disorders.

PubMed

Veilleux, Marie-Pier; Moriyama, Satomi; Yoshioka, Masami; Hinode, Daisuke; Grenier, Daniel

2018-04-18

Kampo medicines prescribed by specialized medical practitioners and Japanese physicians have gradually reemerged in Japan as alternatives to Western medications. Kampo formulations are composed of several plant extracts and, as such, the broad variety of phytochemicals they contain likely act synergistically to provide their beneficial effects. Kampo medicines have traditionally been prescribed for a number of health conditions, including chronic hepatitis, bronchial asthma, anemia, etc. The aim of this article is to review the beneficial effects of Kampos with respect to oral health. Pertinent papers published between 1970 and 2017 were retrieved by searching in PubMed, ScienceDirect, Web of Science, and Scopus using key words followed by evaluation of the relevant articles. In vitro studies have identified a number of properties that give credence to the potential of Kampos for treating or preventing oral diseases/disorders. Given their anti-microbial and anti-inflammatory properties, they may be promising agents for controlling periodontal diseases, oral mucositis, xerostomia, and drug-induced gingival overgrowth. Since some oral diseases have a complex etiology that involves microbial pathogens and the host immune response, agents with dual functionality such as Kampo phytochemicals may offer a therapeutic advantage.

The needs of denture-brushing in geriatrics: clinical aspects and perspectives.

PubMed

Berteretche, Marie-Violaine; Mastari, Fatima; Nicolas, Emmanuel; Hüe, Olivier

2012-06-01

Oral and denture hygiene are often defective in particular with dependent persons such as geriatric subjects. The reasons are the lack of hygiene education of the subjects or those caring for them. Consequently, oral hygiene is often neglected, resulting in poor oral health and an increase in the presence of local or general infections. This paper is a report of brushing effectiveness on microbial biofilm deposits on dentures of subjects participating in a specific oral hygiene programme. Thirty-nine dentures of 30 subjects were assessed for 2 weeks following an educational brushing programme. Microbial biofilm was recovered using fluoresceine and then scanned and quantified by 'Mesurim' software three times: before study, after 1 and 2 weeks. The repeated measurement procedures showed a decrease in the percentage of biofilm present (F = 15, p < 0.001) whatever the type of denture (partial or complete) and for all biomaterials. Regular denture-brushing can improve local hygiene. Consequently, decreasing the biofilm surface can reduce the prevalence of oral pathogens, thereby contributing to the general prevention of the risks of infections such as pneumotisis. © 2011 The Gerodontology Society and John Wiley & Sons A/S.

Variations in the Oral Anaerobic Microbial Flora in Relation to Pregnancy

PubMed Central

Basavaraju, Anuradha; Durga S., Vijaya; Vanitha, B.

2012-01-01

Introduction Pregnancy gingivitis is a major oral infection. Periodontium acts as a reservoir of inflammatory mediators and sub gingival biofilms of bacteria. Aim: To evaluate the anaerobic oral microbial flora in pregnant women before delivery and after delivery by comparing them with control group. Material and Methods: The study group included fifteen cases of pregnant women before and after delivery and healthy non-pregnant women of same age as control group. Sub gingival plaque samples were collected with the help of dentists. The samples were inoculated immediately into Thioglycollate broth (MV010), transported to the laboratory, inoculated on to selective media for anaerobes (Hi-media laboratories) incubated anaerobically (Gas pack). Results: Prevotella, Tanerella forsythia, Porphyromonas gingivalis and Fusobacterium nucleatum, Veillonella, Peptostreptococcus were isolated. Discussion: The anaerobic bacteria in pregnant women were Prevotella, Tanerella forsythia and Porphyromonas gingivalis. Viellonella and Peptostreptococcus were seen in control group and after delivery. Research suggests that periodontal pathogens may travel the blood stream from the oral cavity to the placenta. Conclusion: Pregnancy has significant effect on periodontal tissue. There is a significant alteration of bacterial flora during and after pregnancy. Oral health has to become a part of antenatal care /check up. PMID:23285437

Activity of Potent and Selective Host Defense Peptide Mimetics in Mouse Models of Oral Candidiasis

PubMed Central

Ryan, Lisa K.; Freeman, Katie B.; Masso-Silva, Jorge A.; Falkovsky, Klaudia; Aloyouny, Ashwag; Markowitz, Kenneth; Hise, Amy G.; Fatahzadeh, Mahnaz; Scott, Richard W.

2014-01-01

There is a strong need for new broadly active antifungal agents for the treatment of oral candidiasis that not only are active against many species of Candida, including drug-resistant strains, but also evade microbial countermeasures which may lead to resistance. Host defense peptides (HDPs) can provide a foundation for the development of such agents. Toward this end, we have developed fully synthetic, small-molecule, nonpeptide mimetics of the HDPs that improve safety and other pharmaceutical properties. Here we describe the identification of several HDP mimetics that are broadly active against C. albicans and other species of Candida, rapidly fungicidal, and active against yeast and hyphal cultures and that exhibit low cytotoxicity for mammalian cells. Importantly, specificity for Candida over commensal bacteria was also evident, thereby minimizing potential damage to the endogenous microbiome which otherwise could favor fungal overgrowth. Three compounds were tested as topical agents in two different mouse models of oral candidiasis and were found to be highly active. Following single-dose administrations, total Candida burdens in tongues of infected animals were reduced up to three logs. These studies highlight the potential of HDP mimetics as a new tool in the antifungal arsenal for the treatment of oral candidiasis. PMID:24752272

Cost-effectiveness analysis of oral probiotics for the prevention of Clostridium difficile-associated diarrhoea in children and adolescents.

PubMed

Li, Na; Zheng, Bin; Cai, Hong-Fu; Chen, Yan-Hui; Qiu, Ming-Qi; Liu, Mao-Bai

2018-04-17

The incidence of Clostridium difficile-associated diarrhoea (CDAD) in hospitalized children and adolescents has been increasing year-on-year. Paediatric CDAD represents a significant economic burden on healthcare systems. Probiotics are live organisms thought to improve the microbial balance of the host, counteract disturbances in intestinal flora, and reduce the risk of colonization by pathogenic bacteria. We conducted a cost-effectiveness analysis to assess the economy of probiotics for the prevention of CDAD in children and adolescents receiving antibiotics. A decision tree model combined clinical effectiveness, utility, and cost data was used. Sensitivity analyses were conducted to determine the robustness of the model outcomes. The Oral probiotics strategy and No probiotics strategy offered patients 0.05876 and 0.056 QALY at a cost of $16668.70 and $20355.28, respectively. The Oral probiotics strategy exhibited higher QALY and lower cost, so it is the cost-saving strategy. The results were robust for sensitivity analyses. From the perspective of the medical system, oral probiotics as a preventive strategy for CDAD in hospitalized children and adolescents who are receiving a therapeutic course of antibiotics reduced the risk of CDAD, and it is a cost-saving strategy. Copyright © 2018. Published by Elsevier Ltd.

Oral Microbial Ecology and the Role of Salivary Immunoglobulin A

PubMed Central

Marcotte, Harold; Lavoie, Marc C.

1998-01-01

In the oral cavity, indigenous bacteria are often associated with two major oral diseases, caries and periodontal diseases. These diseases seem to appear following an inbalance in the oral resident microbiota, leading to the emergence of potentially pathogenic bacteria. To define the process involved in caries and periodontal diseases, it is necessary to understand the ecology of the oral cavity and to identify the factors responsible for the transition of the oral microbiota from a commensal to a pathogenic relationship with the host. The regulatory forces influencing the oral ecosystem can be divided into three major categories: host related, microbe related, and external factors. Among host factors, secretory immunoglobulin A (SIgA) constitutes the main specific immune defense mechanism in saliva and may play an important role in the homeostasis of the oral microbiota. Naturally occurring SIgA antibodies that are reactive against a variety of indigenous bacteria are detectable in saliva. These antibodies may control the oral microbiota by reducing the adherence of bacteria to the oral mucosa and teeth. It is thought that protection against bacterial etiologic agents of caries and periodontal diseases could be conferred by the induction of SIgA antibodies via the stimulation of the mucosal immune system. However, elucidation of the role of the SIgA immune system in controlling the oral indigenous microbiota is a prerequisite for the development of effective vaccines against these diseases. The role of SIgA antibodies in the acquisition and the regulation of the indigenous microbiota is still controversial. Our review discusses the importance of SIgA among the multiple factors that control the oral microbiota. It describes the oral ecosystems, the principal factors that may control the oral microbiota, a basic knowledge of the secretory immune system, the biological functions of SIgA, and, finally, experiments related to the role of SIgA in oral microbial ecology. PMID:9529888

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

PubMed Central

Warinner, Christina; Speller, Camilla; Collins, Matthew J.

2015-01-01

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes. PMID:25487328

Effect of Coffea canephora aqueous extract on microbial counts in ex vivo oral biofilms: a case study.

PubMed

Antonio, Andréa Gonçalves; Iorio, Natália Lopes Pontes; Farah, Adriana; Netto dos Santos, Kátia Regina; Maia, Lucianne Cople

2012-05-01

In the present study, the ex vivo antimicrobial effect of brewed coffee was tested on oral biofilms. For this, unsweetened and sweetened (10 % sucrose) brewed light-roasted Coffea canephora at 20 % was used in biofilms formed by non-stimulated saliva from three volunteers. After 30 min contact with unsweetened and sweetened brews, the average microorganism count in the biofilms reduced by 15.2 % and 12.4 %, respectively, with no statistical difference among them. We also observed a drop of microorganisms in the biofilms after treatment with sucrose solution at 5 % compared to control (saline) and to sucrose at 1 % and 3 %. In conclusion, Coffea canephora extract reduces the microbial count in oral biofilm, and our data suggest that sucrose concentration in coffee brew can influence its antimicrobial property against the referred biofilm. Georg Thieme Verlag KG Stuttgart · New York.

Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease

PubMed Central

Wang, Jinfeng; Qi, Ji; Zhao, Hui; He, Shu; Zhang, Yifei; Wei, Shicheng; Zhao, Fangqing

2013-01-01

Although attempts have been made to reveal the relationships between bacteria and human health, little is known about the species and function of the microbial community associated with oral diseases. In this study, we report the sequencing of 16 metagenomic samples collected from dental swabs and plaques representing four periodontal states. Insights into the microbial community structure and the metabolic variation associated with periodontal health and disease were obtained. We observed a strong correlation between community structure and disease status, and described a core disease-associated community. A number of functional genes and metabolic pathways including bacterial chemotaxis and glycan biosynthesis were over-represented in the microbiomes of periodontal disease. A significant amount of novel species and genes were identified in the metagenomic assemblies. Our study enriches the understanding of the oral microbiome and sheds light on the contribution of microorganisms to the formation and succession of dental plaques and oral diseases. PMID:23673380

The Fungal Biome of the Oral Cavity.

PubMed

Chandra, Jyotsna; Retuerto, Mauricio; Mukherjee, Pranab K; Ghannoum, Mahmoud

2016-01-01

Organisms residing in the oral cavity (oral microbiota) contribute to health and disease, and influence diseases like gingivitis, periodontitis, and oral candidiasis (the most common oral complication of HIV-infection). These organisms are also associated with cancer and other systemic diseases including upper respiratory infections. There is limited knowledge regarding how oral microbes interact together and influence the host immune system. Characterizing the oral microbial community (oral microbiota) in health and disease represents a critical step in gaining insight into various members of this community. While most of the studies characterizing oral microbiota have focused on bacterial community, there are few encouraging studies characterizing the oral mycobiome (the fungal component of the oral microbiota). Our group recently characterized the oral mycobiome in health and disease focusing on HIV. In this chapter we will describe the methods used by our group for characterization of the oral mycobiome.

Oral microbial and respiratory status of persons with mental retardation/intellectual and developmental disability: an observational cohort study.

PubMed

Binkley, Catherine J; Haugh, Gilbert S; Kitchens, Dinah H; Wallace, Debra L; Sessler, Daniel I

2009-11-01

The objective of this study was to determine the prevalence of select microorganisms in oral biofilms and to investigate relationships between oral and respiratory status in persons with mental retardation/intellectual and developmental disabilities (IDD). We conducted a 6-month-long observational cohort study with 63 persons with IDD. Oral examinations, oral sampling, and medical record reviews were performed at baseline and then monthly. Polymerase chain reaction (PCR) was used to analyze all baseline oral samples for the presence of Streptococcus pneumoniae, Methicillin-resistant Staphylococcus aureus (MRSA), Prevotella melaninogenica, and Candida albicans. PCR analyses were also performed on participants' samples collected in the month before being diagnosed with a respiratory infection. All subjects had P. melaninogenica detected by PCR in their oral samples. Fifty-five percent (35 of 63) of participants had S. pneumoniae, MRSA, and C. albicans in their oral samples at baseline. No dental decay was detected clinically, oral hygiene was fair, and dysphagia was common. During the 6 months of the study, there were 22 respiratory infections (35% of participants)-12 pneumonias, 7 sinusitis, 1 bronchitis, and 1 upper respiratory tract infection. Participants with microorganisms in their baseline samples were significantly more likely to develop any respiratory infection and those who had poor oral status were significantly more likely to develop pneumonia. Almost 60% of participants who developed respiratory infections had the same microorganism detected in the sample collected in the month before infection as had been detected in their baseline sample. Potentially pathogenic microorganisms in the oral cavity and poor oral status significantly increased the risk of developing respiratory infections, including pneumonia, in persons with IDD. The results suggest that colonization with these microorganisms may persist despite routine tooth brushing. Meticulous comprehensive oral hygiene of the oral cavity may be needed to reduce oropharyngeal microbial load.

Linkages between oral commensal bacteria and atherosclerotic plaques in coronary artery disease patients.

PubMed

Chhibber-Goel, Jyoti; Singhal, Varsha; Bhowmik, Debaleena; Vivek, Rahul; Parakh, Neeraj; Bhargava, Balram; Sharma, Amit

2016-01-01

Coronary artery disease is an inflammatory disorder characterized by narrowing of coronary arteries due to atherosclerotic plaque formation. To date, the accumulated epidemiological evidence supports an association between oral bacterial diseases and coronary artery disease, but has failed to prove a causal link between the two. Due to the recent surge in microbial identification and analyses techniques, a number of bacteria have been independently found in atherosclerotic plaque samples from coronary artery disease patients. In this study, we present meta-analysis from published studies that have independently investigated the presence of bacteria within atherosclerotic plaque samples in coronary artery disease patients. Data were collated from 63 studies covering 1791 patients spread over a decade. Our analysis confirms the presence of 23 oral commensal bacteria, either individually or in co-existence, within atherosclerotic plaques in patients undergoing carotid endarterectomy, catheter-based atherectomy, or similar procedures. Of these 23 bacteria, 5 ( Campylobacter rectus , Porphyromonas gingivalis , Porphyromonas endodontalis , Prevotella intermedia , Prevotella nigrescens ) are unique to coronary plaques, while the other 18 are additionally present in non-cardiac organs, and associate with over 30 non-cardiac disorders. We have cataloged the wide spectrum of proteins secreted by above atherosclerotic plaque-associated bacteria, and discuss their possible roles during microbial migration via the bloodstream. We also highlight the prevalence of specific poly-microbial communities within atherosclerotic plaques. This work provides a resource whose immediate implication is the necessity to systematically catalog landscapes of atherosclerotic plaque-associated oral commensal bacteria in human patient populations.

The oral cavity microbiota: between health, oral disease, and cancers of the aerodigestive tract.

PubMed

Le Bars, Pierre; Matamoros, Sébastien; Montassier, Emmanuel; Le Vacon, Françoise; Potel, Gilles; Soueidan, Assem; Jordana, Fabienne; de La Cochetière, Marie-France

2017-06-01

Many studies show that the human microbiome plays a critical role in the chronic pathologies of obesity, inflammatory bowel diseases, and diabetes. More recently, the interaction between cancer and the microbiome has been highlighted. Most studies have focused on the gut microbiota because it represents the most extensive bacterial community, and the body of evidence correlating it with gut syndromes is increasing. However, in the strict sense, the gastrointestinal (GI) tract begins in the oral cavity, and special attention should be paid to the specific flora of this cavity. This study reviewed the current knowledge about the various microbial ecosystems of the upper part of the GI tract and discussed their potential link to carcinogenesis. The overall composition of the microbial communities, as well as the presence or absence of "key species", in relation to carcinogenesis is addressed. Alterations in the oral microbiota can potentially be used to predict the risk of cancer. Molecular advances and the further monitoring of the microbiota will increase our understanding of the role of the microbiota in carcinogenesis and open new perspectives for future therapeutic and prophylactic modalities.

Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients.

PubMed

Tian, Na; Faller, Lina; Leffler, Daniel A; Kelly, Ciaran P; Hansen, Joshua; Bosch, Jos A; Wei, Guoxian; Paster, Bruce J; Schuppan, Detlef; Helmerhorst, Eva J

2017-03-15

Celiac disease (CD) is a chronic immune-mediated enteropathy induced by dietary gluten in genetically predisposed individuals. Saliva harbors the second highest bacterial load of the gastrointestinal (GI) tract after the colon. We hypothesized that enzymes produced by oral bacteria may be involved in gluten processing in the intestine and susceptibility to celiac disease. The aim of this study was to investigate salivary enzymatic activities and oral microbial profiles in healthy subjects versus patients with classical and refractory CD. Stimulated whole saliva was collected from patients with CD in remission ( n = 21) and refractory CD (RCD; n = 8) and was compared to healthy controls (HC; n = 20) and subjects with functional GI complaints ( n = 12). Salivary gluten-degrading activities were monitored with the tripeptide substrate Z-Tyr-Pro-Gln-pNA and the α-gliadin-derived immunogenic 33-mer peptide. The oral microbiome was profiled by 16S rRNA-based MiSeq analysis. Salivary glutenase activities were higher in CD patients compared to controls, both before and after normalization for protein concentration or bacterial load. The oral microbiomes of CD and RCD patients showed significant differences from that of healthy subjects, e.g., higher salivary levels of lactobacilli ( P < 0.05), which may partly explain the observed higher gluten-degrading activities. While the pathophysiological link between the oral and gut microbiomes in CD needs further exploration, the presented data suggest that oral microbe-derived enzyme activities are elevated in subjects with CD, which may impact gluten processing and the presentation of immunogenic gluten epitopes to the immune system in the small intestine. IMPORTANCE Ingested gluten proteins are the triggers of intestinal inflammation in celiac disease (CD). Certain immunogenic gluten domains are resistant to intestinal proteases but can be hydrolyzed by oral microbial enzymes. Very little is known about the endogenous proteolytic processing of gluten proteins in the oral cavity. Given that this occurs prior to gluten reaching the small intestine, such enzymes are likely to contribute to the composition of the gluten digest that ultimately reaches the small intestine and causes CD. We demonstrated that endogenous salivary protease activities are incomplete, likely liberating peptides from larger gluten proteins. The potentially responsible microbes were identified. The study included refractory CD patients, who have been studied less with regard to CD pathogenesis. Copyright © 2017 American Society for Microbiology.

Metagenomic sequencing reveals altered metabolic pathways in the oral microbiota of sailors during a long sea voyage

PubMed Central

Zheng, Weiwei; Zhang, Ze; Liu, Cuihua; Qiao, Yuanyuan; Zhou, Dianrong; Qu, Jia; An, Huaijie; Xiong, Ming; Zhu, Zhiming; Zhao, Xiaohang

2015-01-01

Seafaring is a difficult occupation, and sailors face higher health risks than individuals on land. Commensal microbiota participates in the host immune system and metabolism, reflecting the host's health condition. However, the interaction mechanisms between the microbiota and the host's health condition remain unclear. This study reports the influence of long sea voyages on human health by utilising a metagenomic analysis of variation in the microbiota of the buccal mucosa. Paired samples collected before and after a sea-voyage were analysed. After more than 120 days of ocean sailing, the oral microbial diversity of sailors was reduced by approximately 5 fold, and the levels of several pathogens (e.g., Streptococcus pneumonia) increased. Moreover, 69.46% of the identified microbial sequences were unclassified microbiota. Notably, several metabolic pathways were dramatically decreased, including folate biosynthesis, carbohydrate, lipid and amino acid pathways. Clinical examination of the hosts confirmed the identified metabolic changes, as demonstrated by decreased serum levels of haemoglobin and folic acid, a decreased neutrophil-to-lymphocyte ratio, and increased levels of triglycerides, cholesterol and homocysteine, which are consistent with the observed microbial variation. Our study suggests that oral mucosal bacteria may reflect host health conditions and could provide approaches for improving the health of sailors. PMID:26154405

A Simplified Extemporaneously Prepared Potassium Chloride Oral Solution.

PubMed

Tannous, Elias; Tal, Yana; Amarny, Kamal

2016-01-01

Although commercial preparations of oral potassium supplements are usually available, there are times when our Medical Center is faced with situations in which the oral solution of potassium chloride is not available. This solution is necessary for our pediatric outpatients who cannot swallow tablets and need an oral solution. Moreover, there are no studies available which describe an extemporaneously prepared potassium chloride oral solution on which we can rely for assigning a beyond-use date. The aim of this study was to formulate an extemporaneous pediatric oral solution of potassium chloride and to determine the physical and chemical stability of this preparation. We prepared 1 mMoL/mL by withdrawing 25 mL of potassium chloride 14.9%. Ora-Sweet SF was added to 50 mL in a metered flask. The solution was kept refrigerated (2°C to 8°C). Samples were withdrawn to measure potassium concentration, pH, and microbial overgrowth. The test was performed by our biochemical laboratory. The oral solution of potassium chloride 1 mMoL/mL stored at 2°C to 8°C maintained at least 91% of the initial concentration for 28 days. There were no notable changes in pH, and the solution remained physically stable with no visual microbial growth. The oral solution of potassium chloride 1 mMoL/mL prepared in Ora-Sweet and stored at 2°C to 8°C in amber glass bottles is expected to remain stable for 28 days. Copyright© by International Journal of Pharmaceutical Compounding, Inc.

The effect of polyvinylpyrrolidone-sodium hyaluronate gel (Gelclair) on oral microbial colonization and pain control compared with other rinsing solutions in patients with oral mucositis after allogeneic stem cells transplantation

PubMed Central

Vokurka, Samuel; Skardova, Jana; Hruskova, Renata; Kabatova-Maxova, Klara; Svoboda, Tomas; Bystricka, Eva; Steinerova, Katerina; Koza, Vladimir

2011-01-01

Summary Background Gelclair is an oral lubricating gel used in the management of oral mucositis (OM). We evaluated its efficacy, tolerance and impact on oral cavity microbial colonization in patients with OM after allogeneic hematopoietic stem cells transplantation. Material/Method Gelclair was administered in a group of 22 patients with active OM. A control group of 15 patients used other rinsing solutions (chlorhexidine, benzydamine, salvia). Tests with oral cavity swabs for microbiology analysis were performed once a week. Results The characteristics of OM in both groups were comparable, and rinsing solutions had satisfactory tolerability. There was no difference in the median improvement of oral intake and OM-related pain relief, which was assessed mostly as “slight effect”. In the Gelclair group, the effect duration was longer (median 3 [0–5] vs. 1 [0–3] hours, p=0.001). There was significant increase of Enterococcus faecalis and Candida sp. colonization of the oral cavity over the course of the hospitalization and significantly reduced incidence of such colonization in patients with OM in the Gelclair group: 1/22 (5%) vs. 6/15 (40%), p=0.01. In vitro tests showed inhibited growth of Enterococcus faecalis and Candida sp. colonies within the area of the Gelclair application. Conclusions Gelclair may be individually helpful in the management of OM and pain in patients after allogeneic stem cells transplantation. Its use did not lead to worsened oral bacterial and yeast colonization and probably even helped to protect mucosa from Enterococcus and Candida sp. Further studies based on larger cohorts are needed. PMID:21959611

Antimicrobial activity of jasmine oil against oral microorganisms

NASA Astrophysics Data System (ADS)

Thaweboon, S.; Thaweboon, B.; Kaypetch, R.

2018-02-01

Jasmine sambac is a species of jasmine indigenous to the tropical and warm temperature regions in particular West and Southeast Asia. Essential oil extracted from the flowers of J. sambac has been shown to have anti-oxidant activity. However, very little information regarding antimicrobial activity especially oral microorganisms exists. Objective: To investigate antimicrobial effect of essential oil extracted from flowers of J. sambac against various oral microorganisms. Materials and Methods: Oral microbial strains used in the study were Streptococcus mutans KPSK2, Staphylococcus aureus ATCC 5638, Lactobacillus casei ATCC 6363, Klebsiella pneumoniae (clinical isolate), Escherichia coli ATCC 25922, Candida albicans ATCC 10231, Candida krusei ATCC 6258, Candida parapsilosis ATCC 22019, Candida tropicalis (clinical isolate), Candida glabrata ATCC 90030, Candida pseudotropicalis (clinical isolate) and Candida stellatoidia (clinical isolate). The potential of microbial growth inhibition of the oil was firstly screened by Kirby-Bauer disk diffusion method and then the minimum inhibitory concentration (MIC) was determined by agar dilution method. Results: Jasmine oil showed antimicrobial activities against S. mutans, L. casei, E. coli and all strains of Candida species with the zones of inhibition ranging from 9 to 26 mm and MIC values of 0.19-1.56 %v/v. Conclusion: Results from the present study are scientific evidence to demonstrate that jasmine oil could be employed as a natural antimicrobial agent against oral microorganisms.

Intraindividual variation in core microbiota in peri-implantitis and periodontitis

PubMed Central

Maruyama, Noriko; Maruyama, Fumito; Takeuchi, Yasuo; Aikawa, Chihiro; Izumi, Yuichi; Nakagawa, Ichiro

2014-01-01

The oral microbiota change dramatically with each part of the oral cavity, even within the same mouth. Nevertheless, the microbiota associated with peri-implantitis and periodontitis have been considered the same. To improve our knowledge of the different communities of complex oral microbiota, we compared the microbial features between peri-implantitis and periodontitis in 20 patients with both diseases. Although the clinical symptoms of peri-implantitis were similar to those of periodontitis, the core microbiota of the diseases differed. Correlation analysis revealed the specific microbial co-occurrence patterns and found some of the species were associated with the clinical parameters in a disease-specific manner. The proportion of Prevotella nigrescens was significantly higher in peri-implantitis than in periodontitis, while the proportions of Peptostreptococcaceae sp. and Desulfomicrobium orale were significantly higher in periodontitis than in peri-implantitis. The severity of the peri-implantitis was also species-associated, including with an uncultured Treponema sp. that correlated to 4 clinical parameters. These results indicate that peri-implantitis and periodontitis are both polymicrobial infections with different causative pathogens. Our study provides a framework for the ecologically different bacterial communities between peri-implantitis and periodontitis, and it will be useful for further studies to understand the complex microbiota and pathogenic mechanisms of oral polymicrobial diseases. PMID:25308100

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

PubMed Central

Chen, Tsute; Yu, Wen-Han; Izard, Jacques; Baranova, Oxana V.; Lakshmanan, Abirami; Dewhirst, Floyd E.

2010-01-01

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD—taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org PMID:20624719

Combinatorial Effects of Arginine and Fluoride on Oral Bacteria

PubMed Central

Zheng, X.; Cheng, X.; Wang, L.; Qiu, W.; Wang, S.; Zhou, Y.; Li, M.; Li, Y.; Cheng, L.; Li, J.; Zhou, X.

2015-01-01

Dental caries is closely associated with the microbial disequilibrium between acidogenic/aciduric pathogens and alkali-generating commensal residents within the dental plaque. Fluoride is a widely used anticaries agent, which promotes tooth hard-tissue remineralization and suppresses bacterial activities. Recent clinical trials have shown that oral hygiene products containing both fluoride and arginine possess a greater anticaries effect compared with those containing fluoride alone, indicating synergy between fluoride and arginine in caries management. Here, we hypothesize that arginine may augment the ecological benefit of fluoride by enriching alkali-generating bacteria in the plaque biofilm and thus synergizes with fluoride in controlling dental caries. Specifically, we assessed the combinatory effects of NaF/arginine on planktonic and biofilm cultures of Streptococcus mutans, Streptococcus sanguinis, and Porphyromonas gingivalis with checkerboard microdilution assays. The optimal NaF/arginine combinations were selected, and their combinatory effects on microbial composition were further examined in single-, dual-, and 3-species biofilm using bacterial species–specific fluorescence in situ hybridization and quantitative polymerase chain reaction. We found that arginine synergized with fluoride in suppressing acidogenic S. mutans in both planktonic and biofilm cultures. In addition, the NaF/arginine combination synergistically reduced S. mutans but enriched S. sanguinis within the multispecies biofilms. More importantly, the optimal combination of NaF/arginine maintained a “streptococcal pressure” against the potential growth of oral anaerobe P. gingivalis within the alkalized biofilm. Taken together, we conclude that the combinatory application of fluoride and arginine has a potential synergistic effect in maintaining a healthy oral microbial equilibrium and thus represents a promising ecological approach to caries management. PMID:25477312

The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci

PubMed Central

Sandberg, Scott; Reyes, Iris; Fritsche, Thomas R.

2017-01-01

Allergic and autoimmune diseases had been attributed to lack of exposure to biodiversity, an important factor in regulating immune homeostasis in a healthy host. We posit that the microbiome of healthy dairy farmers (DF) will be richer than non-farmers (NF) living in urban settings due to exposure to a greater biodiversity in the dairy environment. However, no studies have investigated the relationships between microbiota of dairy farmers (DF) compared with urban non-farmers (NF). We compared the nasal and oral microbiota of dairy farmers (N_DF, O_DF, respectively) with nasal and oral microbiota of NF in the same geographical area. The N_DF showed high microbial diversity with hundreds of unique genera that reflected environmental/occupational exposures. The nasal and oral microbiomes clustered separately from each other using Principal Coordinate Analysis, and with DF harboring two-fold and 1.5-fold greater exclusive genera in their nose and mouth respectively, than did non-farmers. Additionally, the N_DF group had a lower burden of Staphylococcus spp. suggesting a correlation between higher microbial diversity and competition for colonization by staphylococci. The N_DF samples were negative for the mecA gene, a marker of methicillin-resistance in staphylococci. The lower burden of staphylococci was found to be independent of the abundance of Corynebacterium spp. Exposure to greater biodiversity could enhance microbial competition, thereby reducing colonization with opportunistic pathogens. Future studies will analyze whether exposure to livestock microbiomes offers protection from acute and chronic diseases. PMID:28850578

The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci.

PubMed

Shukla, Sanjay K; Ye, Zhan; Sandberg, Scott; Reyes, Iris; Fritsche, Thomas R; Keifer, Matthew

2017-01-01

Allergic and autoimmune diseases had been attributed to lack of exposure to biodiversity, an important factor in regulating immune homeostasis in a healthy host. We posit that the microbiome of healthy dairy farmers (DF) will be richer than non-farmers (NF) living in urban settings due to exposure to a greater biodiversity in the dairy environment. However, no studies have investigated the relationships between microbiota of dairy farmers (DF) compared with urban non-farmers (NF). We compared the nasal and oral microbiota of dairy farmers (N_DF, O_DF, respectively) with nasal and oral microbiota of NF in the same geographical area. The N_DF showed high microbial diversity with hundreds of unique genera that reflected environmental/occupational exposures. The nasal and oral microbiomes clustered separately from each other using Principal Coordinate Analysis, and with DF harboring two-fold and 1.5-fold greater exclusive genera in their nose and mouth respectively, than did non-farmers. Additionally, the N_DF group had a lower burden of Staphylococcus spp. suggesting a correlation between higher microbial diversity and competition for colonization by staphylococci. The N_DF samples were negative for the mecA gene, a marker of methicillin-resistance in staphylococci. The lower burden of staphylococci was found to be independent of the abundance of Corynebacterium spp. Exposure to greater biodiversity could enhance microbial competition, thereby reducing colonization with opportunistic pathogens. Future studies will analyze whether exposure to livestock microbiomes offers protection from acute and chronic diseases.

The role of the gut microbiota in food allergy.

PubMed

Rachid, Rima; Chatila, Talal A

2016-12-01

The rise in the prevalence of food allergy over the past decades has focused attention of factors that may impact disease development, most notably the gut microbiota. The gut microbial communities play a crucial role in promoting oral tolerance. Their alteration by such factors as Cesarean section delivery, diet and antibiotics may influence disease development. This review highlights recent progress in our understanding of the role of the gut microbiota in the development of food allergy. Food allergy is associated with alterations in the gut microbiota or dysbiosis early in life that may be predictive of disease persistence versus tolerance acquisition. Evidence for the benefits of adjunct therapy with probiotics for the prevention of food allergies and for potentiating oral immunotherapy remains circumstantial, with further studies needed to validate its use. Studies in murine models of food allergy suggest that microbial therapy with protolerogenic bacteria such as certain Clostridial species holds promise in future applications for prevention or therapy of food allergy. Progress in understanding the role of dysbiosis in food allergy and the factors that promote its development, such as antibiotic therapy, diet, modes of infant delivery, and environmental exposures, offer windows of opportunity for both preventive and therapeutic interventions to stem the rising tide of the food allergy epidemic.

The Oral Microbiota in Health and Disease: An Overview of Molecular Findings.

PubMed

Siqueira, José F; Rôças, Isabela N

2017-01-01

Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity may be even much larger. Nucleic acid technologies have also been helpful in profiling bacterial communities and identifying disease-related patterns. This chapter provides an overview of the diversity and taxonomy of oral bacteria associated with health and disease.

Oral Health Measurement in Nursing Research: State of the Science

PubMed Central

Munro, Cindy L.; Grap, Mary Jo; Jablonski, Rita; Boyle, Anne

2008-01-01

Oral health can impact general health and systemic disease. Changes in dental plaque, oral microbial flora, and local oral immunity may be important in the development or exacerbation of disease in critically ill patients, trauma patients, adults with chronic obstructive pulmonary disease, and frail elderly. Inasmuch as oral health potentially can be influenced by nursing interventions, nursing research in this area can contribute greatly to improved patient outcomes in these diverse populations. The authors’ research teams have conducted several federally funded projects focused on oral health and have developed synergy in research methods. A unifying theme for these research projects is the measurement of oral health. Standardized measures of components of oral health are available and applicable across populations, and their uses and relationship to nursing research and patient outcomes will be discussed. PMID:16766627

Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China.

PubMed

Chen, Xingdong; Winckler, Björn; Lu, Ming; Cheng, Hongwei; Yuan, Ziyu; Yang, Yajun; Jin, Li; Ye, Weimin

2015-01-01

Poor oral health has been linked with an increased risk of esophageal squamous cell carcinoma (ESCC). We investigated whether alteration of oral microbiota is associated with ESCC risk. Fasting saliva samples were collected from 87 incident and histopathologicallly diagnosed ESCC cases, 63 subjects with dysplasia and 85 healthy controls. All subjects were also interviewed with a questionnaire. V3-V4 region of 16S rRNA was amplified and sequenced by 454-pyrosequencing platform. Carriage of each genus was compared by means of multivariate-adjusted odds ratios derived from logistic regression model. Relative abundance was compared using Metastats method. Beta diversity was estimated using Unifrac and weighted Unifrac distances. Principal coordinate analysis (PCoA) was applied to ordinate dissimilarity matrices. Multinomial logistic regression was used to compare the coordinates between different groups. ESCC subjects had an overall decreased microbial diversity compared to control and dysplasia subjects (P<0.001). Decreased carriage of genera Lautropia, Bulleidia, Catonella, Corynebacterium, Moryella, Peptococcus and Cardiobacterium were found in ESCC subjects compared to non-ESCC subjects. Multinomial logistic regression analyses on PCoA coordinates also revealed that ESCC subjects had significantly different levels for several coordinates compared to non-ESCC subjects. In conclusion, we observed a correlation between altered salivary bacterial microbiota and ESCC risk. The results of our study on the saliva microbiome are of particular interest as it reflects the shift in microbial communities. Further studies are warranted to verify this finding, and if being verified, to explore the underlying mechanisms.

In-vitro analysis of APA microcapsules for oral delivery of live bacterial cells.

PubMed

Chen, H; Ouyang, W; Jones, M; Haque, T; Lawuyi, B; Prakash, S

2005-08-01

Oral administration of microcapsules containing live bacterial cells has potential as an alternative therapy for several diseases. This article evaluates the suitability of the alginate-poly-L-lysine-alginate (APA) microcapsules for oral delivery of live bacterial cells, in-vitro, using a dynamic simulated human gastro-intestinal (GI) model. Results showed that the APA microcapsules were morphologically stable in the simulated stomach conditions, but did not retain their structural integrity after a 3-day exposure in simulated human GI media. The microbial populations of the tested bacterial cells and the activities of the tested enzymes in the simulated human GI suspension were not substantially altered by the presence of the APA microcapsules, suggesting that there were no significant adverse effects of oral administration of the APA microcapsules on the flora of the human gastrointestinal tract. When the APA microcapsules containing Lactobacillus plantarum 80 (LP80) were challenged in the simulated gastric medium (pH = 2.0), 80.0% of the encapsulated cells remained viable after a 5-min incubation; however, the viability decreased considerably (8.3%) after 15 min and dropped to 2.6% after 30 min and lower than 0.2% after 60 min, indicating the limitations of the currently obtainable APA membrane for oral delivery of live bacteria. Further in-vivo studies are required before conclusions can be made concerning the inadequacy of APA microcapsules for oral delivery of live bacterial cells.

Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments

PubMed Central

Whiteson, Katrine L.; Lazarevic, Vladimir; Tangomo-Bento, Manuela; Girard, Myriam; Maughan, Heather; Pittet, Didier; Francois, Patrice; Schrenzel, Jacques

2014-01-01

We aim to understand the microbial ecology of noma (cancrum oris), a devastating ancient illness which causes severe facial disfigurement in>140,000 malnourished children every year. The cause of noma is still elusive. A chaotic mix of microbial infection, oral hygiene and weakened immune system likely contribute to the development of oral lesions. These lesions are a plausible entry point for unidentified microorganisms that trigger gangrenous facial infections. To catalog bacteria present in noma lesions and identify candidate noma-triggering organisms, we performed a cross-sectional sequencing study of 16S rRNA gene amplicons from sixty samples of gingival fluid from twelve healthy children, twelve children suffering from noma (lesion and healthy sites), and twelve children suffering from Acute Necrotizing Gingivitis (ANG) (lesion and healthy sites). Relative to healthy individuals, samples taken from lesions in diseased mouths were enriched with Spirochaetes and depleted for Proteobacteria. Samples taken from healthy sites of diseased mouths had proportions of Spirochaetes and Proteobacteria that were similar to healthy control individuals. Samples from noma mouths did not have a higher abundance of Fusobacterium, casting doubt on its role as a causative agent of noma. Microbial communities sampled from noma and ANG lesions were dominated by the same Prevotella intermedia OTU, which was much less abundant in healthy sites sampled from the same mouths. Multivariate analysis confirmed that bacterial communities in healthy and lesion sites were significantly different. Several OTUs in the Orders Erysipelotrichales, Clostridiales, Bacteroidales, and Spirochaetales were identified as indicators of noma, suggesting that one or more microbes within these Orders is associated with the development of noma lesions. Future studies should include longitudinal sampling of viral and microbial components of this community, before and early in noma lesion development. PMID:25474262

Smokeless tobacco impacts oral microbiota in a Syrian Golden hamster cheek pouch carcinogenesis model.

PubMed

Jin, Jinshan; Guo, Lei; VonTungeln, Linda; Vanlandingham, Michelle; Cerniglia, Carl E; Chen, Huizhong

2018-05-28

The use of smokeless tobacco products (STPs) can cause many serious health problems. The oral microbiota plays important roles in oral and systemic health, and the disruption in the oral microbial population is linked to periodontal disease and other health problems. To assess the impact of smokeless tobacco on oral microbiota in vivo, high-throughput sequencing was used to examine the oral microbiota present in Syrian Golden hamster cheek pouches. Sixteen hamsters were divided into four groups and treated with the STP Grizzly snuff (0, 2.5, 25, or 250 mg) twice daily for 4 weeks. After 0, 1, 2, 3, and 4 weeks of treatment, bacterial genomic DNA was extracted from oral swabs sampled from the cheek pouches of the hamsters. The oral bacterial communities present in different hamster groups were characterized by sequencing the hypervariable regions V1-V2 and V4 of 16S rRNA using the Illumina MiSeq platform. Fifteen phyla, 27 classes, 59 orders, 123 families, and 250 genera were identified from 4,962,673 sequence reads from the cheek pouch samples. The bacterial diversity and taxonomic abundances for the different treatment groups were compared to the non-treated hamsters. Bacterial diversity was significantly decreased after 4 weeks of exposure to 2.5 mg, and significantly increased by exposure to 250 mg STP. Treatment with 250 mg STP significantly increased Firmicutes, transiently increased Cyanobacteria and TM7, and decreased Bacteroidetes and Fusobacteria compared to the control group. At the genus level, 4 weeks of administration of 250 mg STP significantly increased Granulicatella, Streptococcus, Oribacterium, Anaerococcus, Acidaminococcus, Actinomyces, Eubacterium, Negativicoccus, and Staphylococcus, and decreased Bacteroides, Buleidia, Dialister, and Leptotrichia, and transiently decreased Arcanobacterium compared to the control group. For the first time, an animal model was used for evaluating the effects of STP on oral microbiota by metagenomic sequencing. Our results provide a view of the shift of the oral microbiota in response to STP exposure in Syrian Golden hamster. Our findings indicate that the use of smokeless tobacco significantly disrupts the oral microbiota. Published by Elsevier Ltd.

Respiratory pathogen colonization of dental plaque, the lower airways, and endotracheal tube biofilms during mechanical ventilation.

PubMed

Sands, Kirsty M; Wilson, Melanie J; Lewis, Michael A O; Wise, Matt P; Palmer, Nicki; Hayes, Anthony J; Barnes, Rosemary A; Williams, David W

2017-02-01

In mechanically ventilated patients, the endotracheal tube is an essential interface between the patient and ventilator, but inadvertently, it also facilitates the development of ventilator-associated pneumonia (VAP) by subverting pulmonary host defenses. A number of investigations suggest that bacteria colonizing the oral cavity may be important in the etiology of VAP. The present study evaluated microbial changes that occurred in dental plaque and lower airways of 107 critically ill mechanically ventilated patients. Dental plaque and lower airways fluid was collected during the course of mechanical ventilation, with additional samples of dental plaque obtained during the entirety of patients' hospital stay. A "microbial shift" occurred in dental plaque, with colonization by potential VAP pathogens, namely, Staphylococcus aureus and Pseudomonas aeruginosa in 35 patients. Post-extubation analyses revealed that 70% and 55% of patients whose dental plaque included S aureus and P aeruginosa, respectively, reverted back to having a predominantly normal oral microbiota. Respiratory pathogens were also isolated from the lower airways and within the endotracheal tube biofilms. To the best of our knowledge, this is the largest study to date exploring oral microbial changes during both mechanical ventilation and after recovery from critical illness. Based on these findings, it was apparent that during mechanical ventilation, dental plaque represents a source of potential VAP pathogens. Copyright © 2016 Elsevier Inc. All rights reserved.

Subgingival Microbial Communities in Leukocyte Adhesion Deficiency and Their Relationship with Local Immunopathology

PubMed Central

Moutsopoulos, Niki M.; Abusleme, Loreto; Greenwell-Wild, Teresa; Dutzan, Nicolas; Paster, Bruce J.; Munson, Peter J.; Fine, Daniel H.; Uzel, Gulbu; Holland, Steven M.

2015-01-01

Leukocyte Adhesion Deficiency I (LAD-I) is a primary immunodeficiency caused by single gene mutations in the CD18 subunit of β2 integrins which result in defective transmigration of neutrophils into the tissues. Affected patients suffer from recurrent life threatening infections and severe oral disease (periodontitis). Microbial communities in the local environment (subgingival plaque) are thought to be the triggers for inflammatory periodontitis, yet little is known regarding the microbial communities associated with LAD-I periodontitis. Here we present the first comprehensive characterization of the subgingival communities in LAD-I, using a 16S rRNA gene-based microarray, and investigate the relationship of this tooth adherent microbiome to the local immunopathology of periodontitis. We show that the LAD subgingival microbiome is distinct from that of health and Localized Aggressive Periodontitits. Select periodontitis-associated species in the LAD microbiome included Parvimonas micra, Porphyromonas endodontalis, Eubacterium brachy and Treponema species. Pseudomonas aeruginosa, a bacterium not typically found in subgingival plaque is detected in LAD-I. We suggest that microbial products from LAD-associated communities may have a role in stimulating the local inflammatory response. We demonstrate that bacterial LPS translocates into the lesions of LAD-periodontitis potentially triggering immunopathology. We also show in in vitro assays with human macrophages and in vivo in animal models that microbial products from LAD-associated subgingival plaque trigger IL-23-related immune responses, which have been shown to dominate in patient lesions. In conclusion, our current study characterizes the subgingival microbial communities in LAD-periodontitis and supports their role as triggers of disease pathogenesis. PMID:25741691

Subgingival microbial communities in Leukocyte Adhesion Deficiency and their relationship with local immunopathology.

PubMed

Moutsopoulos, Niki M; Chalmers, Natalia I; Barb, Jennifer J; Abusleme, Loreto; Greenwell-Wild, Teresa; Dutzan, Nicolas; Paster, Bruce J; Munson, Peter J; Fine, Daniel H; Uzel, Gulbu; Holland, Steven M

2015-03-01

Leukocyte Adhesion Deficiency I (LAD-I) is a primary immunodeficiency caused by single gene mutations in the CD18 subunit of β2 integrins which result in defective transmigration of neutrophils into the tissues. Affected patients suffer from recurrent life threatening infections and severe oral disease (periodontitis). Microbial communities in the local environment (subgingival plaque) are thought to be the triggers for inflammatory periodontitis, yet little is known regarding the microbial communities associated with LAD-I periodontitis. Here we present the first comprehensive characterization of the subgingival communities in LAD-I, using a 16S rRNA gene-based microarray, and investigate the relationship of this tooth adherent microbiome to the local immunopathology of periodontitis. We show that the LAD subgingival microbiome is distinct from that of health and Localized Aggressive Periodontitits. Select periodontitis-associated species in the LAD microbiome included Parvimonas micra, Porphyromonas endodontalis, Eubacterium brachy and Treponema species. Pseudomonas aeruginosa, a bacterium not typically found in subgingival plaque is detected in LAD-I. We suggest that microbial products from LAD-associated communities may have a role in stimulating the local inflammatory response. We demonstrate that bacterial LPS translocates into the lesions of LAD-periodontitis potentially triggering immunopathology. We also show in in vitro assays with human macrophages and in vivo in animal models that microbial products from LAD-associated subgingival plaque trigger IL-23-related immune responses, which have been shown to dominate in patient lesions. In conclusion, our current study characterizes the subgingival microbial communities in LAD-periodontitis and supports their role as triggers of disease pathogenesis.

Proton Pump Inhibitor Initiation and Withdrawal affects Gut Microbiota and Readmission Risk in Cirrhosis.

PubMed

Bajaj, Jasmohan S; Acharya, Chathur; Fagan, Andrew; White, Melanie B; Gavis, Edith; Heuman, Douglas M; Hylemon, Phillip B; Fuchs, Michael; Puri, Puneet; Schubert, Mitchell L; Sanyal, Arun J; Sterling, Richard K; Stravitz, R Todd; Siddiqui, Mohammad S; Luketic, Velimir; Lee, Hannah; Sikaroodi, Masoumeh; Gillevet, Patrick M

2018-06-06

Cirrhosis is associated with gut microbial dysbiosis, high readmissions and proton pump inhibitor (PPI) overuse, which could be inter-linked. Our aim was to determine the effect of PPI use, initiation and withdrawl on gut microbiota and readmissions in cirrhosis. Four cohorts were enrolled. Readmissions study: Cirrhotic inpatients were followed throughout the hospitalization and 30/90-days post-discharge. PPI initiation, withdrawal/continuation patterns were analyzed between those with/without readmissions. Cross-sectional microbiota study: Cirrhotic outpatients and controls underwent stool microbiota analysis. Beneficial autochthonous and oral-origin taxa analysis vis-à-vis PPI use was performed. Longitudinal studies: Two cohorts of decompensated cirrhotic outpatients were enrolled. Patients on chronic unindicated PPI use were withdrawn for 14 days. Patients not on PPI were started on omeprazole for 14 days. Microbial analysis for oral-origin taxa was performed pre/post-intervention. Readmissions study: 343 inpatients (151 on admission PPI) were enrolled. 21 were withdrawn and 45 were initiated on PPI resulting in a PPI use increase of 21%. PPIs were associated with higher 30 (p = 0.002) and 90-day readmissions (p = 0.008) independent of comorbidities, medications, MELD and age. Cross-sectional microbiota: 137 cirrhotics (59 on PPI) and 45 controls (17 on PPI) were included. PPI users regardless of cirrhosis had higher oral-origin microbiota while cirrhotics on PPI had lower autochthonous taxa compared to the rest. Longitudinal studies: Fifteen decompensated cirrhotics tolerated omeprazole initiation with an increase in oral-origin microbial taxa compared to baseline. PPIs were withdrawn from an additional 15 outpatients, which resulted in a significant reduction of oral-origin taxa compared to baseline. PPIs modulate readmission risk and microbiota composition in cirrhosis, which responds to withdrawal. The systematic withdrawal and judicious use of PPIs is needed from a clinical and microbiological perspective in decompensated cirrhosis.

Comparison of oral microbial profiles between children with severe early childhood caries and caries-free children using the human oral microbe identification microarray.

PubMed

Ma, Chen; Chen, Feng; Zhang, Yifei; Sun, Xiangyu; Tong, Peiyuan; Si, Yan; Zheng, Shuguo

2015-01-01

Early childhood caries (ECC) has become a prevalent public health problem among Chinese preschool children. The bacterial microflora is considered to be an important factor in the formation and progress of dental caries. However, high-throughput and large-scale studies of the primary dentition are lacking. The present study aimed to compare oral microbial profiles between children with severe ECC (SECC) and caries-free children. Both saliva and supragingival plaque samples were obtained from children with SECC (n = 20) and caries-free children (n = 20) aged 3 to 4 years. The samples were assayed using the Human Oral Microbe Identification Microarray (HOMIM). A total of 379 bacterial species were detected in both the saliva and supragingival plaque samples from all children. Thirteen (including Streptococcus) and two (Streptococcus and Actinomyces) bacterial species in supragingival plaque and saliva, respectively, showed significant differences in prevalence between the two groups. Of these, the frequency of Streptococcus mutans detection was significantly higher in both saliva (p = 0.026) and plaque (p = 0.006) samples from the SECC group than in those from the caries-free group. The findings of our study revealed differences in the oral microbiota between the SECC and caries-free groups Several genera, including Streptococcus, Porphyromonas, and Actinomyces, are strongly associated with SECC and can be potential biomarkers of dental caries in the primary dentition.

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress.

PubMed

Bharwani, Aadil; Mian, M Firoz; Surette, Michael G; Bienenstock, John; Forsythe, Paul

2017-01-11

Stress-related disorders involve systemic alterations, including disruption of the intestinal microbial community. Given the putative connections between the microbiota, immunity, neural function, and behaviour, we investigated the potential for microbe-induced gut-to-brain signalling to modulate the impact of stress on host behaviour and immunoregulation. Male C57BL/6 mice treated orally over 28 days with either Lactobacillus rhamnosus (JB-1) ™ or vehicle were subjected to chronic social defeat and assessed for alterations in behaviour and immune cell phenotype. 16S rRNA sequencing and mass spectrometry were employed to analyse the faecal microbial community and metabolite profile. Treatment with JB-1 decreased stress-induced anxiety-like behaviour and prevented deficits in social interaction with conspecifics. However, JB-1 did not alter development of aggressor avoidance following social defeat. Microbial treatment attenuated stress-related activation of dendritic cells while increasing IL-10+ regulatory T cells. Furthermore, JB-1 modulated the effect of stress on faecal metabolites with neuroactive and immunomodulatory properties. Exposure to social defeat altered faecal microbial community composition and reduced species richness and diversity, none of which was prevented by JB-1. Stress-related microbiota disruptions persisted in vehicle-treated mice for 3 weeks following stressor cessation. These data demonstrate that despite the complexity of the gut microbiota, exposure to a single microbial strain can protect against certain stress-induced behaviours and systemic immune alterations without preventing dysbiosis. This work supports microbe-based interventions for stress-related disorders.

Combinatorial effects of arginine and fluoride on oral bacteria.

PubMed

Zheng, X; Cheng, X; Wang, L; Qiu, W; Wang, S; Zhou, Y; Li, M; Li, Y; Cheng, L; Li, J; Zhou, X; Xu, X

2015-02-01

Dental caries is closely associated with the microbial disequilibrium between acidogenic/aciduric pathogens and alkali-generating commensal residents within the dental plaque. Fluoride is a widely used anticaries agent, which promotes tooth hard-tissue remineralization and suppresses bacterial activities. Recent clinical trials have shown that oral hygiene products containing both fluoride and arginine possess a greater anticaries effect compared with those containing fluoride alone, indicating synergy between fluoride and arginine in caries management. Here, we hypothesize that arginine may augment the ecological benefit of fluoride by enriching alkali-generating bacteria in the plaque biofilm and thus synergizes with fluoride in controlling dental caries. Specifically, we assessed the combinatory effects of NaF/arginine on planktonic and biofilm cultures of Streptococcus mutans, Streptococcus sanguinis, and Porphyromonas gingivalis with checkerboard microdilution assays. The optimal NaF/arginine combinations were selected, and their combinatory effects on microbial composition were further examined in single-, dual-, and 3-species biofilm using bacterial species-specific fluorescence in situ hybridization and quantitative polymerase chain reaction. We found that arginine synergized with fluoride in suppressing acidogenic S. mutans in both planktonic and biofilm cultures. In addition, the NaF/arginine combination synergistically reduced S. mutans but enriched S. sanguinis within the multispecies biofilms. More importantly, the optimal combination of NaF/arginine maintained a "streptococcal pressure" against the potential growth of oral anaerobe P. gingivalis within the alkalized biofilm. Taken together, we conclude that the combinatory application of fluoride and arginine has a potential synergistic effect in maintaining a healthy oral microbial equilibrium and thus represents a promising ecological approach to caries management. © International & American Associations for Dental Research 2014.

The microbiome associated with equine periodontitis and oral health.

PubMed

Kennedy, Rebekah; Lappin, David Francis; Dixon, Padraic Martin; Buijs, Mark Johannes; Zaura, Egija; Crielaard, Wim; O'Donnell, Lindsay; Bennett, David; Brandt, Bernd Willem; Riggio, Marcello Pasquale

2016-04-14

Equine periodontal disease is a common and painful condition and its severe form, periodontitis, can lead to tooth loss. Its aetiopathogenesis remains poorly understood despite recent increased awareness of this disorder amongst the veterinary profession. Bacteria have been found to be causative agents of the disease in other species, but current understanding of their role in equine periodontitis is extremely limited. The aim of this study was to use high-throughput sequencing to identify the microbiome associated with equine periodontitis and oral health. Subgingival plaque samples from 24 horses with periodontitis and gingival swabs from 24 orally healthy horses were collected. DNA was extracted from samples, the V3-V4 region of the bacterial 16S rRNA gene amplified by PCR and amplicons sequenced using Illumina MiSeq. Data processing was conducted using USEARCH and QIIME. Diversity analyses were performed with PAST v3.02. Linear discriminant analysis effect size (LEfSe) was used to determine differences between the groups. In total, 1308 OTUs were identified and classified into 356 genera or higher taxa. Microbial profiles at health differed significantly from periodontitis, both in their composition (p < 0.0001, F = 12.24; PERMANOVA) and in microbial diversity (p < 0.001; Mann-Whitney test). Samples from healthy horses were less diverse (1.78, SD 0.74; Shannon diversity index) and were dominated by the genera Gemella and Actinobacillus, while the periodontitis group samples showed higher diversity (3.16, SD 0.98) and were dominated by the genera Prevotella and Veillonella. It is concluded that the microbiomes associated with equine oral health and periodontitis are distinct, with the latter displaying greater microbial diversity.

Microbiota diversity and gene expression dynamics in human oral biofilms

PubMed Central

2014-01-01

Background Micro-organisms inhabiting teeth surfaces grow on biofilms where a specific and complex succession of bacteria has been described by co-aggregation tests and DNA-based studies. Although the composition of oral biofilms is well established, the active portion of the bacterial community and the patterns of gene expression in vivo have not been studied. Results Using RNA-sequencing technologies, we present the first metatranscriptomic study of human dental plaque, performed by two different approaches: (1) A short-reads, high-coverage approach by Illumina sequencing to characterize the gene activity repertoire of the microbial community during biofilm development; (2) A long-reads, lower-coverage approach by pyrosequencing to determine the taxonomic identity of the active microbiome before and after a meal ingestion. The high-coverage approach allowed us to analyze over 398 million reads, revealing that microbial communities are individual-specific and no bacterial species was detected as key player at any time during biofilm formation. We could identify some gene expression patterns characteristic for early and mature oral biofilms. The transcriptomic profile of several adhesion genes was confirmed through qPCR by measuring expression of fimbriae-associated genes. In addition to the specific set of gene functions overexpressed in early and mature oral biofilms, as detected through the short-reads dataset, the long-reads approach detected specific changes when comparing the metatranscriptome of the same individual before and after a meal, which can narrow down the list of organisms responsible for acid production and therefore potentially involved in dental caries. Conclusions The bacteria changing activity during biofilm formation and after meal ingestion were person-specific. Interestingly, some individuals showed extreme homeostasis with virtually no changes in the active bacterial population after food ingestion, suggesting the presence of a microbial community which could be associated to dental health. PMID:24767457

Microbiota diversity and gene expression dynamics in human oral biofilms.

PubMed

Benítez-Páez, Alfonso; Belda-Ferre, Pedro; Simón-Soro, Aurea; Mira, Alex

2014-04-27

Micro-organisms inhabiting teeth surfaces grow on biofilms where a specific and complex succession of bacteria has been described by co-aggregation tests and DNA-based studies. Although the composition of oral biofilms is well established, the active portion of the bacterial community and the patterns of gene expression in vivo have not been studied. Using RNA-sequencing technologies, we present the first metatranscriptomic study of human dental plaque, performed by two different approaches: (1) A short-reads, high-coverage approach by Illumina sequencing to characterize the gene activity repertoire of the microbial community during biofilm development; (2) A long-reads, lower-coverage approach by pyrosequencing to determine the taxonomic identity of the active microbiome before and after a meal ingestion. The high-coverage approach allowed us to analyze over 398 million reads, revealing that microbial communities are individual-specific and no bacterial species was detected as key player at any time during biofilm formation. We could identify some gene expression patterns characteristic for early and mature oral biofilms. The transcriptomic profile of several adhesion genes was confirmed through qPCR by measuring expression of fimbriae-associated genes. In addition to the specific set of gene functions overexpressed in early and mature oral biofilms, as detected through the short-reads dataset, the long-reads approach detected specific changes when comparing the metatranscriptome of the same individual before and after a meal, which can narrow down the list of organisms responsible for acid production and therefore potentially involved in dental caries. The bacteria changing activity during biofilm formation and after meal ingestion were person-specific. Interestingly, some individuals showed extreme homeostasis with virtually no changes in the active bacterial population after food ingestion, suggesting the presence of a microbial community which could be associated to dental health.

Microbial interactions in building of communities

PubMed Central

Wright, Christopher J.; Burns, Logan H.; Jack, Alison A.; Back, Catherine R.; Dutton, Lindsay C.; Nobbs, Angela H.; Lamont, Richard J.; Jenkinson, Howard F.

2012-01-01

SUMMARY Establishment of a community is considered to be essential for microbial growth and survival in the human oral cavity. Biofilm communities have increased resilience to physical forces, antimicrobial agents, and nutritional variations. Specific cell-to-cell adherence processes, mediated by adhesin-receptor pairings on respective microbial surfaces, are able to direct community development. These interactions co-localize species in mutually beneficial relationships, such as streptococci, veillonellae, Porphyromonas gingivalis and Candida albicans. In transition from the planktonic mode of growth to a biofilm community, microorganisms undergo major transcriptional and proteomic changes. These occur in response to sensing of diffusible signals, such as autoinducer molecules, and to contact with host tissues or other microbial cells. Underpinning many of these processes are intracellular phosphorylation events that regulate a large number of microbial interactions relevant to community formation and development. PMID:23253299

Dental plaque biofilm in oral health and disease.

PubMed

Seneviratne, Chaminda Jayampath; Zhang, Cheng Fei; Samaranayake, Lakshman Perera

2011-01-01

Dental plaque is an archetypical biofilm composed of a complex microbial community. It is the aetiological agent for major dental diseases such as dental caries and periodontal disease. The clinical picture of these dental diseases is a net result of the cross-talk between the pathogenic dental plaque biofilm and the host tissue response. In the healthy state, both plaque biofilm and adjacent tissues maintain a delicate balance, establishing a harmonious relationship between the two. However, changes occur during the disease process that transform this 'healthy' dental plaque into a 'pathogenic' biofilm. Recent advances in molecular microbiology have improved the understanding of dental plaque biofilm and produced numerous clinical benefits. Therefore, it is imperative that clinicians keep abreast with these new developments in the field of dentistry. Better understanding of the molecular mechanisms behind dental diseases will facilitate the development of novel therapeutic strategies to establish a 'healthy dental plaque biofilm' by modulating both host and microbial factors. In this review, the present authors aim to summarise the current knowledge on dental plaque as a microbial biofilm and its properties in oral health and disease.

Microbial Reprogramming Inhibits Western Diet-Associated Obesity

PubMed Central

Smillie, Christopher; Levkovich, Tatiana; Perrotta, Alison; Bhela, Siddheshvar; Varian, Bernard J.; Ibrahim, Yassin M.; Lakritz, Jessica R.; Kearney, Sean M.; Chatzigiagkos, Antonis; Hafler, David A.; Alm, Eric J.; Erdman, Susan E.

2013-01-01

A recent epidemiological study showed that eating ‘fast food’ items such as potato chips increased likelihood of obesity, whereas eating yogurt prevented age-associated weight gain in humans. It was demonstrated previously in animal models of obesity that the immune system plays a critical role in this process. Here we examined human subjects and mouse models consuming Westernized ‘fast food’ diet, and found CD4+ T helper (Th)17-biased immunity and changes in microbial communities and abdominal fat with obesity after eating the Western chow. In striking contrast, eating probiotic yogurt together with Western chow inhibited age-associated weight gain. We went on to test whether a bacteria found in yogurt may serve to lessen fat pathology by using purified Lactobacillus reuteri ATCC 6475 in drinking water. Surprisingly, we discovered that oral L. reuteri therapy alone was sufficient to change the pro-inflammatory immune cell profile and prevent abdominal fat pathology and age-associated weight gain in mice regardless of their baseline diet. These beneficial microbe effects were transferable into naïve recipient animals by purified CD4+ T cells alone. Specifically, bacterial effects depended upon active immune tolerance by induction of Foxp3+ regulatory T cells (Treg) and interleukin (Il)-10, without significantly changing the gut microbial ecology or reducing ad libitum caloric intake. Our finding that microbial targeting restored CD4+ T cell balance and yielded significantly leaner animals regardless of their dietary ‘fast food’ indiscretions suggests population-based approaches for weight management and enhancing public health in industrialized societies. PMID:23874682

Quantitative microbial risk assessment of Cryptosporidium and Giardia in well water from a native community of Mexico.

PubMed

Balderrama-Carmona, Ana Paola; Gortáres-Moroyoqui, Pablo; Álvarez-Valencia, Luis Humberto; Castro-Espinoza, Luciano; Balderas-Cortés, José de Jesús; Mondaca-Fernández, Iram; Chaidez-Quiroz, Cristóbal; Meza-Montenegro, María Mercedes

2015-01-01

Cryptosporidium and Giardia are gastrointestinal disease-causing organisms transmitted by the fecal-oral route, zoonotic and prevalent in all socioeconomic segments with greater emphasis in rural communities. The goal of this study was to assess the risk of cryptosporidiosis and giardiasis of Potam dwellers consuming drinking water from communal well water. To achieve the goal, quantitative microbial risk assessment (QMRA) was carried out as follows: (a) identification of Cryptosporidium oocysts and Giardia cysts in well water samples by information collection rule method, (b) assessment of exposure to healthy Potam residents, (c) dose-response modelling, and (d) risk characterization using an exponential model. All well water samples tested were positive for Cryptosporidium and Giardia. The QMRA results indicate a mean of annual risks of 99:100 (0.99) for cryptosporidiosis and 1:1 (1.0) for giardiasis. The outcome of the present study may drive decision-makers to establish an educational and treatment program to reduce the incidence of parasite-borne intestinal infection in the Potam community, and to conduct risk analysis programs in other similar rural communities in Mexico.

Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans.

PubMed

Vanhatalo, Anni; Blackwell, Jamie R; L'Heureux, Joanna; Williams, David W; Smith, Ann; van der Giezen, Mark; Winyard, Paul G; Kelly, James; Jones, Andrew M

2018-05-25

Imbalances in the oral microbial community have been associated with reduced cardiovascular and metabolic health. A possible mechanism linking the oral microbiota to health is the nitrate (NO 3 - )-nitrite (NO 2 - )-nitric oxide (NO) pathway, which relies on oral bacteria to reduce NO 3 - to NO 2 - . NO (generated from both NO 2 - and L-arginine) regulates vascular endothelial function and therefore blood pressure (BP). By sequencing bacterial 16S rRNA genes we examined the relationships between the oral microbiome and physiological indices of NO bioavailability and possible changes in these variables following 10 days of NO 3 - (12mmol/d) and placebo supplementation in young (18-22yrs) and old (70-79yrs) normotensive humans (n=18). NO 3 - supplementation altered the salivary microbiome compared to placebo by increasing the relative abundance of Proteobacteria (+225%) and decreasing the relative abundance of Bacteroidetes (-46%; P<0.05). After NO 3 - supplementation the relative abundances of Rothia (+127%) and Neisseria (+351%) were greater, and Prevotella (-60%) and Veillonella (-65%) were lower than in the placebo condition (all P<0.05). NO 3 - supplementation increased plasma concentration of NO 2 - and reduced systemic blood pressure in old (70-79yrs), but not young (18-22yrs), participants. High abundances of Rothia and Neisseria and low abundances of Prevotella and Veillonella were correlated with greater increases in plasma [NO 2 - ] in response to NO 3 - supplementation. The current findings indicate that the oral microbiome is malleable to change with increased dietary intake of inorganic NO 3 - , and that diet-induced changes in the oral microbial community are related to indices of NO homeostasis and vascular health in vivo. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

OralCard: a bioinformatic tool for the study of oral proteome.

PubMed

Arrais, Joel P; Rosa, Nuno; Melo, José; Coelho, Edgar D; Amaral, Diana; Correia, Maria José; Barros, Marlene; Oliveira, José Luís

2013-07-01

The molecular complexity of the human oral cavity can only be clarified through identification of components that participate within it. However current proteomic techniques produce high volumes of information that are dispersed over several online databases. Collecting all of this data and using an integrative approach capable of identifying unknown associations is still an unsolved problem. This is the main motivation for this work. We present the online bioinformatic tool OralCard, which comprises results from 55 manually curated articles reflecting the oral molecular ecosystem (OralPhysiOme). It comprises experimental information available from the oral proteome both of human (OralOme) and microbial origin (MicroOralOme) structured in protein, disease and organism. This tool is a key resource for researchers to understand the molecular foundations implicated in biology and disease mechanisms of the oral cavity. The usefulness of this tool is illustrated with the analysis of the oral proteome associated with diabetes melitus type 2. OralCard is available at http://bioinformatics.ua.pt/oralcard. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Critical Role for Extracellular DNA in Dental Plaque Formation.

PubMed

Rostami, N; Shields, R C; Yassin, S A; Hawkins, A R; Bowen, L; Luo, T L; Rickard, A H; Holliday, R; Preshaw, P M; Jakubovics, N S

2017-02-01

Extracellular DNA (eDNA) has been identified in the matrix of many different monospecies biofilms in vitro, including some of those produced by oral bacteria. In many cases, eDNA stabilizes the structure of monospecies biofilms. Here, the authors aimed to determine whether eDNA is an important component of natural, mixed-species oral biofilms, such as plaque on natural teeth or dental implants. To visualize eDNA in oral biofilms, approaches for fluorescently stained eDNA with either anti-DNA antibodies or an ultrasensitive cell-impermeant dye, YOYO-1, were first developed using Enterococcus faecalis, an organism that has previously been shown to produce extensive eDNA structures within biofilms. Oral biofilms were modelled as in vitro "microcosms" on glass coverslips inoculated with the natural microbial population of human saliva and cultured statically in artificial saliva medium. Using antibodies and YOYO-1, eDNA was found to be distributed throughout microcosm biofilms, and was particularly abundant in the immediate vicinity of cells. Similar arrangements of eDNA were detected in biofilms on crowns and overdenture abutments of dental implants that had been recovered from patients during the restorative phase of treatment, and in subgingival dental plaque of periodontitis patients, indicating that eDNA is a common component of natural oral biofilms. In model oral biofilms, treatment with a DNA-degrading enzyme, NucB from Bacillus licheniformis, strongly inhibited the accumulation of biofilms. The bacterial species diversity was significantly reduced by treatment with NucB and particularly strong reductions were observed in the abundance of anaerobic, proteolytic bacteria such as Peptostreptococcus, Porphyromonas and Prevotella. Preformed biofilms were not significantly reduced by NucB treatment, indicating that eDNA is more important or more exposed during the early stages of biofilm formation. Overall, these data demonstrate that dental plaque eDNA is potentially an important target for oral biofilm control.

Oral Biofilm Architecture on Natural Teeth

PubMed Central

Zijnge, Vincent; van Leeuwen, M. Barbara M.; Degener, John E.; Abbas, Frank; Thurnheer, Thomas; Gmür, Rudolf; M. Harmsen, Hermie J.

2010-01-01

Periodontitis and caries are infectious diseases of the oral cavity in which oral biofilms play a causative role. Moreover, oral biofilms are widely studied as model systems for bacterial adhesion, biofilm development, and biofilm resistance to antibiotics, due to their widespread presence and accessibility. Despite descriptions of initial plaque formation on the tooth surface, studies on mature plaque and plaque structure below the gum are limited to landmark studies from the 1970s, without appreciating the breadth of microbial diversity in the plaque. We used fluorescent in situ hybridization to localize in vivo the most abundant species from different phyla and species associated with periodontitis on seven embedded teeth obtained from four different subjects. The data showed convincingly the dominance of Actinomyces sp., Tannerella forsythia, Fusobacterium nucleatum, Spirochaetes, and Synergistetes in subgingival plaque. The latter proved to be new with a possibly important role in host-pathogen interaction due to its localization in close proximity to immune cells. The present study identified for the first time in vivo that Lactobacillus sp. are the central cells of bacterial aggregates in subgingival plaque, and that Streptococcus sp. and the yeast Candida albicans form corncob structures in supragingival plaque. Finally, periodontal pathogens colonize already formed biofilms and form microcolonies therein. These in vivo observations on oral biofilms provide a clear vision on biofilm architecture and the spatial distribution of predominant species. PMID:20195365

Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing

PubMed Central

Wang, Yuan; Zhang, Jie; Chen, Xi; Jiang, Wen; Wang, Sa; Xu, Lei; Tu, Yan; Zheng, Pei; Wang, Ying; Lin, Xiaolong; Chen, Hui

2017-01-01

Background: Alterations of oral microbiota are the main cause of the progression of caries. The goal of this study was to characterize the oral microbiota in childhood caries based on single-molecule real-time sequencing. Methods: A total of 21 preschoolers, aged 3–5 years old with severe early childhood caries, and 20 age-matched, caries-free children as controls were recruited. Saliva samples were collected, followed by DNA extraction, Pacbio sequencing, and phylogenetic analyses of the oral microbial communities. Results: Eight hundred and seventy six species derived from 13 known bacterial phyla and 110 genera were detected from 41 children using Pacbio sequencing. At the species level, 38 species, including Veillonella spp., Streptococcus spp., Prevotella spp., and Lactobacillus spp., showed higher abundance in the caries group compared to the caries-free group (p < 0.05). The core microbiota at the genus and species levels was more stable in the caries-free micro-ecological niche. At follow-up, oral examinations 6 months after sample collection, development of new dental caries was observed in 5 children (the transitional group) among the 21 caries free children. Compared with the caries-free children, in the transitional and caries groups, 6 species, which were more abundant in the caries-free group, exhibited a relatively low abundance in both the caries group and the transitional group (p < 0.05). We conclude that Abiotrophia spp., Neisseria spp., and Veillonella spp., might be associated with healthy oral microbial ecosystem. Prevotella spp., Lactobacillus spp., Dialister spp., and Filifactor spp. may be related to the pathogenesis and progression of dental caries. PMID:29187843

Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing.

PubMed

Wang, Yuan; Zhang, Jie; Chen, Xi; Jiang, Wen; Wang, Sa; Xu, Lei; Tu, Yan; Zheng, Pei; Wang, Ying; Lin, Xiaolong; Chen, Hui

2017-01-01

Background: Alterations of oral microbiota are the main cause of the progression of caries. The goal of this study was to characterize the oral microbiota in childhood caries based on single-molecule real-time sequencing. Methods: A total of 21 preschoolers, aged 3-5 years old with severe early childhood caries, and 20 age-matched, caries-free children as controls were recruited. Saliva samples were collected, followed by DNA extraction, Pacbio sequencing, and phylogenetic analyses of the oral microbial communities. Results: Eight hundred and seventy six species derived from 13 known bacterial phyla and 110 genera were detected from 41 children using Pacbio sequencing. At the species level, 38 species, including Veillonella spp., Streptococcus spp., Prevotella spp., and Lactobacillus spp., showed higher abundance in the caries group compared to the caries-free group ( p < 0.05). The core microbiota at the genus and species levels was more stable in the caries-free micro-ecological niche. At follow-up, oral examinations 6 months after sample collection, development of new dental caries was observed in 5 children (the transitional group) among the 21 caries free children. Compared with the caries-free children, in the transitional and caries groups, 6 species, which were more abundant in the caries-free group, exhibited a relatively low abundance in both the caries group and the transitional group ( p < 0.05). We conclude that Abiotrophia spp., Neisseria spp., and Veillonella spp., might be associated with healthy oral microbial ecosystem. Prevotella spp., Lactobacillus spp., Dialister spp., and Filifactor spp. may be related to the pathogenesis and progression of dental caries.

The scientific exploration of saliva in the post-proteomic era: from database back to basic function

PubMed Central

Ruhl, Stefan

2012-01-01

The proteome of human saliva can be considered as being essentially completed. Diagnostic markers for a number of diseases have been identified among salivary proteins and peptides, taking advantage of saliva as an easy-to-obtain biological fluid. Yet, the majority of disease markers identified so far are serum components and not intrinsic proteins produced by the salivary glands. Furthermore, despite the fact that saliva is essential for protecting the oral integuments and dentition, little progress has been made in finding risk predictors in the salivary proteome for dental caries or periodontal disease. Since salivary proteins, and in particular the attached glycans, play an important role in interactions with the microbial world, the salivary glycoproteome and other post-translational modifications of salivary proteins need to be studied. Risk markers for microbial diseases, including dental caries, are likely to be discovered among the highly glycosylated major protein species in saliva. This review will attempt to raise new ideas and also point to under-researched areas that may hold promise for future applicability in oral diagnostics and prediction of oral disease. PMID:22292826

Design and stability study of a paediatric oral solution of methotrexate 2 mg/ml.

PubMed

Vrignaud, Sandy; Briot, Thomas; Launay, Aurélie; Kempf, Marie; Lagarce, Frédéric

2015-06-20

Oral paediatric forms development by pharmaceutical industry is still insufficient. The present study was performed to propose an adapted and pleasant formulation of liquid oral formulation of MTX. The solution is composed of injectable methotrexate, water, Ora Sweet(®) and sodium bicarbonate. After 120 days storage, pH remained stable at about 8 in all formulations, insuring no risk of MTX precipitation. MTX content in solution formulation, determined by high performance liquid chromatography measurements, remained in the specifications of >90% of the initial concentration when stored at 4 and 25°C. Forced degradation of MTX by heat and acidic conditions allowed formation and detection of degradation products by the analytical method. Microbial study of the preparation shows that the solution remains in the specifications during all the storage, or after one sample each week during one month, eventually indicating the microbial properties are not affected by patient use. To conclude, we here propose a new MTX liquid formulation stable for at least 120 days. Copyright © 2015 Elsevier B.V. All rights reserved.

A practical guide to the oral microbiome and its relation to health and disease

PubMed Central

Krishnan, K; Chen, T; Paster, BJ

2016-01-01

The oral microbiome is incredibly complex with the average adult harboring about 50 to 100 billion bacteria in the oral cavity, which represent about 200 predominant bacterial species. Collectively, there are approximately 700 predominant taxa of which less than 1/3 still have not yet been grown in vitro. Compared to other body sites, the oral microbiome is unique and readily accessible. There is extensive literature available describing the oral microbiome and discussing the roles that bacteria may play in oral health and disease. However, the purpose of this review is not to rehash these detailed studies but rather to educate the reader with understanding the essence of the oral microbiome, namely that there are abundant bacteria in numbers and types, that there are molecular methods to rapidly determine bacterial associations, that there is site-specificity for colonization of the host, that there are specific associations with oral health and disease, that oral bacteria may serve as biomarkers for non-oral diseases, and that oral microbial profiles may have potential use to assess disease risk. PMID:27219464

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major).

PubMed

Kropáčková, Lucie; Pechmanová, Hana; Vinkler, Michal; Svobodová, Jana; Velová, Hana; Těšičký, Martin; Martin, Jean-François; Kreisinger, Jakub

2017-01-01

The gastrointestinal tract of vertebrates is inhabited by diverse bacterial communities that induce marked effects on the host physiology and health status. The composition of the gastrointestinal microbiota is characterized by pronounced taxonomic and functional variability among different regions of the vertebrate gastrointestinal tract. Despite the relatively solid knowledge on the among-region variations of the gastrointestinal microbiota in model mammalian species, there are only a few studies concerning among-region variations of the gastrointestinal microbiota in free-living non-mammalian vertebrate taxa. We used Illumina MiSeq sequencing of bacterial 16S rRNA amplicons to compare the diversity as well as taxonomic composition of bacterial communities in proximal vs. distal parts of the gastrointestinal tract (represented by oral swabs and faecal samples, respectively) in a wild passerine bird, the great tit (Parus major). The diversity of the oral microbiota was significantly higher compared to the faecal microbiota, whereas interindividual variation was higher in faecal than in oral samples. We also observed a pronounced difference in taxonomic content between the oral and faecal microbiota. Bacteria belonging to the phyla Proteobacteria, Firmicutes and Actinobacteria typically dominated in both oral and faecal samples. A high abundance of bacteria belonging to Tenericutes was observed only in faecal samples. Surprisingly, we found only a slight correlation between the faecal and oral microbiota at the within-individual level, suggesting that the microbial composition in these body sites is shaped by independent regulatory processes. Given the independence of these two communities at the individual level, we propose that simultaneous sampling of the faecal and oral microbiota will extend our understanding of host vs. microbiota interactions in wild populations.

The microbiology of the peri-implant sulcus following successful implantation of oral prosthetic treatments.

PubMed

Asadzadeh, Nafiseh; Naderynasab, Mahbobeh; Fard, Fojhan Ghorbanian; Rohi, Ali; Haghi, Hamidreza Rajati

2012-01-01

Oral implants are widely used in partially and fully edentulous patients; however, the integration of an implant can be endangered by factors such as intraoral bacteria or inflammatory reactions. The purpose of this study was to evaluate the microbial flora present in the sulcus around dental implants and to assess the relationship between gingival health and microbial flora present. Twenty patients who had received oral implants with no complications were followed for a period of 9 months. Assessment of probing depth, the presence of bleeding on probing and microbial sampling from the peri-implant sulcus were performed at three different time points- 4 weeks after surgery, 1 month and 6 months after loading. The samples were taken by paper points and transferred to the microbiology lab in thioglyocolate cultures. In order to do a colony count and isolate the aerobic capnophilic and anerobic bacteria the samples were cultured and incubated on laboratory media. The colonies were also identified using various diagnostic tests. Alterations in the presence of various bacterial species over time and gum health were tested using analysis of variance (ANOVA) with Tukey's test post hoc. The average pocket depth for each patient ranged from 1.37 ± 0.39 mm to 2.55 ± 0.72 mm. The bacteria isolated from the cultured samples included aerobic, facultative anerobic, obligate anerobic and capnophilic bacteria. The anerobic conditions created in the peri-implant sulcus might with time enhance the number of anerobic bacteria present following dental implant loading.

Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis

PubMed Central

Midura-Kiela, Monica T.; Ramalingam, Rajalakshmy; Larmonier, Claire B.; Chase, John H.; Caporaso, J. Gregory; Besselsen, David G.; Ghishan, Fayez K.; Kiela, Pawel R.

2016-01-01

Inflammatory bowel diseases (IBD) are associated with functional inhibition of epithelial Na+/H+ exchange. In mice, a selective disruption of NHE3 (Slc9a3), a major apical Na+/H+ exchanger, also promotes IBD-like symptoms and gut microbial dysbiosis. We hypothesized that disruption of Na+/H+ exchange is necessary for the development of dysbiosis, which promotes an exacerbated mucosal inflammatory response. Therefore, we performed a temporal analysis of gut microbiota composition, and mucosal immune response to adoptive T cell transfer was evaluated in Rag2-/- and NHE3-/-/Rag2-/- (DKO) mice with and without broad-spectrum antibiotics. Microbiome (16S profiling), colonic histology, T cell and neutrophil infiltration, mucosal inflammatory tone, and epithelial permeability were analyzed. In adoptive T cell transfer colitis model, Slc9a3 status was the most significant determinant of gut microbial community. In DKO mice, NHE3-deficiency and dysbiosis were associated with dramatically accelerated and exacerbated disease, with rapid body weight loss, increased mucosal T cell and neutrophil influx, increased mucosal cytokine expression, increased permeability, and expansion of CD25-FoxP3+ Tregs; this enhanced susceptibility was alleviated by oral broad-spectrum antibiotics. Based on these results and our previous work, we postulate that epithelial electrolyte homeostasis is an important modulator in the progression of colitis, acting through remodeling of the gut microbial community. PMID:27050757

Probiotics as oral health biotherapeutics.

PubMed

Saha, Shyamali; Tomaro-Duchesneau, Catherine; Tabrizian, Maryam; Prakash, Satya

2012-09-01

Oral health is affected by its resident microorganisms. Three prominent oral disorders are dental caries, gingivitis and periodontitis, with the oral microbiota playing a key role in the initiation/progression of all three. Understanding the microbiota and the diseases they may cause is critical to the development of new therapeutics. This review is focused on probiotics for the prevention and/or treatment of oral diseases. This review describes the oral ecosystem and its correlation with oral health/disease. The pathogenesis and current prevention/treatment strategies of periodontal diseases (PD) and dental caries (DC) are depicted. An introduction of probiotics is followed by an analysis of their role in PD and DC, and their potential role(s) in oral health. Finally, a discussion ensues on the future research directions and limitations of probiotics for oral health. An effective oral probiotic formulation should contribute to the prevention/treatment of microbial diseases of the oral cavity. Understanding the oral microbiota's role in oral disease is important for the development of a therapeutic to prevent/treat dental diseases. However, investigations into clinical efficacy, delivery/dose optimization, mechanism(s) of action and other related parameters are yet to be fully explored. Keeping this in mind, investigations into oral probiotic therapies are proving promising.

Saliva and dental plaque.

PubMed

Rudney, J D

2000-12-01

Dental plaque is being redefined as oral biofilm. Diverse overlapping microbial consortia are present on all oral tissues. Biofilms are structured, displaying features like channels and projections. Constituent species switch back and forth between sessile and planktonic phases. Saliva is the medium for planktonic suspension. Several major functions can be defined for saliva in relation to oral biofilm. It serves as a medium for transporting planktonic bacteria within and between mouths. Bacteria in transit may be vulnerable to negative selection. Salivary agglutinins may prevent reattachment to surfaces. Killing by antimicrobial proteins may lead to attachment of dead cells. Salivary proteins form conditioning films on all oral surfaces. This contributes to positive selection for microbial adherence. Saliva carries chemical messengers which allow live adherent cells to sense a critical density of conspecifics. Growth begins, and thick biofilms may become resistant to antimicrobial substances. Salivary macromolecules may be catabolized, but salivary flow also may clear dietary substrates. Salivary proteins act in ways that benefit both host and microbe. All have multiple functions, and many do the same job. They form heterotypic complexes, which may exist in large micelle-like structures. These issues make it useful to compare subjects whose saliva functions differently. We have developed a simultaneous assay for aggregation, killing, live adherence, and dead adherence of oral species. Screening of 149 subjects has defined high killing/low adherence, low killing/high adherence, high killing/high adherence, and low killing/low adherence groups. These will be evaluated for differences in their flora.

Stability of sotalol hydrochloride in extemporaneously prepared oral suspension formulations.

PubMed

Sidhom, Madiha B; Rivera, Nadya; Almoazen, Hassan; Taft, David R; Kirschenbaum, Harold L

2005-01-01

The physical, chemical, and microbial stabilities of extemporaneously compounded oral liquid formulations of sotalol hydrochloride were studied. Sotalol hydrochloride oral liquid suspensions (5mg/mL) were prepared from commercially available tablets (Betapace) in a 1:1 mixture of Ora-Plus: Ora-Sweet, a 1:1 mixture of Ora-Plus:Ora-Sweet SF, and a 1:2.4 mixture of simple syrup:methylcellulose vehicle. Six batches of each formulation were prepared; three were stored at refrigerated temperature (2 deg to 8 deg C) and three at room temperature (20 deg to 25 deg C). Samples were collected from each batch weekly for 6 weeks, and again at 12 weeks. Samples were analyzed by means of a high-performance liquid chromatographic method, and the concentrations obtained were compared to the theoretical time zero value. Samples were examined for pH, odor, color, and consistency changes. The suspensions also were evaluated for their microbial stability. Sotalol hydrochloride oral liquid suspensions (5mg/mL) were chemically stable for 12 weeks regardless of storage conditions (room temperature or refrigerated). Bacterial growth was not supported by any of the formulations. Suspensions stored at refrigerated temperature retained better physical quality (e.g., odor, color, and consistency) than suspensions stored at room temperature. Overall, this study demonstrates that oral formulations of sotalol hydrochloride can be readily prepared with commercially available vehicles. The method of preparation is relatively simple, the materials are relatively inexpensive, and the products have a shelf-life of at least 12 weeks.

The pathogenic persona of community associated oral streptococci

PubMed Central

Whitmore, Sarah E.; Lamont, Richard J.

2011-01-01

Summary The mitis group streptococci (MGS) are widespread in the oral cavity and are traditionally associated with oral health. However, these organisms have many attributes that contribute to the development of pathogenic oral communities. MGS adhere rapidly to saliva-coated tooth surfaces, thereby providing an attachment substratum for more overtly pathogenic organisms such as Porphyromonas gingivalis, and the two species assemble into heterotypic communities. Close physical association facilitates physiologic support, and pathogens such as Actinobacillus actinomycetemcomitans display resource partitioning to favour carbon sources generated by streptococcal metabolism. MGS exchange information with community members through a number of interspecies signaling systems including AI-2 and contact dependent mechanisms. Signal transduction systems induced in P. gingivalis are based on protein dephosphorylation mediated by the tyrosine phosphatase Ltp1, and converge on a LuxR-family transcriptional regulator, CdhR. Phenotypic responses in P. gingivalis include regulation of hemin uptake systems and gingipain activity, processes that are intimately linked to the virulence of the organism. Furthermore, communities of S. gordonii with P. gingivalis or with A. actinomycetemcomitans are more pathogenic in animal models than the constituent species alone. We propose that MGS should be considered accessory pathogens, organisms whose pathogenic potential only becomes evident in the context of a heterotypic microbial community. PMID:21635580

The pathogenic persona of community-associated oral streptococci.

PubMed

Whitmore, Sarah E; Lamont, Richard J

2011-07-01

The mitis group streptococci (MGS) are widespread in the oral cavity and are traditionally associated with oral health. However, these organisms have many attributes that contribute to the development of pathogenic oral communities. MGS adhere rapidly to saliva-coated tooth surfaces, thereby providing an attachment substratum for more overtly pathogenic organisms such as Porphyromonas gingivalis, and the two species assemble into heterotypic communities. Close physical association facilitates physiologic support, and pathogens such as Aggregatibacter actinomycetemcomitans display resource partitioning to favour carbon sources generated by streptococcal metabolism. MGS exchange information with community members through a number of interspecies signalling systems including AI-2 and contact dependent mechanisms. Signal transduction systems induced in P. gingivalis are based on protein dephosphorylation mediated by the tyrosine phosphatase Ltp1, and converge on a LuxR-family transcriptional regulator, CdhR. Phenotypic responses in P. gingivalis include regulation of hemin uptake systems and gingipain activity, processes that are intimately linked to the virulence of the organism. Furthermore, communities of S. gordonii with P. gingivalis or with A. actinomycetemcomitans are more pathogenic in animal models than the constituent species alone. We propose that MGS should be considered accessory pathogens, organisms whose pathogenic potential only becomes evident in the context of a heterotypic microbial community. © 2011 Blackwell Publishing Ltd.

Dental plaque as a biofilm: the significance of pH in health and caries.

PubMed

Marsh, Philip D

2009-03-01

Dental plaque is an example of a biofilm; its presence is natural and it supports the host in its defense against invading microbes. In health, the microbial composition of dental plaque is diverse and remains relatively stable over time (microbial homeostasis). The predominant microorganisms prefer host molecules (eg, salivary mucins) and a neutral pH for growth. Under certain circumstances, this microbial homeostasis can break down and diseases such as caries can occur. In dental caries, there is a shift toward increased proportions of acid-producing and acid-tolerating species, such as mutans streptococci and Lactobacilli, although other species with relevant traits can participate in demineralization. Strategies to control caries include effective oral hygiene practices to reduce biofilm development, and adoption of a low-sugar diet to restrict periods of acidic challenge to teeth. These conventional approaches also should be augmented by interference with the factors that enable the cariogenic bacteria to outcompete the organisms associated with health. Evidence suggests that regular conditions of low pH in plaque select for mutans streptococci and Lactobacilli. Therefore, the suppression of sugar catabolism and acid production by the use of metabolic inhibitors in oral care products, the consumption of nonfermentable sweeteners in snacks, the stimulation of saliva flow, and/or other strategies that maintain supragingival plaque at a pH around neutrality will assist in the maintenance of microbial homeostasis in plaque.

Progress toward understanding the contribution of alkali generation in dental biofilms to inhibition of dental caries

PubMed Central

Liu, Ya-Ling; Nascimento, Marcelle; Burne, Robert A

2012-01-01

Alkali production by oral bacteria is believed to have a major impact on oral microbial ecology and to be inibitory to the initiation and progression of dental caries. A substantial body of evidence is beginning to accumulate that indicates the modulation of the alkalinogenic potential of dental biofilms may be a promising strategy for caries control. This brief review highlights recent progress toward understanding molecular genetic and physiologic aspects of important alkali-generating pathways in oral bacteria, and the role of alkali production in the ecology of dental biofilms in health and disease. PMID:22996271

Managing the complexity of a dynamic biofilm.

PubMed

Thomas, John G; Nakaishi, Lindsay A

2006-11-01

This article provides an overview of the history of oral microbiology, a discussion of dental plaque as both a microbial community and a biofilm, and a review of the measures available to control the oral microflora. The authors reviewed the literature related to oral microbiology and associated infectious diseases. They also examined articles that detailed the structure and physiology of biofilms, including dental plaque biofilms. Biofilms cannot be eliminated. The pathogenic nature of the dental plaque biofilm can be diminished in the oral cavity by reducing the bioburden and effectively maintaining a normal oral flora via oral hygiene procedures that include daily toothbrushing, flossing and rinsing with an antimicrobial mouthrinse. An oral hygiene regimen that includes rinsing with an antimicrobial mouthrinse is a practical approach to the prevention and management of periodontal diseases. This strategy may have wider benefits when the link between periodontal disease and certain systemic diseases is considered. An effective oral hygiene regimen can help control dental plaque biofilm and associated periodontal diseases.

l-Arginine Modifies the Exopolysaccharide Matrix and Thwarts Streptococcus mutans Outgrowth within Mixed-Species Oral Biofilms

PubMed Central

He, Jinzhi; Hwang, Geelsu; Liu, Yuan; Gao, Lizeng; Kilpatrick-Liverman, LaTonya; Santarpia, Peter; Zhou, Xuedong

2016-01-01

ABSTRACT l-Arginine, a ubiquitous amino acid in human saliva, serves as a substrate for alkali production by arginolytic bacteria. Recently, exogenous l-arginine has been shown to enhance the alkalinogenic potential of oral biofilm and destabilize its microbial community, which might help control dental caries. However, l-arginine exposure may inflict additional changes in the biofilm milieu when bacteria are growing under cariogenic conditions. Here, we investigated how exogenous l-arginine modulates biofilm development using a mixed-species model containing both cariogenic (Streptococcus mutans) and arginolytic (Streptococcus gordonii) bacteria in the presence of sucrose. We observed that 1.5% (wt/vol) l-arginine (also a clinically effective concentration) exposure suppressed the outgrowth of S. mutans, favored S. gordonii dominance, and maintained Actinomyces naeslundii growth within biofilms (versus vehicle control). In parallel, topical l-arginine treatments substantially reduced the amounts of insoluble exopolysaccharides (EPS) by >3-fold, which significantly altered the three-dimensional (3D) architecture of the biofilm. Intriguingly, l-arginine repressed S. mutans genes associated with insoluble EPS (gtfB) and bacteriocin (SMU.150) production, while spxB expression (H2O2 production) by S. gordonii increased sharply during biofilm development, which resulted in higher H2O2 levels in arginine-treated biofilms. These modifications resulted in a markedly defective EPS matrix and areas devoid of any bacterial clusters (microcolonies) on the apatitic surface, while the in situ pH values at the biofilm-apatite interface were nearly one unit higher in arginine-treated biofilms (versus the vehicle control). Our data reveal new biological properties of l-arginine that impact biofilm matrix assembly and the dynamic microbial interactions associated with pathogenic biofilm development, indicating the multiaction potency of this promising biofilm disruptor. IMPORTANCE Dental caries is one of the most prevalent and costly infectious diseases worldwide, caused by a biofilm formed on tooth surfaces. Novel strategies that compromise the ability of virulent species to assemble and maintain pathogenic biofilms could be an effective alternative to conventional antimicrobials that indiscriminately kill other oral species, including commensal bacteria. l-Arginine at 1.5% has been shown to be clinically effective in modulating cariogenic biofilms via alkali production by arginolytic bacteria. Using a mixed-species ecological model, we show new mechanisms by which l-arginine disrupts the process of biofilm matrix assembly and the dynamic microbial interactions that are associated with cariogenic biofilm development, without impacting the bacterial viability. These results may aid in the development of enhanced methods to control biofilms using l-arginine. PMID:27161116

The 'sialo-microbial-dental complex' in oral health and disease.

PubMed

Kaidonis, John; Townsend, Grant

2016-01-01

Biofilms are naturally found in all wet environments including the oral structures of nearly all species. Human oral biofilms have existed since our earliest ancestors and have evolved symbiotically with the dentition over many millennia within a Palaeolithic, hunter-gatherer setting. Irrespective of the plant-animal ratio, it can be argued that the Palaeolithic diet was essentially acidic, and acted as a selective force for much of the evolution of the stomatognathic system. The relationship between saliva, biofilm and teeth, the 'sialo-microbial-dental complex', provides oral health benefits and offers a different perspective to the old dental paradigm that only associated oral biofilms (plaque) with disease (caries). This new paradigm emphasises that oral biofilms are essential for the 'mineral maintenance' of teeth. Oral biofilms provide physical protection from dietary acid and together with bacterial metabolic acids cause the resting pH of the biofilm to fall below neutral. This is then followed by the re-establishment of a neutral environment by chemical interactions mediated by the saliva within the biofilm. Such pH fluctuations are often responsible for the cyclic demineralisation, then remineralisation of teeth, a process necessary for tooth maturation. However, since the advent of farming and especially since the industrial revolution, the increase in consumption of carbohydrates, refined sugars and acidic drinks has changed the ecology of biofilms. Biofilm biodiversity is significantly reduced together with a proliferation of acidogenic and aciduric organisms, tipping the balance of the 'demin-remin' cycle towards net mineral loss and hence caries. In addition, the consumption of acidic drinks in today's societies has removed the protective nature of the biofilm, leading to erosion. Erosion and caries are 'modern-day' diseases and reflect an imbalance within the oral biofilm resulting in the demineralisation of teeth. Copyright © 2015 The Authors. Published by Elsevier GmbH.. All rights reserved.

Development of an in vitro periodontal biofilm model for assessing antimicrobial and host modulatory effects of bioactive molecules.

PubMed

Millhouse, Emma; Jose, Anto; Sherry, Leighann; Lappin, David F; Patel, Nisha; Middleton, Andrew M; Pratten, Jonathan; Culshaw, Shauna; Ramage, Gordon

2014-06-28

Inflammation within the oral cavity occurs due to dysregulation between microbial biofilms and the host response. Understanding how different oral hygiene products influence inflammatory properties is important for the development of new products. Therefore, creation of a robust host-pathogen biofilm platform capable of evaluating novel oral healthcare compounds is an attractive option. We therefore devised a multi-species biofilm co-culture model to evaluate the naturally derived polyphenol resveratrol (RSV) and gold standard chlorhexidine (CHX) with respect to anti-biofilm and anti-inflammatory properties. An in vitro multi-species biofilm containing S. mitis, F. nucleatum, P. gingivalis and A. actinomycetemcomitans was created to represent a disease-associated biofilm and the oral epithelial cell in OKF6-TERT2. Cytotoxicity studies were performed using RSV and CHX. Multi-species biofilms were either treated with either molecule, or alternatively epithelial cells were treated with these prior to biofilm co-culture. Biofilm composition was evaluated and inflammatory responses quantified at a transcriptional and protein level. CHX was toxic to epithelial cells and multi-species biofilms at concentrations ranging from 0.01-0.2%. RSV did not effect multi-species biofilm composition, but was toxic to epithelial cells at concentrations greater than 0.01%. In co-culture, CHX-treated biofilms resulted in down regulation of the inflammatory chemokine IL-8 at both mRNA and protein level. RSV-treated epithelial cells in co-culture were down-regulated in the release of IL-8 protein, but not mRNA. CHX possesses potent bactericidal properties, which may impact downstream inflammatory mediators. RSV does not appear to have bactericidal properties against multi-species biofilms, however it did appear to supress epithelial cells from releasing inflammatory mediators. This study demonstrates the potential to understand the mechanisms by which different oral hygiene products may influence gingival inflammation, thereby validating the use of a biofilm co-culture model.

Photodynamic inactivation of Paracoccidioides brasiliensis helps the outcome of oral paracoccidiodomycosis.

PubMed

Dos Santos, Letícia F M; Melo, Nathália B; de Carli, Marina L; Mendes, Ana Carolina S C; Bani, Giulia Maria A C; Verinaud, Liana M; Burger, Eva; de Oliveira I Moraes, Gabriel; Pereira, Alessandro A C; Brigagão, Maísa R L; Hanemann, João Adolfo C; Sperandio, Felipe F

2017-05-01

The antifungal drug therapy often employed to treat paracoccidiodomycosis (PCM), an important neglected fungal systemic infection, leads to offensive adverse effects, besides being very long-lasting. In addition, PCM compromises the oral health of patients by leading to oral lesions that are very painful and disabling. In that way, photodynamic therapy (PDT) arises as a new promising adjuvant treatment for inactivating Paracoccidioides brasiliensis (Pb), the responsible fungus for PCM, and also for helping the patients to deal with such debilitating oral lesions. PDT has been linked to an improved microbial killing, also presenting the advantage of not inducing immediate microbial resistance such as drugs. For the present study, we investigated the generation of reactive oxygen species (ROS) by using the fluorescent probes hydroxyphenyl fluorescein (HPF) and aminophenyl fluorescein (APF) after toluidine blue (TBO-37.5 mg/L)-mediated PDT (660 nm, 40 mW, and 0.04 cm 2 spot area) and the action of TBO-PDT upon Pb cultures grown for 7 or 15 days in semisolid Fava Netto's culture medium; we also targeted oral PCM manifestations by reporting the first clinical cases (three patients) to receive topic PDT for such purpose. We were able to show a significant generation of hydroxyl radicals and hypochlorite after TBO-PDT with doses around 90 J/cm 2 ; such ROS generation was particularly useful to attack and inactivate Pb colonies at 7 and 15 days. All three patients reported herein related an immediate relief when it came to pain, mouth opening, and also the ability to chew and swallow. As extracted from our clinical results, which are in fact based on in vitro outcomes, TBO-PDT is a very safe, inexpensive, and promising therapy for the oral manifestations of PCM.

Evaluation of Buccal Cell Samples for Studies of Oral Microbiota.

PubMed

Yu, Guoqin; Phillips, Steve; Gail, Mitchell H; Goedert, James J; Humphrys, Michael; Ravel, Jacques; Ren, Yanfang; Caporaso, Neil E

2017-02-01

The human microbiota is postulated to affect cancer risk, but collecting microbiota specimens with prospective follow-up for diseases will take time. Buccal cell samples have been obtained from mouthwash for the study of human genomic DNA in many cohort studies. Here, we evaluate the feasibility of using buccal cell samples to examine associations of human microbiota and disease risk. We obtained buccal cells from mouthwash in 41 healthy participants using a protocol that is widely employed to obtain buccal cells for the study of human DNA. We compared oral microbiota from buccal cells with that from eight other oral sample types collected by following the protocols of the Human Microbiome Project. Microbiota profiles were determined by sequencing 16S rRNA gene V3-V4 region. Compared with each of the eight other oral samples, the buccal cell samples had significantly more observed species (P < 0.002) and higher alpha diversity (Shannon index, P < 0.02). The microbial communities were more similar (smaller beta diversity) among buccal cells samples than in the other samples (P < 0.001 for 12 of 16 weighted and unweighted UniFrac distance comparisons). Buccal cell microbial profiles closely resembled saliva but were distinct from dental plaque and tongue dorsum. Stored buccal cell samples in prospective cohort studies are a promising resource to study associations of oral microbiota with disease. The feasibility of using existing buccal cell collections in large prospective cohorts allows investigations of the role of oral microbiota in chronic disease etiology in large population studies possible today. Cancer Epidemiol Biomarkers Prev; 26(2); 249-53. ©2016 AACR. ©2016 American Association for Cancer Research.

[The origin of hydrogen peroxide in oral cavity and its role in oral microecology balance].

PubMed

Keke, Zhang; Xuedong, Zhou; Xin, Xu

2017-04-01

Hydrogen peroxide, an important antimicrobial agent in oral cavity, plays a significant role in the balance of oral microecology. At the early stage of biofilm formation, about 80% of the detected initial colonizers belong to the genus Streptococcus. These oral streptococci use different oxidase to produce hydrogen peroxide. Recent studies showed that the produced hydrogen peroxide plays a critical role in modulating oral microecology. Hydrogen peroxide modulates biofilm development attributed to its growth inhibitory nature. Hydrogen peroxide production is closely associated with extracellular DNA(eDNA) release from microbe and the development of its competent cell which are critical for biofilm development and also serves as source for horizontal gene transfer. Microbe also can reduce the damage to themselves through several detoxification mechanisms. Moreover, hydrogen peroxide is also involved in the regulation of interactions between oral microorganisms and host. Taken together, hydrogen peroxide is an imperative ecological factor that contributes to the microbial equilibrium in the oral cavity. Here we will give a brief review of both the origin and the function in the oral microecology balance of hydrogen peroxide.

The Toll-Dorsal Pathway Is Required for Resistance to Viral Oral Infection in Drosophila

PubMed Central

Ferreira, Álvaro Gil; Naylor, Huw; Esteves, Sara Santana; Pais, Inês Silva; Martins, Nelson Eduardo; Teixeira, Luis

2014-01-01

Pathogen entry route can have a strong impact on the result of microbial infections in different hosts, including insects. Drosophila melanogaster has been a successful model system to study the immune response to systemic viral infection. Here we investigate the role of the Toll pathway in resistance to oral viral infection in D. melanogaster. We show that several Toll pathway components, including Spätzle, Toll, Pelle and the NF-kB-like transcription factor Dorsal, are required to resist oral infection with Drosophila C virus. Furthermore, in the fat body Dorsal is translocated from the cytoplasm to the nucleus and a Toll pathway target gene reporter is upregulated in response to Drosophila C Virus infection. This pathway also mediates resistance to several other RNA viruses (Cricket paralysis virus, Flock House virus, and Nora virus). Compared with control, viral titres are highly increased in Toll pathway mutants. The role of the Toll pathway in resistance to viruses in D. melanogaster is restricted to oral infection since we do not observe a phenotype associated with systemic infection. We also show that Wolbachia and other Drosophila-associated microbiota do not interact with the Toll pathway-mediated resistance to oral infection. We therefore identify the Toll pathway as a new general inducible pathway that mediates strong resistance to viruses with a route-specific role. These results contribute to a better understanding of viral oral infection resistance in insects, which is particularly relevant in the context of transmission of arboviruses by insect vectors. PMID:25473839

Quantitative Molecular Detection of Putative Periodontal Pathogens in Clinically Healthy and Periodontally Diseased Subjects

PubMed Central

Göhler, André; Hetzer, Adrian; Holtfreter, Birte; Geisel, Marie Henrike; Schmidt, Carsten Oliver; Steinmetz, Ivo; Kocher, Thomas

2014-01-01

Periodontitis is a multi-microbial oral infection with high prevalence among adults. Putative oral pathogens are commonly found in periodontally diseased individuals. However, these organisms can be also detected in the oral cavity of healthy subjects. This leads to the hypothesis, that alterations in the proportion of these organisms relative to the total amount of oral microorganisms, namely their abundance, rather than their simple presence might be important in the transition from health to disease. Therefore, we developed a quantitative molecular method to determine the abundance of various oral microorganisms and the portion of bacterial and archaeal nucleic acid relative to the total nucleic acid extracted from individual samples. We applied quantitative real-time PCRs targeting single-copy genes of periodontal bacteria and 16S-rRNA genes of Bacteria and Archaea. Testing tongue scrapings of 88 matched pairs of periodontally diseased and healthy subjects revealed a significantly higher abundance of P. gingivalis and a higher total bacterial abundance in diseased subjects. In fully adjusted models the risk of being periodontally diseased was significantly higher in subjects with high P. gingivalis and total bacterial abundance. Interestingly, we found that moderate abundances of A. actinomycetemcomitans were associated with reduced risk for periodontal disease compared to subjects with low abundances, whereas for high abundances, this protective effect leveled off. Moderate archaeal abundances were health associated compared to subjects with low abundances. In conclusion, our methodological approach unraveled associations of the oral flora with periodontal disease, which would have gone undetected if only qualitative data had been determined. PMID:25029268

Oral Microbiota Distinguishes Acute Lymphoblastic Leukemia Pediatric Hosts from Healthy Populations

PubMed Central

Zhou, Xuedong; You, Meng; Du, Qin; Yang, Xue; He, Jingzhi; Zou, Jing; Cheng, Lei; Li, Mingyun; Li, Yuqing; Zhu, Yiping; Li, Jiyao; Shi, Wenyuan; Xu, Xin

2014-01-01

In leukemia, oral manifestations indicate aberrations in oral microbiota. Microbiota structure is determined by both host and environmental factors. In human hosts, how health status shapes the composition of oral microbiota is largely unknown. Taking advantage of advances in high-throughput sequencing, we compared the composition of supragingival plaque microbiota of acute lymphoblastic leukemia (ALL) pediatric patients with healthy controls. The oral microbiota of leukemia patients had lower richness and less diversity compared to healthy controls. Microbial samples clustered into two major groups, one of ALL patients and another of healthy children, with different structure and composition. Abundance changes of certain taxa including the Phylum Firmicutes, the Class Bacilli, the Order Lactobacillales, the Family Aerococcaceae and Carnobacteriaceae, as well as the Genus Abiotrophia and Granulicatella were associated with leukemia status. ALL patients demonstrated a structural imbalance of the oral microbiota, characterized by reduced diversity and abundance alterations, possibly involved in systemic infections, indicating the importance of immune status in shaping the structure of oral microbiota. PMID:25025462

Gut Microbiota and Salivary Diagnostics: The Mouth Is Salivating to Tell Us Something.

PubMed

Kodukula, Krishna; Faller, Douglas V; Harpp, David N; Kanara, Iphigenia; Pernokas, Julie; Pernokas, Mark; Powers, Whitney R; Soukos, Nikolaos S; Steliou, Kosta; Moos, Walter H

2017-01-01

The microbiome of the human body represents a symbiosis of microbial networks spanning multiple organ systems. Bacteria predominantly represent the diversity of human microbiota, but not to be forgotten are fungi, viruses, and protists. Mounting evidence points to the fact that the "microbial signature" is host-specific and relatively stable over time. As our understanding of the human microbiome and its relationship to the health of the host increases, it is becoming clear that many and perhaps most chronic conditions have a microbial involvement. The oral and gastrointestinal tract microbiome constitutes the bulk of the overall human microbial load, and thus presents unique opportunities for advancing human health prognosis, diagnosis, and therapy development. This review is an attempt to catalog a broad diversity of recent evidence and focus it toward opportunities for prevention and treatment of debilitating illnesses.

A practical guide to the oral microbiome and its relation to health and disease.

PubMed

Krishnan, K; Chen, T; Paster, B J

2017-04-01

The oral microbiome is incredibly complex with the average adult harboring about 50-100 billion bacteria in the oral cavity, which represent about 200 predominant bacterial species. Collectively, there are approximately 700 predominant taxa of which less than one-third still have not yet been grown in vitro. Compared to other body sites, the oral microbiome is unique and readily accessible. There is extensive literature available describing the oral microbiome and discussing the roles that bacteria may play in oral health and disease. However, the purpose of this review is not to rehash these detailed studies but rather to educate the reader with understanding the essence of the oral microbiome, namely that there are abundant bacteria in numbers and types, that there are molecular methods to rapidly determine bacterial associations, that there is site specificity for colonization of the host, that there are specific associations with oral health and disease, that oral bacteria may serve as biomarkers for non-oral diseases, and that oral microbial profiles may have potential use to assess disease risk. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Urease and Dental Plaque Microbial Profiles in Children.

PubMed

Morou-Bermudez, Evangelia; Rodriguez, Selena; Bello, Angel S; Dominguez-Bello, Maria G

2015-01-01

Urease enzymes produced by oral bacteria generate ammonia, which can have a significant impact on the oral ecology and, consequently, on oral health. To evaluate the relationship of urease with dental plaque microbial profiles in children as it relates to dental caries, and to identify the main contributors to this activity. 82 supragingival plaque samples were collected from 44 children at baseline and one year later, as part of a longitudinal study on urease and caries in children. DNA was extracted; the V3-V5 region of the 16S rRNA gene was amplified and sequenced using 454 pyrosequencing. Urease activity was measured using a spectrophotometric assay. Data were analyzed with Qiime. Plaque urease activity was significantly associated with the composition of the microbial communities of the dental plaque (Baseline P = 0.027, One Year P = 0.012). The bacterial taxa whose proportion in dental plaque exhibited significant variation by plaque urease levels in both visits were the family Pasteurellaceae (Baseline P<0.001; One Year P = 0.0148), especially Haemophilus parainfluenzae. No association was observed between these bacteria and dental caries. Bacteria in the genus Leptotrichia were negatively associated with urease and positively associated with dental caries (Bonferroni P<0.001). Alkali production by urease enzymes primarily from species in the family Pasteurellaceae can be an important ecological determinant in children's dental plaque. Further studies are needed to establish the role of urease-associated bacteria in the acid/base homeostasis of the dental plaque, and in the development and prediction of dental caries in children.

Urease and Dental Plaque Microbial Profiles in Children

PubMed Central

Morou-Bermudez, Evangelia; Rodriguez, Selena; Bello, Angel S.; Dominguez-Bello, Maria G.

2015-01-01

Objective Urease enzymes produced by oral bacteria generate ammonia, which can have a significant impact on the oral ecology and, consequently, on oral health. To evaluate the relationship of urease with dental plaque microbial profiles in children as it relates to dental caries, and to identify the main contributors to this activity. Methods 82 supragingival plaque samples were collected from 44 children at baseline and one year later, as part of a longitudinal study on urease and caries in children. DNA was extracted; the V3–V5 region of the 16S rRNA gene was amplified and sequenced using 454 pyrosequencing. Urease activity was measured using a spectrophotometric assay. Data were analyzed with Qiime. Results Plaque urease activity was significantly associated with the composition of the microbial communities of the dental plaque (Baseline P = 0.027, One Year P = 0.012). The bacterial taxa whose proportion in dental plaque exhibited significant variation by plaque urease levels in both visits were the family Pasteurellaceae (Baseline P<0.001; One Year P = 0.0148), especially Haemophilus parainfluenzae. No association was observed between these bacteria and dental caries. Bacteria in the genus Leptotrichia were negatively associated with urease and positively associated with dental caries (Bonferroni P<0.001). Conclusions Alkali production by urease enzymes primarily from species in the family Pasteurellaceae can be an important ecological determinant in children’s dental plaque. Further studies are needed to establish the role of urease-associated bacteria in the acid/base homeostasis of the dental plaque, and in the development and prediction of dental caries in children. PMID:26418220

Effects of probiotic fermented milk on biofilms, oral microbiota, and enamel.

PubMed

Lodi, Carolina Simonetti; Oliveira, Lidiane Viana; Brighenti, Fernanda Lourenção; Delbem, Alberto Carlos Botazzo; Martinhon, Cleide Cristina Rodrigues

2015-01-01

The aim of this study was to evaluate in vitro and in vivo the effects of 2 brands of probiotic fermented milk on biofilms, oral microbiota, and enamel. For the in situ experiment, ten volunteers wore palatine devices containing four blocks of bovine dental enamel over 3 phases, during which 20% sucrose solution, Yakult® (Treatment A), and Batavito® (Treatment B) were dropped on the enamel blocks. Salivary microbial counts were obtained and biofilm samples were analyzed after each phase. For the in vivo experiment, the same ten volunteers drunk Yakult® (Treatment C) and Batavito® (Treatment D) in two phases. Saliva samples were collected for microbial analysis after each phase. The in situ study showed that in comparison with Treatment A, Treatment B resulted in fewer total cultivable anaerobes and facultative microorganisms in biofilms, higher final microhardness, lower percentage change in surface hardness, and smaller integrated subsurface enamel hardness. In the in vivo study, Treatment D resulted in a reduction in the counts of all microorganisms. The results suggested that the probiotic fermented milk Batavito®, but not Yakult®, reduced the amount of oral microorganisms and mineral loss in bovine enamel.

Oral administration of Saccharomyces boulardii ameliorates carbon tetrachloride-induced liver fibrosis in rats via reducing intestinal permeability and modulating gut microbial composition.

PubMed

Li, Ming; Zhu, Lin; Xie, Ao; Yuan, Jieli

2015-02-01

To investigate the effects of orally administrated Saccharomyces boulardii (S. boulardii) on the progress of carbon tetrachloride (CCl4)-induced liver fibrosis, 34 male Wistar rats were randomly divided into four experimental groups including the control group (n = 8), the cirrhotic group (n = 10), the preventive group (n = 8), and the treatment group (n = 8). Results showed that the liver expression levels of collagen, type I, alpha 1 (Col1A1), alpha smooth muscle actin (αSMA), transforming growth factor beta (TGF-β) and the serum levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and malondialdehyde (MDA) increased significantly in cirrhotic rats compared with control and decreased by S. boulardii administration. Treatment of S. boulardii also attenuated the increased endotoxin levels and pro-inflammatory cytokines in CCl4-treated rats. And, these were associated with the changes of intestinal permeability and fecal microbial composition. Our study suggested that oral administration of S. boulardii can promote the liver function of CCl4-treated rats, and the preventive treatment of this probiotic yeast may decelerate the progress of liver fibrosis.

Plant and Fungal Food Components with Potential Activity on the Development of Microbial Oral Diseases

PubMed Central

Daglia, Maria; Papetti, Adele; Mascherpa, Dora; Grisoli, Pietro; Giusto, Giovanni; Lingström, Peter; Pratten, Jonathan; Signoretto, Caterina; Spratt, David A.; Wilson, Michael; Zaura, Egija; Gazzani, Gabriella

2011-01-01

This paper reports the content in macronutrients, free sugars, polyphenols, and inorganic ions, known to exert any positive or negative action on microbial oral disease such as caries and gingivitis, of seven food/beverages (red chicory, mushroom, raspberry, green and black tea, cranberry juice, dark beer). Tea leaves resulted the richest material in all the detected ions, anyway tea beverages resulted the richest just in fluoride. The highest content in zinc was in chicory, raspberry and mushroom. Raspberry is the richest food in strontium and boron, beer in selenium, raspberry and mushroom in copper. Beer, cranberry juice and, especially green and black tea are very rich in polyphenols, confirming these beverages as important sources of such healthy substances. The fractionation, carried out on the basis of the molecular mass (MM), of the water soluble components occurring in raspberry, chicory, and mushroom extracts (which in microbiological assays revealed the highest potential action against oral pathogens), showed that both the high and low MM fractions are active, with the low MM fractions displaying the highest potential action for all the fractionated extracts. Our findings show that more compounds that can play a different active role occur in these foods. PMID:22013381

Interruption of Electrical Conductivity of Titanium Dental Implants Suggests a Path Towards Elimination Of Corrosion

PubMed Central

Pozhitkov, Alex E.; Daubert, Diane; Brochwicz Donimirski, Ashley; Goodgion, Douglas; Vagin, Mikhail Y.; Leroux, Brian G.; Hunter, Colby M.; Flemmig, Thomas F.; Noble, Peter A.; Bryers, James D.

2015-01-01

Peri-implantitis is an inflammatory disease that results in the destruction of soft tissue and bone around the implant. Titanium implant corrosion has been attributed to the implant failure and cytotoxic effects to the alveolar bone. We have documented the extent of titanium release into surrounding plaque in patients with and without peri-implantitis. An in vitro model was designed to represent the actual environment of an implant in a patient’s mouth. The model uses actual oral microbiota from a volunteer, allows monitoring electrochemical processes generated by biofilms growing on implants and permits control of biocorrosion electrical current. As determined by next generation DNA sequencing, microbial compositions in experiments with the in vitro model were comparable with the compositions found in patients with implants. It was determined that the electrical conductivity of titanium implants was the key factor responsible for the biocorrosion process. The interruption of the biocorrosion current resulted in a 4–5 fold reduction of corrosion. We propose a new design of dental implant that combines titanium in zero oxidation state for osseointegration and strength, interlaid with a nonconductive ceramic. In addition, we propose electrotherapy for manipulation of microbial biofilms and to induce bone healing in peri-implantitis patients. PMID:26461491

Interruption of Electrical Conductivity of Titanium Dental Implants Suggests a Path Towards Elimination Of Corrosion.

PubMed

Pozhitkov, Alex E; Daubert, Diane; Brochwicz Donimirski, Ashley; Goodgion, Douglas; Vagin, Mikhail Y; Leroux, Brian G; Hunter, Colby M; Flemmig, Thomas F; Noble, Peter A; Bryers, James D

2015-01-01

Peri-implantitis is an inflammatory disease that results in the destruction of soft tissue and bone around the implant. Titanium implant corrosion has been attributed to the implant failure and cytotoxic effects to the alveolar bone. We have documented the extent of titanium release into surrounding plaque in patients with and without peri-implantitis. An in vitro model was designed to represent the actual environment of an implant in a patient's mouth. The model uses actual oral microbiota from a volunteer, allows monitoring electrochemical processes generated by biofilms growing on implants and permits control of biocorrosion electrical current. As determined by next generation DNA sequencing, microbial compositions in experiments with the in vitro model were comparable with the compositions found in patients with implants. It was determined that the electrical conductivity of titanium implants was the key factor responsible for the biocorrosion process. The interruption of the biocorrosion current resulted in a 4-5 fold reduction of corrosion. We propose a new design of dental implant that combines titanium in zero oxidation state for osseointegration and strength, interlaid with a nonconductive ceramic. In addition, we propose electrotherapy for manipulation of microbial biofilms and to induce bone healing in peri-implantitis patients.

Oral microbiome in HIV-associated periodontitis.

PubMed

Noguera-Julian, Marc; Guillén, Yolanda; Peterson, Jessica; Reznik, David; Harris, Erica V; Joseph, Sandeep J; Rivera, Javier; Kannanganat, Sunil; Amara, Rama; Nguyen, Minh Ly; Mutembo, Simon; Paredes, Roger; Read, Timothy D; Marconi, Vincent C

2017-03-01

HIV-associated periodontal diseases (PD) could serve as a source of chronic inflammation. Here, we sought to characterize the oral microbial signatures of HIV+ and HIV- individuals at different levels of PD severity.This cross-sectional study included both HIV+ and HIV- patients with varying degrees of PD. Two tooth, 2 cheek, and 1 saliva samples were obtained for microbiome analysis. Mothur/SILVADB were used to classify sequences. R/Bioconductor (Vegan, PhyloSeq, and DESeq2) was employed to assess overall microbiome structure differences and differential abundance of bacterial genera between groups. Polychromatic flow cytometry was used to assess immune activation in CD4 and CD8 cell populations.Around 250 cheek, tooth, and saliva samples from 50 participants (40 HIV+ and 10 HIV-) were included. Severity of PD was classified clinically as None/Mild (N), Moderate (M), and Severe (S) with 18 (36%), 16 (32%), and 16 (32%) participants in each category, respectively. Globally, ordination analysis demonstrated clustering by anatomic site (R2 = 0.25, P < 0.001). HIV status and PD severity showed a statistically significant impact on microbiome composition but only accounted for a combined 2% of variation. HIV+ samples were enriched in genera Abiotrophia, Neisseria, Kingella, and unclassified Neisseriaceae and depleted in Leptotrichia and Selenomonas. The Neisseria genus was consistently enriched in HIV+ participants regardless of sampling site and PD level. Immune markers were altered in HIV+ participants but did not show association with the oral microbiome.HIV-associated changes in oral microbiome result in subtle microbial signatures along different stages of PD that are common in independent oral anatomic sites.

Oral microbiome in HIV-associated periodontitis

PubMed Central

Noguera-Julian, Marc; Guillén, Yolanda; Peterson, Jessica; Reznik, David; Harris, Erica V.; Joseph, Sandeep J.; Rivera, Javier; Kannanganat, Sunil; Amara, Rama; Nguyen, Minh Ly; Mutembo, Simon; Paredes, Roger; Read, Timothy D.; Marconi, Vincent C.

2017-01-01

Abstract HIV-associated periodontal diseases (PD) could serve as a source of chronic inflammation. Here, we sought to characterize the oral microbial signatures of HIV+ and HIV– individuals at different levels of PD severity. This cross-sectional study included both HIV+ and HIV– patients with varying degrees of PD. Two tooth, 2 cheek, and 1 saliva samples were obtained for microbiome analysis. Mothur/SILVADB were used to classify sequences. R/Bioconductor (Vegan, PhyloSeq, and DESeq2) was employed to assess overall microbiome structure differences and differential abundance of bacterial genera between groups. Polychromatic flow cytometry was used to assess immune activation in CD4 and CD8 cell populations. Around 250 cheek, tooth, and saliva samples from 50 participants (40 HIV+ and 10 HIV–) were included. Severity of PD was classified clinically as None/Mild (N), Moderate (M), and Severe (S) with 18 (36%), 16 (32%), and 16 (32%) participants in each category, respectively. Globally, ordination analysis demonstrated clustering by anatomic site (R2 = 0.25, P < 0.001). HIV status and PD severity showed a statistically significant impact on microbiome composition but only accounted for a combined 2% of variation. HIV+ samples were enriched in genera Abiotrophia, Neisseria, Kingella, and unclassified Neisseriaceae and depleted in Leptotrichia and Selenomonas. The Neisseria genus was consistently enriched in HIV+ participants regardless of sampling site and PD level. Immune markers were altered in HIV+ participants but did not show association with the oral microbiome. HIV-associated changes in oral microbiome result in subtle microbial signatures along different stages of PD that are common in independent oral anatomic sites. PMID:28328799

Mouthguards: does the indigenous microbiome play a role in maintaining oral health?

PubMed

Kumar, Purnima S; Mason, Matthew R

2015-01-01

The existence of symbiotic relationships between bacteria and their hosts in various ecosystems have long been known to science. The human body also hosts vast numbers of bacteria in several habitats. Emerging evidence from the gastro-intestinal tract, genito-urinary tract and respiratory indicates that there are several health benefits to hosting a complex and diverse microbial community. Bacteria colonize the oral cavity within a few minutes after birth and form stable communities. Our knowledge of the oral microbiome has expanded exponentially with development of novel exploratory methods that allow us to examine diversity, structure, function, and topography without the need to cultivate the individual components of the biofilm. The purpose of this perspective, therefore, is to examine the strength of current evidence supporting a role for the oral microbiome in maintaining oral health. While several lines of evidence are emerging to suggest that indigenous oral microbiota may have a role in immune education and preventing pathogen expansion, much more work is needed to definitively establish whether oral bacteria do indeed contribute to sustaining oral health, and if so, the mechanisms underlying this role.

The oral microbiome - an update for oral healthcare professionals.

PubMed

Kilian, M; Chapple, I L C; Hannig, M; Marsh, P D; Meuric, V; Pedersen, A M L; Tonetti, M S; Wade, W G; Zaura, E

2016-11-18

For millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a 'superorganism' or holobiont, with the microbiome playing a significant role in our physiology and health. The mouth houses the second most diverse microbial community in the body, harbouring over 700 species of bacteria that colonise the hard surfaces of teeth and the soft tissues of the oral mucosa. Through recent advances in technology, we have started to unravel the complexities of the oral microbiome and gained new insights into its role during both health and disease. Perturbations of the oral microbiome through modern-day lifestyles can have detrimental consequences for our general and oral health. In dysbiosis, the finely-tuned equilibrium of the oral ecosystem is disrupted, allowing disease-promoting bacteria to manifest and cause conditions such as caries, gingivitis and periodontitis. For practitioners and patients alike, promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This article aims to give an update on our current knowledge of the oral microbiome in health and disease and to discuss implications for modern-day oral healthcare.

The numerous microbial species in oral biofilms: how could antibacterial therapy be effective?

PubMed

ten Cate, J M; Zaura, E

2012-09-01

Hundreds of bacterial species inhabit the oral cavity. Many of these have never been cultivated and can be assessed only with DNA-based techniques. This new understanding has changed the paradigm of the etiology of oral disease from that associated with 'traditional pathogens' as being primarily responsible for all diseases. Increasingly, associations between oral bacteria and systemic diseases are being reported. The emergence of antibiotic resistance is alarming and calls for in-depth studies of biofilms, bacterial physiology, and a body-wide approach to infectious diseases. We propose that the borderline between commensal bacteria and pathogens is no longer discrete. In a field of science where so many of the established paradigms are being undermined, a thorough analysis of threats and opportunities is required. This article addresses some of the questions that can be raised and serves to identify research opportunities and needs to leverage the prevention of oral diseases through novel antimicrobial strategies.

Gut Microbiota and Salivary Diagnostics: The Mouth Is Salivating to Tell Us Something

PubMed Central

Kodukula, Krishna; Faller, Douglas V.; Harpp, David N.; Kanara, Iphigenia; Pernokas, Julie; Pernokas, Mark; Powers, Whitney R.; Soukos, Nikolaos S.; Steliou, Kosta; Moos, Walter H.

2017-01-01

Abstract The microbiome of the human body represents a symbiosis of microbial networks spanning multiple organ systems. Bacteria predominantly represent the diversity of human microbiota, but not to be forgotten are fungi, viruses, and protists. Mounting evidence points to the fact that the “microbial signature” is host-specific and relatively stable over time. As our understanding of the human microbiome and its relationship to the health of the host increases, it is becoming clear that many and perhaps most chronic conditions have a microbial involvement. The oral and gastrointestinal tract microbiome constitutes the bulk of the overall human microbial load, and thus presents unique opportunities for advancing human health prognosis, diagnosis, and therapy development. This review is an attempt to catalog a broad diversity of recent evidence and focus it toward opportunities for prevention and treatment of debilitating illnesses. PMID:29098118

High-affinity monoclonal IgA regulates gut microbiota and prevents colitis in mice.

PubMed

Okai, Shinsaku; Usui, Fumihito; Yokota, Shuhei; Hori-I, Yusaku; Hasegawa, Makoto; Nakamura, Toshinobu; Kurosawa, Manabu; Okada, Seiji; Yamamoto, Kazuya; Nishiyama, Eri; Mori, Hiroshi; Yamada, Takuji; Kurokawa, Ken; Matsumoto, Satoshi; Nanno, Masanobu; Naito, Tomoaki; Watanabe, Yohei; Kato, Tamotsu; Miyauchi, Eiji; Ohno, Hiroshi; Shinkura, Reiko

2016-07-04

Immunoglobulin A (IgA) is the main antibody isotype secreted into the intestinal lumen. IgA plays a critical role in the defence against pathogens and in the maintenance of intestinal homeostasis. However, how secreted IgA regulates gut microbiota is not completely understood. In this study, we isolated monoclonal IgA antibodies from the small intestine of healthy mouse. As a candidate for an efficient gut microbiota modulator, we selected a W27 IgA, which binds to multiple bacteria, but not beneficial ones such as Lactobacillus casei. W27 could suppress the cell growth of Escherichia coli but not L. casei in vitro, indicating an ability to improve the intestinal environment. Indeed W27 oral treatment could modulate gut microbiota composition and have a therapeutic effect on both lymphoproliferative disease and colitis models in mice. Thus, W27 IgA oral treatment is a potential remedy for inflammatory bowel disease, acting through restoration of host-microbial symbiosis.

Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species

PubMed Central

Moor, Kathrin; Wotzka, Sandra Y.; Toska, Albulena; Diard, Médéric; Hapfelmeier, Siegfried; Slack, Emma

2016-01-01

Our mucosal surfaces are the main sites of non-vector-borne pathogen entry, as well as the main interface with our commensal microbiota. We are still only beginning to understand how mucosal adaptive immunity interacts with commensal and pathogenic microbes to influence factors such as infectivity, phenotypic diversity, and within-host evolution. This is in part due to difficulties in generating specific mucosal adaptive immune responses without disrupting the mucosal microbial ecosystem itself. Here, we present a very simple tool to generate inactivated mucosal vaccines from a broad range of culturable bacteria. Oral gavage of 1010 peracetic acid-inactivated bacteria induces high-titer-specific intestinal IgA in the absence of any measurable inflammation or species invasion. As a proof of principle, we demonstrate that this technique is sufficient to provide fully protective immunity in the murine model of invasive non-typhoidal Salmonellosis, even in the face of severe innate immune deficiency. PMID:26904024

Innate Immunity and Saliva in Candida albicans–mediated Oral Diseases

PubMed Central

Salvatori, O.; Puri, S.; Tati, S.; Edgerton, M.

2016-01-01

The oral cavity is a unique niche where Candida albicans infections occur in immunocompetent as well as immunosuppressed individuals. Here we critically review the significance of human innate immune response in preventing oral candidiasis. One important line of defense against oropharyngeal candidiasis is the oral microbiota that prevents infection by competing for space and nutrients as well as by secreting antagonistic molecules and triggering local inflammatory responses. C. albicans is able to induce mucosal defenses through activation of immune cells and production of cytokines. Also, saliva contains various proteins that affect C. albicans growth positively by promoting mucosal adherence and negatively through immune exclusion and direct fungicidal activity. We further discuss the role of saliva in unifying host innate immune defenses against C. albicans as a communicating medium and how C. albicans overgrowth in the oral cavity may be a result of aberrations ranging from microbial dysbiosis and salivary dysfunction to epithelial damage. Last we underscore select oral diseases in which C. albicans is a contributory microorganism in immune-competent individuals. PMID:26747422

Oral Bacterial and Fungal Microbiome Impacts Colorectal Carcinogenesis.

PubMed

Klimesova, Klara; Jiraskova Zakostelska, Zuzana; Tlaskalova-Hogenova, Helena

2018-01-01

Host's physiology is significantly influenced by microbiota colonizing the epithelial surfaces. Complex microbial communities contribute to proper mucosal barrier function, immune response, and prevention of pathogen invasion and have many other crucial functions. The oral cavity and large intestine are distant parts of the digestive tract, both heavily colonized by commensal microbiota. Nevertheless, they feature different proportions of major bacterial and fungal phyla, mostly due to distinct epithelial layers organization and different oxygen levels. A few obligate anaerobic strains inhabiting the oral cavity are involved in the pathogenesis of oral diseases. Interestingly, these microbiota components are also enriched in gut inflammatory and tumor tissue. An altered microbiota composition - dysbiosis - and formation of polymicrobial biofilms seem to play important roles in the development of oral diseases and colorectal cancer. In this review, we describe the differences in composition of commensal microbiota in the oral cavity and large intestine and the mechanisms by which microbiota affect the inflammatory and carcinogenic response of the host.

Antimicrobial and Attractant Roles for Chemerin in the Oral Cavity during Inflammatory Gum Disease.

PubMed

Godlewska, Urszula; Brzoza, Piotr; Sroka, Aneta; Majewski, Pawel; Jentsch, Holger; Eckert, Martin; Eick, Sigrun; Potempa, Jan; Zabel, Brian A; Cichy, Joanna

2017-01-01

Periodontal inflammation is one of the most common chronic inflammatory conditions in humans. Despite recent advances in identifying and characterizing oral microbiota dysbiosis in the pathogenesis of gum disease, just how host factors maintain a healthy homeostatic oral microbial community or prevent the development of a pathogenic oral microbiota remains poorly understood. An important determinant of microbiota fate is local antimicrobial proteins. Here, we report that chemoattractant protein chemerin, which we recently identified as a potent endogenous antimicrobial agent in body barriers such as the skin, is present in the oral cavity under homeostatic and inflammatory conditions. Chemerin and a chemerin-derived antimicrobial peptide are bactericidal against select bacteria strategically positioned in dental biofilm. Gingival crevicular samples from patients with gingivitis but not periodontitis contain abundant bioactive chemerin capable of inducing CMKLR1-dependent leukocyte migration. Gingipains secreted by the periodontopathogen P. gingivalis inactivate chemerin. Together, these data suggest that as an antimicrobial agent and leukocyte chemoattractant, chemerin likely contributes to antimicrobial immune defense in the oral cavity.

The Oral Microbiota.

PubMed

Arweiler, Nicole B; Netuschil, Lutz

2016-01-01

The oral microbiota represents an important part of the human microbiota, and includes several hundred to several thousand diverse species. It is a normal part of the oral cavity and has an important function to protect against colonization of extrinsic bacteria which could affect systemic health. On the other hand, the most common oral diseases caries, gingivitis and periodontitis are based on microorganisms. While (medical) research focused on the planktonic phase of bacteria over the last 100 years, it is nowadays generally known, that oral microorganisms are organised as biofilms. On any non-shedding surfaces of the oral cavity dental plaque starts to form, which meets all criteria for a microbial biofilm and is subject to the so-called succession. When the sensitive ecosystem turns out of balance - either by overload or weak immune system - it becomes a challenge for local or systemic health. Therefore, the most common strategy and the golden standard for the prevention of caries, gingivitis and periodontitis is the mechanical removal of this biofilms from teeth, restorations or dental prosthesis by regular toothbrushing.

High Diversity of the Saliva Microbiome in Batwa Pygmies

PubMed Central

Schroeder, Roland; Creasey, Jean L.; Li, Mingkun; Stoneking, Mark

2011-01-01

We describe the saliva microbiome diversity in Batwa Pygmies, a former hunter-gatherer group from Uganda, using next-generation sequencing of partial 16S rRNA sequences. Microbial community diversity in the Batwa is significantly higher than in agricultural groups from Sierra Leone and the Democratic Republic of Congo. We found 40 microbial genera in the Batwa, which have previously not been described in the human oral cavity. The distinctive composition of the salvia microbiome of the Batwa may have been influenced by their recent different lifestyle and diet. PMID:21858083

Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon

DOE PAGES

Kortman, Guus A. M.; Dutilh, Bas E.; Maathuis, Annet J. H.; ...

2016-01-06

Oral iron administration in African children can increase the risk for infections. However, it remains unclear to what extent supplementary iron affects the intestinal microbiome. We here explored the impact of iron preparations on microbial growth and metabolism in the well-controlled TNO's in vitro model of the large intestine (TIM-2). The model was inoculated with a human microbiota, without supplementary iron, or with 50 or 250 μmol/L ferrous sulfate, 50 or 250 μmol/L ferric citrate, or 50 μmol/L hemin. High resolution responses of the microbiota were examined by 16S rDNA pyrosequencing, microarray analysis, and metagenomic sequencing. The metabolome was assessedmore » by fatty acid quantification, gas chromatography-mass spectrometry (GC-MS), and 1H-NMR spectroscopy. Cultured intestinal epithelial Caco-2 cells were used to assess fecal water toxicity. Microbiome analysis showed, among others, that supplementary iron induced decreased levels of Bifidobacteriaceae and Lactobacillaceae, while it caused higher levels of Roseburia and Prevotella. Metagenomic analyses showed an enrichment of microbial motility-chemotaxis systems, while the metabolome markedly changed from a saccharolytic to a proteolytic profile in response to iron. Branched chain fatty acids and ammonia levels increased significantly, in particular with ferrous sulfate. Importantly, the metabolite-containing effluent from iron-rich conditions showed increased cytotoxicity to Caco-2 cells. In conclusion, our explorations indicate that in the absence of host influences, iron induces a more hostile environment characterized by a reduction of microbes that are generally beneficial, and increased levels of bacterial metabolites that can impair the barrier function of a cultured intestinal epithelial monolayer.« less

Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kortman, Guus A. M.; Dutilh, Bas E.; Maathuis, Annet J. H.

Oral iron administration in African children can increase the risk for infections. However, it remains unclear to what extent supplementary iron affects the intestinal microbiome. We here explored the impact of iron preparations on microbial growth and metabolism in the well-controlled TNO's in vitro model of the large intestine (TIM-2). The model was inoculated with a human microbiota, without supplementary iron, or with 50 or 250 μmol/L ferrous sulfate, 50 or 250 μmol/L ferric citrate, or 50 μmol/L hemin. High resolution responses of the microbiota were examined by 16S rDNA pyrosequencing, microarray analysis, and metagenomic sequencing. The metabolome was assessedmore » by fatty acid quantification, gas chromatography-mass spectrometry (GC-MS), and 1H-NMR spectroscopy. Cultured intestinal epithelial Caco-2 cells were used to assess fecal water toxicity. Microbiome analysis showed, among others, that supplementary iron induced decreased levels of Bifidobacteriaceae and Lactobacillaceae, while it caused higher levels of Roseburia and Prevotella. Metagenomic analyses showed an enrichment of microbial motility-chemotaxis systems, while the metabolome markedly changed from a saccharolytic to a proteolytic profile in response to iron. Branched chain fatty acids and ammonia levels increased significantly, in particular with ferrous sulfate. Importantly, the metabolite-containing effluent from iron-rich conditions showed increased cytotoxicity to Caco-2 cells. In conclusion, our explorations indicate that in the absence of host influences, iron induces a more hostile environment characterized by a reduction of microbes that are generally beneficial, and increased levels of bacterial metabolites that can impair the barrier function of a cultured intestinal epithelial monolayer.« less

Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities

PubMed Central

Biswas, Kristi; Taylor, Michael W.; Gear, Kim

2017-01-01

The application of high-throughput, next-generation sequencing technologies has greatly improved our understanding of the human oral microbiome. While deciphering this diverse microbial community using such approaches is more accurate than traditional culture-based methods, experimental bias introduced during critical steps such as DNA extraction may compromise the results obtained. Here, we systematically evaluate four commonly used microbial DNA extraction methods (MoBio PowerSoil® DNA Isolation Kit, QIAamp® DNA Mini Kit, Zymo Bacterial/Fungal DNA Mini PrepTM, phenol:chloroform-based DNA isolation) based on the following criteria: DNA quality and yield, and microbial community structure based on Illumina amplicon sequencing of the V3–V4 region of the 16S rRNA gene of bacteria and the internal transcribed spacer (ITS) 1 region of fungi. Our results indicate that DNA quality and yield varied significantly with DNA extraction method. Representation of bacterial genera in plaque and saliva samples did not significantly differ across DNA extraction methods and DNA extraction method showed no effect on the recovery of fungal genera from plaque. By contrast, fungal diversity from saliva was affected by DNA extraction method, suggesting that not all protocols are suitable to study the salivary mycobiome. PMID:28099455

Intestinal mucus affinity and biological activity of an orally administered antibacterial and anti-inflammatory peptide.

PubMed

Dupont, Aline; Kaconis, Yani; Yang, Ines; Albers, Thorben; Woltemate, Sabrina; Heinbockel, Lena; Andersson, Mats; Suerbaum, Sebastian; Brandenburg, Klaus; Hornef, Mathias W

2015-02-01

Antimicrobial peptides (AMP) provide protection from infection by pathogenic microorganisms and restrict bacterial growth at epithelial surfaces to maintain mucosal homeostasis. In addition, they exert a significant anti-inflammatory activity. Here we analysed the anatomical distribution and biological activity of an orally administered AMP in the context of bacterial infection and host-microbial homeostasis. The anatomical distribution as well as antibacterial and anti-inflammatory activity of the endogenous AMP cryptdin 2 and the synthetic peptide Pep19-2.5 at the enteric mucosal surface were analysed by immunostaining, functional viability and stimulation assays, an oral Salmonella enterica subsp. enterica sv. Typhimurium (S. Typhimurium) model and comparative microbiota analysis. Endogenous cryptdin 2 was found attached to bacteria of the enteric microbiota within the intestinal mucus layer. Similarly, the synthetic peptide Pep19-2.5 attached rapidly to bacterial cells, exhibited a marked affinity for the intestinal mucus layer in vivo, altered the structural organisation of endotoxin in a mucus matrix and demonstrated potent anti-inflammatory and antibacterial activity. Oral Pep19-2.5 administration induced significant changes in the composition of the enteric microbiota as determined by high-throughput 16S rDNA sequencing. This may have contributed to the only transient improvement of the clinical symptoms after oral infection with S. Typhimurium. Our findings demonstrate the anti-inflammatory activity and mucus affinity of the synthetic AMP Pep19-2.5 and characterise the influence on microbiota composition and enteropathogen infection after oral administration. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Changes in the oral ecosystem induced by the use of 8% arginine toothpaste.

PubMed

Koopman, Jessica E; Hoogenkamp, Michel A; Buijs, Mark J; Brandt, Bernd W; Keijser, Bart J F; Crielaard, Wim; Ten Cate, Jacob M; Zaura, Egija

2017-01-01

Bacterial metabolism of arginine in the oral cavity has a pH-raising and thus, potential anti-caries effect. However, the influence of arginine on the oral microbial ecosystem remains largely unresolved. In this pilot study, nine healthy individuals used toothpaste containing 8% arginine for eight weeks. Saliva was collected to determine arginolytic potential and sucrose metabolic activity at the Baseline, Week 4, Week 8 and after a two weeks Wash-out period. To follow the effects on microbial ecology, 16S rDNA sequencing on saliva and plaque samples at Baseline and Week 8 and metagenome sequencing on selected saliva samples of the same time-points was performed. During the study period, the arginolytic potential of saliva increased, while the sucrose metabolism in saliva decreased. These effects were reversed during the Wash-out period. Although a few operational taxonomic units (OTUs) in plaque changed in abundance during the study period, there was no real shift in the plaque microbiome. In the saliva microbiome there was a significant compositional shift, specifically the genus Veillonella had increased significantly in abundance at Week 8. Indeed, the presence of arginine in toothpaste affects the arginolytic capacity of saliva and reduces its sucrose metabolic activity. Additionally, it leads to a shift in the salivary microbiome composition towards a healthy ecology from a caries point of view. Therefore, arginine can be regarded as a genuine oral prebiotic. Copyright © 2016 Elsevier Ltd. All rights reserved.

l-Arginine Modifies the Exopolysaccharide Matrix and Thwarts Streptococcus mutans Outgrowth within Mixed-Species Oral Biofilms.

PubMed

He, Jinzhi; Hwang, Geelsu; Liu, Yuan; Gao, Lizeng; Kilpatrick-Liverman, LaTonya; Santarpia, Peter; Zhou, Xuedong; Koo, Hyun

2016-10-01

l-Arginine, a ubiquitous amino acid in human saliva, serves as a substrate for alkali production by arginolytic bacteria. Recently, exogenous l-arginine has been shown to enhance the alkalinogenic potential of oral biofilm and destabilize its microbial community, which might help control dental caries. However, l-arginine exposure may inflict additional changes in the biofilm milieu when bacteria are growing under cariogenic conditions. Here, we investigated how exogenous l-arginine modulates biofilm development using a mixed-species model containing both cariogenic (Streptococcus mutans) and arginolytic (Streptococcus gordonii) bacteria in the presence of sucrose. We observed that 1.5% (wt/vol) l-arginine (also a clinically effective concentration) exposure suppressed the outgrowth of S. mutans, favored S. gordonii dominance, and maintained Actinomyces naeslundii growth within biofilms (versus vehicle control). In parallel, topical l-arginine treatments substantially reduced the amounts of insoluble exopolysaccharides (EPS) by >3-fold, which significantly altered the three-dimensional (3D) architecture of the biofilm. Intriguingly, l-arginine repressed S. mutans genes associated with insoluble EPS (gtfB) and bacteriocin (SMU.150) production, while spxB expression (H2O2 production) by S. gordonii increased sharply during biofilm development, which resulted in higher H2O2 levels in arginine-treated biofilms. These modifications resulted in a markedly defective EPS matrix and areas devoid of any bacterial clusters (microcolonies) on the apatitic surface, while the in situ pH values at the biofilm-apatite interface were nearly one unit higher in arginine-treated biofilms (versus the vehicle control). Our data reveal new biological properties of l-arginine that impact biofilm matrix assembly and the dynamic microbial interactions associated with pathogenic biofilm development, indicating the multiaction potency of this promising biofilm disruptor. Dental caries is one of the most prevalent and costly infectious diseases worldwide, caused by a biofilm formed on tooth surfaces. Novel strategies that compromise the ability of virulent species to assemble and maintain pathogenic biofilms could be an effective alternative to conventional antimicrobials that indiscriminately kill other oral species, including commensal bacteria. l-Arginine at 1.5% has been shown to be clinically effective in modulating cariogenic biofilms via alkali production by arginolytic bacteria. Using a mixed-species ecological model, we show new mechanisms by which l-arginine disrupts the process of biofilm matrix assembly and the dynamic microbial interactions that are associated with cariogenic biofilm development, without impacting the bacterial viability. These results may aid in the development of enhanced methods to control biofilms using l-arginine. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Investigation of Acrylic Resin Disinfection Using Chemicals and Ultrasound.

PubMed

Muscat, Ylainia; Farrugia, Cher; Camilleri, Liberato; Arias-Moliz, Maria Teresa; Valdramidis, Vasilis; Camilleri, Josette

2018-06-01

Dental prosthetic and orthodontic appliances are transported from the clinic to the laboratory for additions and repairs. These appliances, containing microbes from the oral flora, are a high risk for cross-contamination. The aim of this study was to evaluate the effect of chemical and ultrasound disinfection against two in vitro biofilms and an in vivo formed biofilm grown on unprepared and polished polymethyl methacrylate (PMMA) surfaces. Rough and polished self-curing PMMA surfaces were infected with strains of both Candida albicans and Streptococcus oralis. After incubation, the samples were treated with different disinfection methods, including ultrasound treatment for both 15 and 30 seconds, and immersion in glutaraldehyde and alcohol-based chemical disinfectants (MD520 and Minuten, respectively). The disinfecting efficacy was assessed by colony forming units (CFU) analysis and by scanning electron microscopy (SEM). Furthermore the adequacy of bacterial elimination of application of 30-second ultrasound and MD520 was assessed on PMMA retrieved from ten volunteers by CFU analyses. ANOVA with p = 0.05 followed by the Tukey post hoc test and the Student t-test was used to analyze the data. The ultrasound treatment for 30 seconds, MD520, and Minuten were the most effective disinfectant methods as they reduced the microbial counts compared to the control (p < 0.05) as shown in the in vitro analyses. S. oralis adhered more to rough acrylic resin surfaces (p < 0.05). Ultrasound treatment was the most effective way to reduce microbial counts on PMMA exposed to oral flora (p = 0.043). Ultrasound treatment for 30 seconds was effective against C. albicans, S. oralis, and the oral flora as shown by testing microbial growth on agar plates and SEM. © 2016 by the American College of Prosthodontists.

Anti-microbial Efficacy of Soursop Leaf Extract (Annona muricata) on Oral Pathogens: An In-vitro Study

PubMed Central

Rajesh, Gururagavendra; Shenoy, Ramya; Rao, Ashwini

2016-01-01

Introduction Annona muricata also called as Soursop is a, flowering evergreen tree native to Mexico, Cuba, Central America and parts of India. The miracle tree as it is widely known as a natural cancer killer that is 10,000 times stronger than chemotherapy. Based on these miraculous claims, the leaves of these plants were used as an extract at varying concentrations as an antibacterial agent against oral pathogens. Aim The aim of the study was to assess antimicrobial efficacy of Soursop leaf extarct (Annona muricata) on Streptococcus mutans, Streptococcus mitis, Porphyromonas gingivalis, Prevotella intermedia and Candida albicans using disc diffusion method. Materials and Methods Extracts of Annona muricata leaves of concentrations of 1%, 5%, 10%, 15% and 20% were prepared. The anti-microbial efficacy was evaluated using disc diffusion method against Streptococcus mutans, Streptococcus mitis, Porphyromonas gingivalis, Prevotella intermedia and Candida albicans on agar plates. Results All concentrations of extracts were effective on the microbiota except for the P. Intermedia. The Soursop extract was highly effective on Candida species, with all concentrations exhibiting bactericidal and fungicidal property. The extracts at different concentration were effective when compared to the gold standard controls and the effect was statistically significant (p<0.05). Data obtained was analysed using one way analysis of variance (ANOVA) and Tukey’s post-hoc test. Conclusion The Soursop extracts were efficient for all test organisms expect P. intermedia. The present study demonstrated the in-vitro efficacy of Soursop was highest against S. mutans followed by C. albicans and least on P. intermedia. Hence, this study proves to an extent that the Soursop extract when used against oral microbiota has sufficient anti-microbial and fungicidal property. PMID:28050493

Microbiota, cirrhosis, and the emerging oral-gut-liver axis

PubMed Central

Acharya, Chathur; Bajaj, Jasmohan S.

2017-01-01

Cirrhosis is a prevalent cause of morbidity and mortality, especially for those at an advanced decompensated stage. Cirrhosis development and progression involves several important interorgan communications, and recently, the gut microbiome has been implicated in pathophysiology of the disease. Dysbiosis, defined as a pathological change in the microbiome, has a variable effect on the compensated versus decompensated stage of cirrhosis. Adverse microbial changes, both in composition and function, can act at several levels within the gut (stool and mucosal) and have also been described in the blood and oral cavity. While dysbiosis in the oral cavity could be a source of systemic inflammation, current cirrhosis treatment modalities are targeted toward the gut-liver axis and do not address the oral microbiome. As interventions designed to modulate oral dysbiosis may delay progression of cirrhosis, a better understanding of this process is of the utmost importance. The concept of oral microbiota dysbiosis in cirrhosis is relatively new; therefore, this review will highlight the emerging role of the oral-gut-liver axis and introduce perspectives for future research. PMID:28978799

Oral microbial community assembly under the influence of periodontitis.

PubMed

Chen, Hongju; Peng, Shuting; Dai, Lin; Zou, Quan; Yi, Bin; Yang, Xianghong; Ma, Zhanshan Sam

2017-01-01

Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.'s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher's exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or 'phenotype' of community assembly), it does not seem to cause the 'mutation' of the 'genotype" (mechanism) of community assembly. We argue that the 'phenotypic' changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation.

Oral microbial community assembly under the influence of periodontitis

PubMed Central

Chen, Hongju; Peng, Shuting; Dai, Lin; Zou, Quan; Yi, Bin; Yang, Xianghong

2017-01-01

Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell’s neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.’s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher’s exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or ‘phenotype’ of community assembly), it does not seem to cause the ‘mutation’ of the ‘genotype” (mechanism) of community assembly. We argue that the ‘phenotypic’ changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation. PMID:28813450

The Same Microbiota and a Potentially Discriminant Metabolome in the Saliva of Omnivore, Ovo-Lacto-Vegetarian and Vegan Individuals

PubMed Central

De Filippis, Francesca; Vannini, Lucia; La Storia, Antonietta; Laghi, Luca; Piombino, Paola; Stellato, Giuseppina; Serrazanetti, Diana I.; Gozzi, Giorgia; Turroni, Silvia; Ferrocino, Ilario; Lazzi, Camilla; Di Cagno, Raffaella; Gobbetti, Marco; Ercolini, Danilo

2014-01-01

The salivary microbiota has been linked to both oral and non-oral diseases. Scant knowledge is available on the effect of environmental factors such as long-term dietary choices on the salivary microbiota and metabolome. This study analyzed the microbial diversity and metabolomic profiles of the saliva of 161 healthy individuals who followed an omnivore or ovo-lacto-vegetarian or vegan diet. A large core microbiota was identified, including 12 bacterial genera, found in >98% of the individuals. The subjects could be stratified into three “salivary types” that differed on the basis of the relative abundance of the core genera Prevotella, Streptococcus/Gemella and Fusobacterium/Neisseria. Statistical analysis indicated no effect of dietary habit on the salivary microbiota. Phylogenetic beta-diversity analysis consistently showed no differences between omnivore, ovo-lacto-vegetarian and vegan individuals. Metabolomic profiling of saliva using 1H-NMR and GC-MS/SPME identified diet-related biomarkers that enabled a significant discrimination between the 3 groups of individuals on the basis of their diet. Formate, urea, uridine and 5-methyl-3-hexanone could discriminate samples from omnivores, whereas 1-propanol, hexanoic acid and proline were characteristic of non-omnivore diets. Although the salivary metabolome can be discriminating for diet, the microbiota has a remarkable inter-individual stability and did not vary with dietary habits. Microbial homeostasis might be perturbed with sub-standard oral hygiene or other environmental factors, but there is no current indication that a choice of an omnivore, ovo-lacto-vegetarian or vegan diet can lead to a specific composition of the oral microbiota with consequences on the oral homeostasis. PMID:25372853

The same microbiota and a potentially discriminant metabolome in the saliva of omnivore, ovo-lacto-vegetarian and Vegan individuals.

PubMed

De Filippis, Francesca; Vannini, Lucia; La Storia, Antonietta; Laghi, Luca; Piombino, Paola; Stellato, Giuseppina; Serrazanetti, Diana I; Gozzi, Giorgia; Turroni, Silvia; Ferrocino, Ilario; Lazzi, Camilla; Di Cagno, Raffaella; Gobbetti, Marco; Ercolini, Danilo

2014-01-01

The salivary microbiota has been linked to both oral and non-oral diseases. Scant knowledge is available on the effect of environmental factors such as long-term dietary choices on the salivary microbiota and metabolome. This study analyzed the microbial diversity and metabolomic profiles of the saliva of 161 healthy individuals who followed an omnivore or ovo-lacto-vegetarian or vegan diet. A large core microbiota was identified, including 12 bacterial genera, found in >98% of the individuals. The subjects could be stratified into three "salivary types" that differed on the basis of the relative abundance of the core genera Prevotella, Streptococcus/Gemella and Fusobacterium/Neisseria. Statistical analysis indicated no effect of dietary habit on the salivary microbiota. Phylogenetic beta-diversity analysis consistently showed no differences between omnivore, ovo-lacto-vegetarian and vegan individuals. Metabolomic profiling of saliva using (1)H-NMR and GC-MS/SPME identified diet-related biomarkers that enabled a significant discrimination between the 3 groups of individuals on the basis of their diet. Formate, urea, uridine and 5-methyl-3-hexanone could discriminate samples from omnivores, whereas 1-propanol, hexanoic acid and proline were characteristic of non-omnivore diets. Although the salivary metabolome can be discriminating for diet, the microbiota has a remarkable inter-individual stability and did not vary with dietary habits. Microbial homeostasis might be perturbed with sub-standard oral hygiene or other environmental factors, but there is no current indication that a choice of an omnivore, ovo-lacto-vegetarian or vegan diet can lead to a specific composition of the oral microbiota with consequences on the oral homeostasis.

Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction.

PubMed

Larsen, Peter; Hamada, Yuki; Gilbert, Jack

2012-07-31

Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science. Copyright © 2012 Elsevier B.V. All rights reserved.

Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology.

PubMed

Guo, Lihong; McLean, Jeffrey S; Yang, Youngik; Eckert, Randal; Kaplan, Christopher W; Kyme, Pierre; Sheikh, Omid; Varnum, Brian; Lux, Renate; Shi, Wenyuan; He, Xuesong

2015-06-16

One major challenge to studying human microbiome and its associated diseases is the lack of effective tools to achieve targeted modulation of individual species and study its ecological function within multispecies communities. Here, we show that C16G2, a specifically targeted antimicrobial peptide, was able to selectively kill cariogenic pathogen Streptococcus mutans with high efficacy within a human saliva-derived in vitro oral multispecies community. Importantly, a significant shift in the overall microbial structure of the C16G2-treated community was revealed after a 24-h recovery period: several bacterial species with metabolic dependency or physical interactions with S. mutans suffered drastic reduction in their abundance, whereas S. mutans' natural competitors, including health-associated Streptococci, became dominant. This study demonstrates the use of targeted antimicrobials to modulate the microbiome structure allowing insights into the key community role of specific bacterial species and also indicates the therapeutic potential of C16G2 to achieve a healthy oral microbiome.

Periodontal diseases.

PubMed

Kinane, Denis F; Stathopoulou, Panagiota G; Papapanou, Panos N

2017-06-22

Periodontal diseases comprise a wide range of inflammatory conditions that affect the supporting structures of the teeth (the gingiva, bone and periodontal ligament), which could lead to tooth loss and contribute to systemic inflammation. Chronic periodontitis predominantly affects adults, but aggressive periodontitis may occasionally occur in children. Periodontal disease initiation and propagation is through a dysbiosis of the commensal oral microbiota (dental plaque), which then interacts with the immune defences of the host, leading to inflammation and disease. This pathophysiological situation persists through bouts of activity and quiescence, until the affected tooth is extracted or the microbial biofilm is therapeutically removed and the inflammation subsides. The severity of the periodontal disease depends on environmental and host risk factors, both modifiable (for example, smoking) and non-modifiable (for example, genetic susceptibility). Prevention is achieved with daily self-performed oral hygiene and professional removal of the microbial biofilm on a quarterly or bi-annual basis. New treatment modalities that are actively explored include antimicrobial therapy, host modulation therapy, laser therapy and tissue engineering for tissue repair and regeneration.

Resistance to tetracycline and β-lactams and distribution of resistance markers in enteric microorganisms and pseudomonads isolated from the oral cavity

PubMed Central

RAMOS, Marcelle Marie Buso; GAETTI-JARDIM, Ellen Cristina; GAETTI-JARDIM, Elerson

2009-01-01

ABSTRACT This study evaluated the occurrence of enteric bacteria and pseudomonads resistant to tetracycline and β-lactams in the oral cavity of patients exhibiting gingivitis (n=89), periodontitis (n=79), periodontally healthy (n=50) and wearing complete dentures (n=41). Microbial identification and presence of resistance markers associated with the production of β-lactamases and tetracycline resistance were performed by using biochemical tests and PCR. Susceptibility tests were carried out in 201 isolates of enteric cocci and rods. Resistance to ampicillin, amoxicillin/clavulanic acid, imipenem, meropenem and tetracycline was detected in 57.4%, 34.6%, 2.4%, 1.9% and 36.5% of the isolates, respectively. β-lactamase production was observed in 41.2% of tested microorganisms, while the most commonly found β-lactamase genetic determinant was gene blaTEM. Tetracycline resistance was disseminated and a wide scope of tet genes were detected in all studied microbial genus. PMID:21499650

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements.

PubMed

Korsch, Michael; Marten, Silke-Mareike; Dötsch, Andreas; Jáuregui, Ruy; Pieper, Dietmar H; Obst, Ursula

2016-12-01

Cementing dental restorations on implants poses the risk of undetected excess cement. Such cement remnants may favor the development of inflammation in the peri-implant tissue. The effect of excess cement on the bacterial community is not yet known. The aim of this study was to analyze the effect of two different dental cements on the composition of the microbial peri-implant community. In a cohort of 38 patients, samples of the peri-implant tissue were taken with paper points from one implant per patient. In 15 patients, the suprastructure had been cemented with a zinc oxide-eugenol cement (Temp Bond, TB) and in 23 patients with a methacrylate cement (Premier Implant Cement, PIC). The excess cement found as well as suppuration was documented. Subgingival samples of all patients were analyzed for taxonomic composition by means of 16S amplicon sequencing. None of the TB-cemented implants had excess cement or suppuration. In 14 (61%) of the PIC, excess cement was found. Suppuration was detected in 33% of the PIC implants without excess cement and in 100% of the PIC implants with excess cement. The taxonomic analysis of the microbial samples revealed an accumulation of oral pathogens in the PIC patients independent of the presence of excess cement. Significantly fewer oral pathogens occurred in patients with TB compared to patients with PIC. Compared with TB, PIC favors the development of suppuration and the growth of periodontal pathogens. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Bovine mastitis may be associated with the deprivation of gut Lactobacillus.

PubMed

Ma, C; Zhao, J; Xi, X; Ding, J; Wang, H; Zhang, H; Kwok, L Y

2016-02-01

Bovine mastitis is an economical important microbial disease in dairy industry. Some recent human clinical trials have shown that oral probiotics supplementation could effectively control clinical mastitis, suggesting that the mechanism of mastitis protection might be achieved via the host gut microbiota. We aimed to test our hypothesis that bovine mastitis was related to changes in both the mammary and gut microbial profiles. By quantitative PCR, the milk and faecal microbial profiles of cows with low (<3×10 5 cells/ml) and high (>1×10 6 cells/ml) somatic cell count (SCC) were compared. Firstly, we observed drastic differences in both the milk and faecal microbial compositions at genus and Lactobacillus-species levels between the two groups. Secondly, the pattern of faecal microbial community changes of mastitis cows was similar to that of the milk, characterised by a general increase in the mastitis pathogens (Enterococcus, Streptococcus and Staphylococcus) and deprivation of Lactobacillus and its members (L. salivarius, L. sakei, L. ruminis, L. delbrueckii, L. buchneri, and L. acidophilus). Thirdly, only the faecal lactobacilli, but not bifidobacteria correlated with the milk microbial communities and SCC. Our data together hint to a close association between bovine mastitis, the host gut and milk microbiota.

Soft, chewable gelatin-based pharmaceutical oral formulations: a technical approach.

PubMed

Dille, Morten J; Hattrem, Magnus N; Draget, Kurt I

2018-06-01

Hard tablets and capsules for oral drug delivery cause problems for people experiencing dysphagia. This work describes the formulation and properties of a gelatin based, self-preserved, and soft chewable tablet as an alternative and novel drug delivery format. Gelatin (8.8-10% in 24.7-29% water) constituted the matrix of the soft, semi-solid tablets. Three different pharmaceuticals (Ibuprofen 10%, Acetaminophen 15%, and Meloxicam 1.5%) were tested in this formulation. Microbial stability was controlled by lowering the water activity with a mixture of sorbitol and xylitol (45.6-55%). Rheological properties were tested applying small strain oscillation measurements. Taste masking of ibuprofen soft-chew tablets was achieved by keeping the ibuprofen insoluble at pH 4.5 and keeping the processing temperature below the crystalline-to-amorphous transition temperature. Soft-chew formulations showed good stability for all three pharmaceuticals (up to 24 months), and the ibuprofen containing formulation exhibited comparable dissolution to a standard oral tablet as well as good microbial stability. The rheological properties of the ibuprofen/gelatin formulation had the fingerprint of a true gelatin gel, albeit higher moduli, and melting temperature. The results suggest that easy-to-swallow and well taste-masked soft chewable tablet formulations with extended shelf life are within reach for several active pharmaceutical ingredients (APIs).

Identification of oral bacteria on titanium implant surfaces by 16S rDNA sequencing.

PubMed

de Melo, Fabiana; do Nascimento, Cássio; Souza, Diogo Onofre; de Albuquerque, Rubens F

2017-06-01

To characterize the profile of microbial communities colonizing titanium implants with different surface treatments after exposure to the oral environment at the genus or higher taxonomic level. Sixteen titanium disks, machined or sandblasted large-grit and acid-etched (SLA), were mounted on removable intraoral splints worn by four patients. After 24 h of intraoral exposure, biofilm samples were collected from disks and supra/subgingival teeth areas. The 16S rDNA genes from each sample were amplified, sequenced with the Miseq Illumina instrument and analyzed. A total of 29 genera and seven more inclusive taxa, representing the phyla Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria and candidate division TM7 were identified in both titanium surfaces and teeth. No differences were found in relation to the operational taxonomic units (OTUs) and microbial diversity, assessed by Chao 1 and Shannon indices, when comparing SLA and machined titanium surfaces. Machined and SLA surfaces are colonized by similar numbers of prokaryotic OTUs after 24 h of exposure to the oral environment. Higher complexity of the titanium surface topography in the initial phase of biofilm maturation does not seem to significantly influence the colonizing microbiota. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

GUT MICROBIOTA DYSBIOSIS IS LINKED TO HYPERTENSION

PubMed Central

Yang, Tao; Santisteban, Monica M.; Rodriguez, Vermali; Li, Eric; Ahmari, Niousha; Carvajal, Jessica Marulanda; Zadeh, Mojgan; Gong, Minghao; Qi, Yanfei; Zubcevic, Jasenka; Sahay, Bikash; Pepine, Carl J.; Raizada, Mohan K.; Mohamadzadeh, Mansour

2015-01-01

Emerging evidence suggests that gut microbiota is critical in the maintenance of physiological homeostasis. The present study was designed to test the hypothesis that dysbiosis in gut microbiota is associated with hypertension since genetic, environmental, and dietary factors profoundly influence both gut microbiota and blood pressure. Bacterial DNA from fecal samples of two rat models of hypertension and a small cohort of patients was used for bacterial genomic analysis. We observed a significant decrease in microbial richness, diversity, and evenness in the spontaneously hypertensive rat, in addition to an increased Firmicutes to Bacteroidetes ratio. These changes were accompanied with decreases in acetate- and butyrate-producing bacteria. Additionally, the microbiota of a small cohort of human hypertension patients was found to follow a similar dysbiotic pattern, as it was less rich and diverse than that of control subjects. Similar changes in gut microbiota were observed in the chronic angiotensin II infusion rat model, most notably decreased microbial richness and an increased Firmicutes to Bacteroidetes ratio. In this model, we evaluated the efficacy of oral minocycline in restoring gut microbiota. In addition to attenuating high blood pressure, minocycline was able to rebalance the dysbiotic hypertension gut microbiota by reducing the Firmicutes to Bacteroidetes ratio. These observations demonstrate that high BP is associated with gut microbiota dysbiosis, both in animal and human hypertension. They suggest that dietary intervention to correct gut microbiota could be an innovative nutritional therapeutic strategy for hypertension. PMID:25870193

Programmable probiotics for detection of cancer in urine

PubMed Central

Danino, Tal; Prindle, Arthur; Kwong, Gabriel A.; Skalak, Matthew; Li, Howard; Allen, Kaitlin; Hasty, Jeff; Bhatia, Sangeeta N.

2015-01-01

Rapid advances in the forward engineering of genetic circuitry in living cells has positioned synthetic biology as a potential means to solve numerous biomedical problems, including disease diagnosis and therapy. One challenge in exploiting synthetic biology for translational applications is to engineer microbes that are well tolerated by patients and seamlessly integrate with existing clinical methods. We use the safe and widely used probiotic Escherichia coli Nissle 1917 to develop an orally administered diagnostic that can noninvasively indicate the presence of liver metastasis by producing easily detectable signals in urine. Our microbial diagnostic generated a high-contrast urine signal through selective expansion in liver metastases (106-fold enrichment) and high expression of a lacZ reporter maintained by engineering a stable plasmid system. The lacZ reporter cleaves a substrate to produce a small molecule that can be detected in urine. E. coli Nissle 1917 robustly colonized tumor tissue in rodent models of liver metastasis after oral delivery but did not colonize healthy organs or fibrotic liver tissue. We saw no deleterious health effects on the mice for more than 12 months after oral delivery. Our results demonstrate that probiotics can be programmed to safely and selectively deliver synthetic gene circuits to diseased tissue microenvironments in vivo. PMID:26019220

Downstream Processing, Formulation Development and Antithrombotic Evaluation of Microbial Nattokinase.

PubMed

Kapoor, Rohit; Harde, Harshad; Jain, Sanyog; Panda, Amulya Kumar; Panda, Bibhu Prasad

2015-07-01

The present research work describes the downstreaming of nattokinase (NK) produced by Bacillus subtilis under solid state fermentation; and the role of efficient oral formulation of purified NK in the management of thrombotic disorders. Molecular weight of purified NK was estimated to be 28 kDa with specific activity of 504.4 FU/mg. Acid stable nattokinase loaded chitosan nanoparticles (sNLCN) were fabricated for oral delivery of this enzyme. Box-Behnken design (BBD) was employed to investigate and validate the effect of process (independent) variables on the quality attributes (dependent variables) of nanoparticles. The integrity, conformational stability and preservation of fibrinolytic activity of NK (in both free and sNLCN forms) were established by SDS-PAGE, CD analysis and in vitro clot lytic examination, respectively. A 'tail thrombosis model' demonstrated significant decrease in frequency of thrombosis in Wistar rats upon peroral administration of sNLCN in comparison with negative control and free NK group. Furthermore, coagulation analysis, namely the measurement of prothrombin and activated partial thromboplastin time illustrated that sNLCN showed significantly (p < 0.001) higher anti-thrombotic potential in comparison to the free NK. Further, sNLCN showed anti-thrombotic profile similar to warfarin. This study signifies the potential of sNLCN in oral delivery of NK for the management of thrombotic disorders.

Microbial contamination of used dental handpieces.

PubMed

Smith, Gordon; Smith, Andrew

2014-09-01

Microbial contamination of used, unprocessed internal components of dental handpieces (HPs) was assessed. HPs were dismantled aseptically, immersed in phosphate-buffered saline, ultrasonicated, and cultured. A median of 200 CFU per turbine (n = 40), 400 CFU per spray channel (n = 40), and 1000 CFU per item of surgical gear (n = 20) was detected. Isolates included oral streptococci, Pseudomonas spp, and Staphylococcus aureus. Recovery of S aureus confirms the need for appropriate HP cleaning and sterilization after each patient to prevent cross-infection. Copyright © 2014 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

Insights into the human oral microbiome.

PubMed

Verma, Digvijay; Garg, Pankaj Kumar; Dubey, Ashok Kumar

2018-05-01

Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions.

PubMed

Adler, Christina J; Dobney, Keith; Weyrich, Laura S; Kaidonis, John; Walker, Alan W; Haak, Wolfgang; Bradshaw, Corey J A; Townsend, Grant; Sołtysiak, Arkadiusz; Alt, Kurt W; Parkhill, Julian; Cooper, Alan

2013-04-01

The importance of commensal microbes for human health is increasingly recognized, yet the impacts of evolutionary changes in human diet and culture on commensal microbiota remain almost unknown. Two of the greatest dietary shifts in human evolution involved the adoption of carbohydrate-rich Neolithic (farming) diets (beginning ∼10,000 years before the present) and the more recent advent of industrially processed flour and sugar (in ∼1850). Here, we show that calcified dental plaque (dental calculus) on ancient teeth preserves a detailed genetic record throughout this period. Data from 34 early European skeletons indicate that the transition from hunter-gatherer to farming shifted the oral microbial community to a disease-associated configuration. The composition of oral microbiota remained unexpectedly constant between Neolithic and medieval times, after which (the now ubiquitous) cariogenic bacteria became dominant, apparently during the Industrial Revolution. Modern oral microbiotic ecosystems are markedly less diverse than historic populations, which might be contributing to chronic oral (and other) disease in postindustrial lifestyles.

Oral pharmacokinetics of baicalin, wogonoside, oroxylin A 7-O-β-d-glucuronide and their aglycones from an aqueous extract of Scutellariae Radix in the rat.

PubMed

Cai, Yu; Li, Sai; Li, Ting; Zhou, Ruina; Wai, Alfred Tai-Seng; Yan, Ru

2016-07-15

Scutellariae Radix (SR) has been extensively prescribed in folk medicines due to its notable beneficial activities. The flavonoid glucuronides baicalin (BG), wogonoside (WG), oroxylin A 7-O-β-d-glucuronide (OG) and their aglycones baicalein, wogonin and oroxylin A, are the main components of the herb. So far, majority of previous studies failed to report the pharmacokinetics and none offered an explanation for the systemic exposures of these six flavonoids when the herbal extract was orally administered. In this study, when a SR extract was orally dosed to rats (800mg/kg, equivalent to BG 324.80, WG 124.00, OG 43.04, baicalein 25.36, wogonin 24.40, and oroxylin A 5.79mg/kg), all six flavonoids were detectable throughout the experimental period (48h) using an LC-MS/MS method with the Cmax and AUC0-48h of the glucuronides 10-130 times that of respective aglycones. As the lowest among the three glucuronides in the herb, OG was the most abundant in vivo, while the systemic exposure of wogonin was the highest amongst the three aglycones. The dose-normalized AUC0-48h descended in orders of OG/oroxylin A, WG/wogonin and BG/baicalein. Two di-conjugates of baicalein (BG glucuronide and BG glucoside), two BG isomers (minor BM1 and major BM2), and one WG isomer (wogonin 5-O-glucuronide) were detected in rat plasma. Semi-quantitation of the isomers with peak area data revealed that the AUPs (area under peak area ratio-time curves) of BG isomers were ∼3 times that of BG, yet the AUP of wogonin 5-O-glucuronide was only one seventh of WG. BM2, tentatively assigned as baicalein 6-O-glucuronide, was formed from both microbial isomerization of BG and hepatic glucuronidation of baicalein. Wogonin 5-O-glucuronide was only formed in hepatic glucuronidation of wogonin. Demethylated wogonin was observed in gut bacteria, offering an optional origin of BM1 apart from baicalein glucuronidation. Microbial isomerization of BG and extensive hepatic glucuronidation of baicalein to form BM2as well as a poorer intestinal permeability of baicalein (Papp×10(-6)cm/s) should account for the lower systemic exposures of BG and baicalein. Faster microbial hydrolysis of WG, high intestinal permeability (Papp×10(-5)cm/s) and less hepatic glucuronidation of wogonin explain the relatively high systemic exposure of wogonin. Sole microbial deglycosylation of OG, high intestinal permeability (Papp×10(-5)cm/s) and extensive hepatic glucuronidation of oroxylin A supported the highest systemic exposure of OG. Taken together, the oral kinetics of six flavonoid glucuronides and aglycones in the SR extract were simultaneously obtained. Microbial conversion, intestinal epithelial permeability and hepatic glucuronidation are determinant factors for their systemic exposures. Copyright © 2015 Elsevier B.V. All rights reserved.

Effectiveness of enamel matrix derivative on the clinical and microbiological outcomes following surgical regenerative treatment of peri-implantitis. A randomized controlled trial.

PubMed

Isehed, Catrine; Holmlund, Anders; Renvert, Stefan; Svenson, Björn; Johansson, Ingegerd; Lundberg, Pernilla

2016-10-01

This randomized clinical trial aimed at comparing radiological, clinical and microbial effects of surgical treatment of peri-implantitis alone or in combination with enamel matrix derivative (EMD). Twenty-six subjects were treated with open flap debridement and decontamination of the implant surfaces with gauze and saline preceding adjunctive EMD or no EMD. Bone level (BL) change was primary outcome and secondary outcomes were changes in pocket depth (PD), plaque, pus, bleeding and the microbiota of the peri-implant biofilm analyzed by the Human Oral Microbe Identification Microarray over a time period of 12 months. In multivariate modelling, increased marginal BL at implant site was significantly associated with EMD, the number of osseous walls in the peri-implant bone defect and a Gram+/aerobic microbial flora, whereas reduced BL was associated with a Gram-/anaerobic microbial flora and presence of bleeding and pus, with a cross-validated predictive capacity (Q(2) ) of 36.4%. Similar, but statistically non-significant, trends were seen for BL, PD, plaque, pus and bleeding in univariate analysis. Adjunctive EMD to surgical treatment of peri-implantitis was associated with prevalence of Gram+/aerobic bacteria during the follow-up period and increased marginal BL 12 months after treatment. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Antimicrobial and Attractant Roles for Chemerin in the Oral Cavity during Inflammatory Gum Disease

PubMed Central

Godlewska, Urszula; Brzoza, Piotr; Sroka, Aneta; Majewski, Pawel; Jentsch, Holger; Eckert, Martin; Eick, Sigrun; Potempa, Jan; Zabel, Brian A.; Cichy, Joanna

2017-01-01

Periodontal inflammation is one of the most common chronic inflammatory conditions in humans. Despite recent advances in identifying and characterizing oral microbiota dysbiosis in the pathogenesis of gum disease, just how host factors maintain a healthy homeostatic oral microbial community or prevent the development of a pathogenic oral microbiota remains poorly understood. An important determinant of microbiota fate is local antimicrobial proteins. Here, we report that chemoattractant protein chemerin, which we recently identified as a potent endogenous antimicrobial agent in body barriers such as the skin, is present in the oral cavity under homeostatic and inflammatory conditions. Chemerin and a chemerin-derived antimicrobial peptide are bactericidal against select bacteria strategically positioned in dental biofilm. Gingival crevicular samples from patients with gingivitis but not periodontitis contain abundant bioactive chemerin capable of inducing CMKLR1-dependent leukocyte migration. Gingipains secreted by the periodontopathogen P. gingivalis inactivate chemerin. Together, these data suggest that as an antimicrobial agent and leukocyte chemoattractant, chemerin likely contributes to antimicrobial immune defense in the oral cavity. PMID:28424689

Microbial Metabolism. Part 11. Metabolites of Flutamide

USDA-ARS?s Scientific Manuscript database

Flutamide, a nonsteroidal antiandrogen is a commonly used drug to treat advanced prostate cancer,2) which is one of the leading causes of death in men in the United States.3) It is absorbed rapidly from the gastrointestinal track of humans and rats after oral administration and undergoes extensive m...

A microbial biogeochemistry network for soil carbon and nitrogen cycling and methane flux: model structure and application to Asia

NASA Astrophysics Data System (ADS)

Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

2017-12-01

A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.

Oral microbiota species in acute apical endodontic abscesses.

PubMed

George, Noelle; Flamiatos, Erin; Kawasaki, Kellie; Kim, Namgu; Carriere, Charles; Phan, Brian; Joseph, Raphael; Strauss, Shay; Kohli, Richie; Choi, Dongseok; Baumgartner, J Craig; Sedgley, Christine; Maier, Tom; Machida, Curtis A

2016-01-01

Acute apical abscesses are serious endodontic diseases resulting from pulpal infection with opportunistic oral microorganisms. The objective of this study was to identify and compare the oral microbiota in patients (N=18) exhibiting acute apical abscesses, originating from the demographic region in Portland, Oregon. The study hypothesis is that abscesses obtained from this demographic region may contain unique microorganisms not identified in specimens from other regions. Endodontic abscesses were sampled from patients at the Oregon Health & Science University (OHSU) School of Dentistry. DNA from abscess specimens was subjected to polymerase chain reaction amplification using 16S rRNA gene-specific primers and Cy3-dCTP labeling. Labeled DNA was then applied to microbial microarrays (280 species) generated by the Human Oral Microbial Identification Microarray Laboratory (Forsyth Institute, Cambridge, MA). The most prevalent microorganisms, found across multiple abscess specimens, include Fusobacterium nucleatum, Parvimonas micra, Megasphaera species clone CS025, Prevotella multisaccharivorax, Atopobium rimae, and Porphyromonas endodontalis. The most abundant microorganisms, found in highest numbers within individual abscesses, include F. nucleatum, P. micra, Streptococcus Cluster III, Solobacterium moorei, Streptococcus constellatus, and Porphyromonas endodontalis. Strong bacterial associations were identified between Prevotella multisaccharivorax, Acidaminococcaceae species clone DM071, Megasphaera species clone CS025, Actinomyces species clone EP053, and Streptococcus cristatus (all with Spearman coefficients >0.9). Cultivable and uncultivable bacterial species have been identified in endodontic abscesses obtained from the Portland, Oregon demographic region, and taxa identifications correlated well with other published studies, with the exception of Treponema and Streptococcus cristae, which were not commonly identified in endodontic abscesses between the demographic region in Portland, Oregon and other regions.

Khat (Catha edulis) alters the phenotype and anti-microbial activity of peripheral blood mononuclear cells.

PubMed

Murdoch, Craig; Aziz, Hesham Abdul; Fang, Hsin-Yu; Jezan, Hussun; Musaid, Raga; Muthana, Munitta

2011-12-08

The habit of khat chewing has been associated with increased risk of systemic and oral disease. Although research has been conducted on the affects of khat on oral epithelial cells, little is known about its influence on immune cells. This study examined the biological effects of khat on the phenotype and function of peripheral blood mononuclear cells (PBMCs). Khat-stimulated PBMCs were examined for signs of cytotoxicity, apoptosis and changes in cell surface receptor and cytokine expression. Khat-induced regulation of transcription factors and stress-related factors were examined, as was PBMC phagocytic activity against oral bacteria. Khat was cytotoxic to PBMC in a dose- and time-dependent manner and cell death was mediated by apoptosis. Khat-treated PBMC showed increased expression of co-stimulatory molecules (CD80, CD86 and MHC II) and pattern recognition receptors (TLR-2, TLR-4 and TREM-1) but secretion of inflammatory cytokines (TNFα, IL-6, CCL5, CXCL8) was inhibited. In contrast, khat induced an increase in the anti-inflammatory cytokine IL-10 as well as IL-2, IFN-γ, FasL and HSP70. These khat-induced alterations were accompanied by increased expression of transcription factors p38 MAPK and HIF-1α, whilst expression of NFκB p65 was inhibited. Although the ability of PBMC to phagocytose dextran and oral bacteria was inhibited, production of reactive oxygen species was increased. These data suggest that khat may severely influence the effectiveness of immune surveillance and anti-microbial capacity of PBMCs. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Mycobacterium smegmatis infection of a prosthetic total knee arthroplasty.

PubMed

Saffo, Zaid; Ognjan, Anthony

2016-01-01

The most common organisms causing prosthetic knee joint infections are staphylococci. However, arthroplasty infections with atypical microbial pathogens, such as Mycobacteria can occur. Due to the rarity of mycobacterial prosthetic joint infections, diagnosis, treatment, and management of these atypical infections represent a clinical challenge. A 71-year old female post-operative day 40 after a left total knee arthroplasty was hospitalized secondary to left knee pain and suspected arthroplasty infection. She had failed outpatient oral antimicrobial treatment for superficial stitch abscess; and outpatient IV/Oral antimicrobials for a clinical postoperative septic bursitis. Ultimately, resection arthroplasty with operative tissue acid fast bacterial cultures demonstrated growth of the Mycobacterium smegmatis group. Post-operatively, she completed a combination course of oral doxycycline and levofloxacin and successfully completed a replacement arthroplasty with clinical and microbial resolution of the infection. To our knowledge, literature review demonstrates three case of knee arthroplasty infection caused by the Mycobacterium smegmatis group. Correspondingly, optimal surgical procedures and antimicrobial management including antimicrobial selection, treatment duration are not well defined. Presently, the best treatment options consists of two step surgical management including prosthesis hardware removal followed by extended antimicrobial therapy, followed by consideration for re-implantation arthroplasty. Our case illustrates importance of considering atypical mycobacterial infections in post-operative arthroplasty infections not responding to traditional surgical manipulations and antimicrobials. For an arthroplasty infection involving the atypical Mycobacterium smegmatis group, two step arthroplasty revision, including arthroplasty resection, with a combination of oral doxycycline and levofloxacin can lead to successful infection resolution, allowing for a successful replacement arthroplasty.

Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

NASA Astrophysics Data System (ADS)

He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

2014-12-01

Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

Human neutrophils and oral microbiota: a constant tug-of-war between a harmonious and a discordant coexistence

PubMed Central

Uriarte, Silvia M.; Edmisson, Jacob S.; Jimenez-Flores, Emeri

2017-01-01

Summary Neutrophils are a major component of the innate host response, and the outcome of the interaction between the oral microbiota and neutrophils is a key determinant of oral health status. The composition of the oral microbiome is very complex and different in health and disease. Neutrophils are constantly recruited to the oral cavity, and their protective role is highlighted in cases where their number or functional responses are impeded, resulting in different forms of periodontal disease. Periodontitis, one of the more severe and irreversible forms of periodontal disease, is a microbial-induced chronic inflammatory disease that affects the gingival tissues supporting the tooth. This chronic inflammatory disease is the result of a shift of the oral bacterial symbiotic community to a dysbiotic more complex community. Chronic inflammatory infectious diseases such as periodontitis can occur because the pathogens are able to evade or disable the innate immune system. In this review, we discuss how human neutrophils interact with both the symbiotic and the dysbiotic oral community; an understanding of which is essential to increase our knowledge of the periodontal disease process. PMID:27558341

Signature of Microbial Dysbiosis in Periodontitis.

PubMed

Meuric, Vincent; Le Gall-David, Sandrine; Boyer, Emile; Acuña-Amador, Luis; Martin, Bénédicte; Fong, Shao Bing; Barloy-Hubler, Frederique; Bonnaure-Mallet, Martine

2017-07-15

Periodontitis is driven by disproportionate host inflammatory immune responses induced by an imbalance in the composition of oral bacteria; this instigates microbial dysbiosis, along with failed resolution of the chronic destructive inflammation. The objectives of this study were to identify microbial signatures for health and chronic periodontitis at the genus level and to propose a model of dysbiosis, including the calculation of bacterial ratios. Published sequencing data obtained from several different studies (196 subgingival samples from patients with chronic periodontitis and 422 subgingival samples from healthy subjects) were pooled and subjected to a new microbiota analysis using the same Visualization and Analysis of Microbial Population Structures (VAMPS) pipeline, to identify microbiota specific to health and disease. Microbiota were visualized using CoNet and Cytoscape. Dysbiosis ratios, defined as the percentage of genera associated with disease relative to the percentage of genera associated with health, were calculated to distinguish disease from health. Correlations between the proposed dysbiosis ratio and the periodontal pocket depth were tested with a different set of data obtained from a recent study, to confirm the relevance of the ratio as a potential indicator of dysbiosis. Beta diversity showed significant clustering of periodontitis-associated microbiota, at the genus level, according to the clinical status and independent of the methods used. Specific genera ( Veillonella , Neisseria , Rothia , Corynebacterium , and Actinomyces ) were highly prevalent (>95%) in health, while other genera ( Eubacterium , Campylobacter , Treponema , and Tannerella ) were associated with chronic periodontitis. The calculation of dysbiosis ratios based on the relative abundance of the genera found in health versus periodontitis was tested. Nonperiodontitis samples were significantly identifiable by low ratios, compared to chronic periodontitis samples. When applied to a subgingival sample set with well-defined clinical data, the method showed a strong correlation between the dysbiosis ratio, as well as a simplified ratio ( Porphyromonas , Treponema , and Tannerella to Rothia and Corynebacterium ), and pocket depth. Microbial analysis of chronic periodontitis can be correlated with the pocket depth through specific signatures for microbial dysbiosis. IMPORTANCE Defining microbiota typical of oral health or chronic periodontitis is difficult. The evaluation of periodontal disease is currently based on probing of the periodontal pocket. However, the status of pockets "on the mend" or sulci at risk of periodontitis cannot be addressed solely through pocket depth measurements or current microbiological tests available for practitioners. Thus, a more specific microbiological measure of dysbiosis could help in future diagnoses of periodontitis. In this work, data from different studies were pooled, to improve the accuracy of the results. However, analysis of multiple species from different studies intensified the bacterial network and complicated the search for reproducible microbial signatures. Despite the use of different methods in each study, investigation of the microbiota at the genus level showed that some genera were prevalent (up to 95% of the samples) in health or disease, allowing the calculation of bacterial ratios (i.e., dysbiosis ratios). The correlation between the proposed ratios and the periodontal pocket depth was tested, which confirmed the link between dysbiosis ratios and the severity of the disease. The results of this work are promising, but longitudinal studies will be required to improve the ratios and to define the microbial signatures of the disease, which will allow monitoring of periodontal pocket recovery and, conceivably, determination of the potential risk of periodontitis among healthy patients. Copyright © 2017 American Society for Microbiology.

Photodynamic inactivation of Staphylococcus aureus and Escherichia coli biofilms by malachite green and phenothiazine dyes: an in vitro study.

PubMed

Vilela, Simone Furgeri Godinho; Junqueira, Juliana Campos; Barbosa, Junia Oliveira; Majewski, Marta; Munin, Egberto; Jorge, Antonio Olavo Cardoso

2012-06-01

The organization of biofilms in the oral cavity gives them added resistance to antimicrobial agents. The action of phenothiazinic photosensitizers on oral biofilms has already been reported. However, the action of the malachite green photosensitizer upon biofilm-organized microorganisms has not been described. The objective of the present work was to compare the action of malachite green with the phenothiazinic photosensitizers (methylene blue and toluidine blue) on Staphylococcus aureus and Escherichia coli biofilms. The biofilms were grown on sample pieces of acrylic resin and subjected to photodynamic therapy using a 660-nm diode laser and photosensitizer concentrations ranging from 37.5 to 3000 μM. After photodynamic therapy, cells from the biofilms were dispersed in a homogenizer and cultured in Brain Heart Infusion broth for quantification of colony-forming units per experimental protocol. For each tested microorganism, two control groups were maintained: one exposed to the laser radiation without the photosensitizer (L+PS-) and other treated with the photosensitizer without exposure to the red laser light (L-PS+). The results were subjected to descriptive statistical analysis. The best results for S. aureus and E. coli biofilms were obtained with photosensitizer concentrations of approximately 300 μM methylene blue, with microbial reductions of 0.8-1.0 log(10); 150 μM toluidine blue, with microbial reductions of 0.9-1.0 log(10); and 3000 μM malachite green, with microbial reductions of 1.6-4.0 log(10). Greater microbial reduction was achieved with the malachite green photosensitizer when used at higher concentrations than those employed for the phenothiazinic dyes. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Inflammasome and Danger Molecule Signaling: At the Crossroads of Inflammation and Pathogen Persistence in the Oral Cavity

PubMed Central

Yilmaz, Özlem; Lee, Kyu Lim

2014-01-01

Inflammasomes are an oligomeric assembly of multiprotein complexes that activate the caspase-1-dependent maturation and the subsequent secretion of inflammatory interleukin-1β and interleukin-18 cytokines in response to a ‘danger signal’ in vertebrates. The assessment of their significance continues to grow rapidly as the complex biology of various chronic inflammatory conditions are better dissected. Increasing evidence links inflammasomes and host-derived small ‘danger molecule ATP’-signaling strongly with the modulation of the host immune response by microbial colonizers as well as potential altering of the microbiome structure and inter-microbial interactions in host. All of these factors eventually lead to the destructive chronic inflammatory disease state. In the oral cavity, a highly dynamic and multifaceted interplay takes place between the endogenous danger molecule signaling and colonizing microbes on the mucosal surfaces. This interaction may redirect the local microenvironment to favor the conversion of the resident microbiome towards pathogenicity. This review outlines the major components of the known inflammasome complexes/mechanisms and highlights their regulation, in particular, by oral microorganisms in relation to the periodontal disease pathology. Better characterizations of the cellular and molecular biology of the inflammasome will likely present important potential therapeutic targets in the treatment and prevention of periodontal disease as well as other debilitating chronic diseases. PMID:26252403

Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease, using transposon-aided capture (TRACA).

PubMed

Warburton, Philip J; Allan, Elaine; Hunter, Stephanie; Ward, John; Booth, Veronica; Wade, William G; Mullany, Peter

2011-11-01

The human oral cavity is host to a complex microbial community estimated to comprise >700 bacterial species, of which at least half are thought to be not yet cultivable in vitro. To investigate the plasmids present in this community, we used a transposon-aided capture system, which allowed the isolation of plasmids from human oral supra- and subgingival plaque samples. Thirty-two novel plasmids and a circular molecule that could be an integrase-generated circular intermediate were isolated. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Using data to inform soil microbial carbon model structure and parameters

NASA Astrophysics Data System (ADS)

Hagerty, S. B.; Schimel, J.

2016-12-01

There is increasing consensus that explicitly representing microbial mechanisms in soil carbon models can improve model predictions of future soil carbon stocks. However, which microbial mechanisms must be represented in these new models and how remains under debate. One of the major challenges in developing microbially explicit soil carbon models is that there is little data available to validate model structure. Empirical studies of microbial mechanisms often fail to capture the full range of microbial processes; from the cellular processes that occur within minutes to hours of substrate consumption to community turnover which may occur over weeks or longer. We added isotopically labeled 14C-glucose to soil incubated in the lab and traced its movement into the microbial biomass, carbon dioxide, and K2SO4 extractable carbon pool. We measured the concentration of 14C in each of these pools at 1, 3, 6, 24, and 72 hours and at 7, 14, and 21 days. We used this data to compare data fits among models that match our conceptual understanding of microbial carbon transformations and to estimate microbial parameters that control the fate of soil carbon. Over 90% of the added glucose was consumed within the first hour after it was added and concentration of the label was highest in biomass at this time. After the first hour, the label in biomass declined, with the rate that the label moved from the biomass slowing after 24hours, because of this models representing the microbial biomass as two pools fit best. Recovery of the label decreased with incubation time, from nearly 80% in the first hour to 67% after three weeks, indicating that carbon is moving into unextractable pools in the soil likely as microbial products and necromass sorb to soil particles and that these mechanisms must be represented in microbial models. This data fitting exercise demonstrates how isotopic data can be useful in validating model structure and estimating microbial model parameters. Future studies can apply this inverse modeling approach to compare the response of microbial parameters to changes in environmental conditions.

Pseudomonas aeruginosa RhlR is required to neutralize the cellular immune response in a Drosophila melanogaster oral infection model

PubMed Central

Limmer, Stefanie; Haller, Samantha; Drenkard, Eliana; Lee, Janice; Yu, Shen; Kocks, Christine; Ausubel, Frederick M.; Ferrandon, Dominique

2011-01-01

An in-depth mechanistic understanding of microbial infection necessitates a molecular dissection of host–pathogen relationships. Both Drosophila melanogaster and Pseudomonas aeruginosa have been intensively studied. Here, we analyze the infection of D. melanogaster by P. aeruginosa by using mutants in both host and pathogen. We show that orally ingested P. aeruginosa crosses the intestinal barrier and then proliferates in the hemolymph, thereby causing the infected flies to die of bacteremia. Host defenses against ingested P. aeruginosa included an immune deficiency (IMD) response in the intestinal epithelium, systemic Toll and IMD pathway responses, and a cellular immune response controlling bacteria in the hemocoel. Although the observed cellular and intestinal immune responses appeared to act throughout the course of the infection, there was a late onset of the systemic IMD and Toll responses. In this oral infection model, P. aeruginosa PA14 did not require its type III secretion system or other well-studied virulence factors such as the two-component response regulator GacA or the protease AprA for virulence. In contrast, the quorum-sensing transcription factor RhlR, but surprisingly not LasR, played a key role in counteracting the cellular immune response against PA14, possibly at an early stage when only a few bacteria are present in the hemocoel. These results illustrate the power of studying infection from the dual perspective of host and pathogen by revealing that RhlR plays a more complex role during pathogenesis than previously appreciated. PMID:21987808

Optimise the microbial flora with milk and yoghurt to prevent disease.

PubMed

Morris, James A

2018-05-01

Pathogenic bacteria, which are temporary or permanent members of our microbial flora, cause or contribute to a wide range of human disease at all ages. Conditions include Alzheimer's disease, atherosclerosis, diabetes mellitus, obesity, cancer, autoimmunity and psychosis, amongst others. The mechanism of damage is inflammation which can be chronic or acute. An optimal microbial flora includes a wide range of pathogenic bacteria in low dose. This allows specific immunity to be developed and maintained with minimal inflammatory damage. Human milk has evolved to deliver an optimal microbial flora to the infant. Cow's milk has the potential, following appropriate fortification, to maintain an optimal human microbial flora throughout life. Yoghurt is a fermented milk product in which bacteria normally present in milk convert sugars to lactic acid. The acid suppresses the growth of pathogens in the oral cavity, oropharynx and oesophagus. Thus yoghurt can restore an optimal flora in these regions in the short term. Since bacteria are transported between epithelial surfaces, yoghurt will also optimise the flora elsewhere. The judicious use of milk and yogurt could prevent a high proportion of human disease. Copyright © 2018 The Author. Published by Elsevier Ltd.. All rights reserved.

Insights from intercomparison of microbial and conventional soil models

NASA Astrophysics Data System (ADS)

Allison, S. D.; Li, J.; Luo, Y.; Mayes, M. A.; Wang, G.

2014-12-01

Changing the structure of soil biogeochemical models to represent coupling between microbial biomass and carbon substrate pools could improve predictions of carbon-climate feedbacks. So-called "microbial models" with this structure make very different predictions from conventional models based on first-order decay of carbon substrate pools. Still, the value of microbial models is uncertain because microbial physiological parameters are poorly constrained and model behaviors have not been fully explored. To address these issues, we developed an approach for inter-comparing microbial and conventional models. We initially focused on soil carbon responses to microbial carbon use efficiency (CUE) and temperature. Three scenarios were implemented in all models at a common reference temperature (20°C): constant CUE (held at 0.31), varied CUE (-0.016°C-1), and 50% acclimated CUE (-0.008°C-1). Whereas the conventional model always showed soil carbon losses with increasing temperature, the microbial models each predicted a temperature threshold above which warming led to soil carbon gain. The location of this threshold depended on CUE scenario, with higher temperature thresholds under the acclimated and constant scenarios. This result suggests that the temperature sensitivity of CUE and the structure of the soil carbon model together regulate the long-term soil carbon response to warming. Compared to the conventional model, all microbial models showed oscillatory behavior in response to perturbations and were much less sensitive to changing inputs. Oscillations were weakest in the most complex model with explicit enzyme pools, suggesting that multi-pool coupling might be a more realistic representation of the soil system. This study suggests that model structure and CUE parameterization should be carefully evaluated when scaling up microbial models to ecosystems and the globe.

Microbial role in periodontitis: Have we reached the top? Some unsung bacteria other than red complex

PubMed Central

Arora, Nupur; Mishra, Ashank; Chugh, Samir

2014-01-01

The microbial etiology of periodontal disease has been the focus of researchers for a long time. The search for the pathogens of periodontal diseases has been underway for more than 100 years, and continues up today. Despite the increasing knowledge about oral microbiota, we are not able to implicate any one particular organism that can be considered as a candidate pathogen. In fact the term “candidate pathogen” has lost its steam with a myriad of microorganisms being incriminated from time to time. Most studies of the bacterial etiology of periodontitis have used either culture-based or targeted deoxyribonucleic acid approaches and so it is likely that pathogens remain undiscovered. The advent of 16S cloning and sequencing has facilitated identification of several uncultivable bacteria in the oral cavity. The concept that not one single organism, but several organisms contained in the biofilm orchestrating in a medley of the show appears to be more plausible. The present review highlights some lesser known bacteria associated with periodontal destruction. PMID:24744537

Influences of pH and Iron Concentration on the Salivary Microbiome in Individual Humans with and without Caries

PubMed Central

Zhou, Jianye; Jiang, Nan; Wang, Zhenzhen; Li, Longqing; Zhang, Jumei; Ma, Rui; Nie, Hongbing

2016-01-01

ABSTRACT This study aimed to identify the differences in the oral microbial communities in saliva from patients with and without caries by performing sequencing with the Illumina MiSeq platform, as well as to further assess their relationships with environmental factors (salivary pH and iron concentration). Forty-three volunteers were selected, including 21 subjects with and 22 without caries, from one village in Gansu, China. Based on 966,255 trimmed sequences and clustering at the 97% similarity level, 1,303 species-level operational taxonomic units were generated. The sequencing data for the two groups revealed that (i) particular distribution patterns (synergistic effects or competition) existed in the subjects with and without caries at both the genus and species levels and (ii) both the salivary pH and iron concentration had significant influences on the microbial community structure. IMPORTANCE The significant influences of the oral environment observed in this study increase the current understanding of the salivary microbiome in caries. These results will be useful for expanding research directions and for improving disease diagnosis, prognosis, and therapy. PMID:27940544

Influences of pH and Iron Concentration on the Salivary Microbiome in Individual Humans with and without Caries.

PubMed

Zhou, Jianye; Jiang, Nan; Wang, Zhenzhen; Li, Longqing; Zhang, Jumei; Ma, Rui; Nie, Hongbing; Li, Zhiqiang

2017-02-15

This study aimed to identify the differences in the oral microbial communities in saliva from patients with and without caries by performing sequencing with the Illumina MiSeq platform, as well as to further assess their relationships with environmental factors (salivary pH and iron concentration). Forty-three volunteers were selected, including 21 subjects with and 22 without caries, from one village in Gansu, China. Based on 966,255 trimmed sequences and clustering at the 97% similarity level, 1,303 species-level operational taxonomic units were generated. The sequencing data for the two groups revealed that (i) particular distribution patterns (synergistic effects or competition) existed in the subjects with and without caries at both the genus and species levels and (ii) both the salivary pH and iron concentration had significant influences on the microbial community structure. The significant influences of the oral environment observed in this study increase the current understanding of the salivary microbiome in caries. These results will be useful for expanding research directions and for improving disease diagnosis, prognosis, and therapy. Copyright © 2017 Zhou et al.

Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth System Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Xiaofeng; Schimel, Joshua; Thornton, Peter E

2014-01-01

Microbial assimilation of soil organic carbon is one of the fundamental processes of global carbon cycling and it determines the magnitude of microbial biomass in soils. Mechanistic understanding of microbial assimilation of soil organic carbon and its controls is important for to improve Earth system models ability to simulate carbon-climate feedbacks. Although microbial assimilation of soil organic carbon is broadly considered to be an important parameter, it really comprises two separate physiological processes: one-time assimilation efficiency and time-dependent microbial maintenance energy. Representing of these two mechanisms is crucial to more accurately simulate carbon cycling in soils. In this study, amore » simple modeling framework was developed to evaluate the substrate and environmental controls on microbial assimilation of soil organic carbon using a new term: microbial annual active period (the length of microbes remaining active in one year). Substrate quality has a positive effect on microbial assimilation of soil organic carbon: higher substrate quality (lower C:N ratio) leads to higher ratio of microbial carbon to soil organic carbon and vice versa. Increases in microbial annual active period from zero stimulate microbial assimilation of soil organic carbon; however, when microbial annual active period is longer than an optimal threshold, increasing this period decreases microbial biomass. The simulated ratios of soil microbial biomass to soil organic carbon are reasonably consistent with a recently compiled global dataset at the biome-level. The modeling framework of microbial assimilation of soil organic carbon and its controls developed in this study offers an applicable ways to incorporate microbial contributions to the carbon cycling into Earth system models for simulating carbon-climate feedbacks and to explain global patterns of microbial biomass.« less

Comparative effect of a stannous fluoride toothpaste and a sodium fluoride toothpaste on a multispecies biofilm.

PubMed

Cheng, Xingqun; Liu, Jinman; Li, Jiyao; Zhou, Xuedong; Wang, Lijiang; Liu, Jiquan; Xu, Xin

2017-02-01

This paper aimed to compare the mode of action of a stannous fluoride-containing toothpaste with a conventional sodium fluoride-containing toothpaste on anti-biofilm properties. A three-species biofilm model that consists of Streptococcus mutans, Streptococcus sanguinis and Porphyromonas gingivalis was established to compare the anti-biofilm properties of a stannous fluoride-containing toothpaste (CPH), a conventional sodium fluoride-containing toothpaste (CCP) and a negative control (PBS). The 48h biofilms were subjected to two-minute episodes of treatment with test agents twice a day for 5 consecutive days. Crystal violet staining and XTT assays were used to evaluate the biomass and viability of the treated biofilm. Live/dead staining and bacteria/extracellular polysaccharides (EPS) double-staining were used to visualize the biofilm structure and to quantify microbial/extracellular components of the treated biofilms. Species-specific fluorescent in situ hybridization and quantitative polymerase chain reaction (qPCR) were used to analyze microbial composition of the biofilms after treatment. The biomass and viability of the biofilms were significantly reduced after CPH toothpaste treatment. The inhibitory effect was further confirmed by the live/dead staining. The EPS amounts of the three-species biofilm were significantly reduced by CCP and CPH treatments, and CPH toothpaste demonstrated significant inhibition on EPS production. More importantly, CPH toothpaste significantly suppressed S. mutans and P. gingvalis, and enriched S. sanguinis in the three-species biofilm. In all experiments CPH had a significantly greater effect than CCP (p<0.05) and CCP had a greater effect than PBS (p<0.05). Stannous fluoride-containing toothpaste not only showed better inhibitory effect against oral microbial biofilm, but was also able to modulate microbial composition within multi-species biofilm compared with conventional sodium fluoride-containing toothpaste. Copyright © 2016 Elsevier Ltd. All rights reserved.

Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

NASA Astrophysics Data System (ADS)

He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, Anthony D.; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

2015-12-01

Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil RH (7.5 ± 2.4 Pg C yr-1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4-0.6) in the simulated spatial pattern of soil RH with both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = -0.43 to -0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

USGS Publications Warehouse

He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, A. David; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

2015-01-01

Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil RH (7.5 ± 2.4 Pg C yr−1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4–0.6) in the simulated spatial pattern of soil RHwith both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = −0.43 to −0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Cliff S.; Martin, Melanie Ann; Dichosa, Armand E. K.

Background Premastication, the transfer of pre-chewed food, is a common infant and young child feeding practice among the Tsimane, forager-horticulturalists living in the Bolivian Amazon. Research conducted primarily with Western populations has shown that infants harbor distinct oral microbiota from their mothers. Premastication, which is less common in these populations, may influence the colonization and maturation of infant oral microbiota, including via transmission of oral pathogens. We collected premasticated food and saliva samples from Tsimane mothers and infants (9–24 months of age) to test for evidence of bacterial transmission in premasticated foods and overlap in maternal and infant salivary microbiota.more » We extracted bacterial DNA from two premasticated food samples and 12 matched salivary samples from maternal-infant pairs. DNA sequencing was performed with MiSeq (Illumina). We evaluated maternal and infant microbial composition in terms of relative abundance of specific taxa, alpha and beta diversity, and dissimilarity distances. Results The bacteria in saliva and premasticated food were mapped to 19 phyla and 400 genera and were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The oral microbial communities of Tsimane mothers and infants who frequently share premasticated food were well-separated in a non-metric multi-dimensional scaling ordination (NMDS) plot. Infant microbiotas clustered together, with weighted Unifrac distances significantly differing between mothers and infants. Infant saliva contained more Firmicutes ( p  < 0.01) and fewer Proteobacteria ( p  < 0.05) than did maternal saliva. Many genera previously associated with dental and periodontal infections, e.g.  Neisseria , Gemella , Rothia , Actinomyces , Fusobacterium , and Leptotrichia , were more abundant in mothers than in infants. Conclusions Salivary microbiota of Tsimane infants and young children up to two years of age do not appear closely related to those of their mothers, despite frequent premastication and preliminary evidence that maternal bacteria is transmitted to premasticated foods. Infant physiology and diet may constrain colonization by maternal bacteria, including several oral pathogens.« less

Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication

DOE PAGES

Han, Cliff S.; Martin, Melanie Ann; Dichosa, Armand E. K.; ...

2016-11-03

Background Premastication, the transfer of pre-chewed food, is a common infant and young child feeding practice among the Tsimane, forager-horticulturalists living in the Bolivian Amazon. Research conducted primarily with Western populations has shown that infants harbor distinct oral microbiota from their mothers. Premastication, which is less common in these populations, may influence the colonization and maturation of infant oral microbiota, including via transmission of oral pathogens. We collected premasticated food and saliva samples from Tsimane mothers and infants (9–24 months of age) to test for evidence of bacterial transmission in premasticated foods and overlap in maternal and infant salivary microbiota.more » We extracted bacterial DNA from two premasticated food samples and 12 matched salivary samples from maternal-infant pairs. DNA sequencing was performed with MiSeq (Illumina). We evaluated maternal and infant microbial composition in terms of relative abundance of specific taxa, alpha and beta diversity, and dissimilarity distances. Results The bacteria in saliva and premasticated food were mapped to 19 phyla and 400 genera and were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The oral microbial communities of Tsimane mothers and infants who frequently share premasticated food were well-separated in a non-metric multi-dimensional scaling ordination (NMDS) plot. Infant microbiotas clustered together, with weighted Unifrac distances significantly differing between mothers and infants. Infant saliva contained more Firmicutes ( p  < 0.01) and fewer Proteobacteria ( p  < 0.05) than did maternal saliva. Many genera previously associated with dental and periodontal infections, e.g.  Neisseria , Gemella , Rothia , Actinomyces , Fusobacterium , and Leptotrichia , were more abundant in mothers than in infants. Conclusions Salivary microbiota of Tsimane infants and young children up to two years of age do not appear closely related to those of their mothers, despite frequent premastication and preliminary evidence that maternal bacteria is transmitted to premasticated foods. Infant physiology and diet may constrain colonization by maternal bacteria, including several oral pathogens.« less

The salivary microbiome is altered in the presence of a high salivary glucose concentration

PubMed Central

Hartman, Mor-Li; Shi, Ping; Hasturk, Hatice; Yaskell, Tina; Vargas, Jorel; Song, Xiaoqing; Cugini, Maryann; Barake, Roula; Alsmadi, Osama; Al-Mutawa, Sabiha; Ariga, Jitendra; Soparkar, Pramod; Behbehani, Jawad; Behbehani, Kazem

2017-01-01

Background Type II diabetes (T2D) has been associated with changes in oral bacterial diversity and frequency. It is not known whether these changes are part of the etiology of T2D, or one of its effects. Methods We measured the glucose concentration, bacterial counts, and relative frequencies of 42 bacterial species in whole saliva samples from 8,173 Kuwaiti adolescents (mean age 10.00 ± 0.67 years) using DNA probe analysis. In addition, clinical data related to obesity, dental caries, and gingivitis were collected. Data were compared between adolescents with high salivary glucose (HSG; glucose concentration ≥ 1.0 mg/d, n = 175) and those with low salivary glucose (LSG, glucose concentration < 0.1 mg/dL n = 2,537). Results HSG was associated with dental caries and gingivitis in the study population. The overall salivary bacterial load in saliva decreased with increasing salivary glucose concentration. Under HSG conditions, the bacterial count for 35 (83%) of 42 species was significantly reduced, and relative bacterial frequencies in 27 species (64%) were altered, as compared with LSG conditions. These alterations were stronger predictors of high salivary glucose than measures of oral disease, obesity, sleep or fitness. Conclusions HSG was associated with a reduction in overall bacterial load and alterations to many relative bacterial frequencies in saliva when compared with LSG in samples from adolescents. We propose that hyperglycemia due to obesity and/or T2D results in HSG and subsequent acidification of the oral environment, leading to a generalized perturbation in the oral microbiome. This suggests a basis for the observation that hyperglycemia is associated with an increased risk of dental erosion, dental caries, and gingivitis. We conclude that HSG in adolescents may be predicted from salivary microbial diversity or frequency, and that the changes in the oral microbial composition seen in adolescents with developing metabolic disease may the consequence of hyperglycemia. PMID:28249034

A simple microbial fuel cell model for improvement of biomedical device powering times.

PubMed

Roxby, Daniel N; Tran, Nham; Nguyen, Hung T

2014-01-01

This study describes a Matlab based Microbial Fuel Cell (MFC) model for a suspended microbial population, in the anode chamber for the use of the MFC in powering biomedical devices. The model contains three main sections including microbial growth, microbial chemical uptake and secretion and electrochemical modeling. The microbial growth portion is based on a Continuously Stirred Tank Reactor (CSTR) model for the microbial growth with substrate and electron acceptors. Microbial stoichiometry is used to determine chemical concentrations and their rates of change and transfer within the MFC. These parameters are then used in the electrochemical modeling for calculating current, voltage and power. The model was tested for typically exhibited MFC characteristics including increased electrode distances and surface areas, overpotentials and operating temperatures. Implantable biomedical devices require long term powering which is the main objective for MFCs. Towards this end, our model was tested with different initial substrate and electron acceptor concentrations, revealing a four-fold increase in concentrations decreased the power output time by 50%. Additionally, the model also predicts that for a 35.7% decrease in specific growth rate, a 50% increase in power longevity is possible.

The oral microbiome in human immunodeficiency virus (HIV)-positive individuals.

PubMed

Kistler, James O; Arirachakaran, Pratanporn; Poovorawan, Yong; Dahlén, Gunnar; Wade, William G

2015-09-01

Human immunodeficiency virus (HIV) infection is associated with a range of oral conditions, and increased numbers of disease-associated microbial species have previously been found in HIV-positive subjects. The aim of this study was to use next-generation sequencing to compare the composition of the oral microbiome in HIV-positive and -negative individuals. Plaque and saliva were collected from 37 HIV-positive individuals and 37 HIV-negative individuals, and their bacterial composition determined by pyrosequencing of partial 16S rRNA genes. A total of 855,222 sequences were analysed. The number of species-level operational taxonomic units (OTUs) detected was significantly lower in the saliva of HIV-positive individuals (mean = 303.3) than in that of HIV-negative individuals (mean = 365.5) (P < 0.0003). Principal coordinates analysis (PCoA) based on community membership (Jaccard index) and structure (Yue and Clayton measure of dissimilarity) showed significant separation of plaque and saliva samples [analysis of molecular variance (AMOVA), P < 0.001]. PCoA plots did not show any clear separation based on HIV status. However, AMOVA indicated that there was a significant difference in the community membership of saliva between HIV-positive and -negative groups (P = 0.001). Linear discriminant analysis effect size revealed an OTU identified as Haemophilus parainfluenzae to be significantly associated with HIV-positive individuals, whilst Streptococcus mitis/HOT473 was most significantly associated with HIV-negative individuals. In conclusion, this study has confirmed that the microbial composition of saliva and plaque is different. The oral microbiomes of HIV-positive and -negative individuals were found to be similar overall, although there were minor but significant differences in the composition of the salivary microbiota of the two groups.

Oral microbiota species in acute apical endodontic abscesses

PubMed Central

George, Noelle; Flamiatos, Erin; Kawasaki, Kellie; Kim, Namgu; Carriere, Charles; Phan, Brian; Joseph, Raphael; Strauss, Shay; Kohli, Richie; Choi, Dongseok; Craig Baumgartner, J.; Sedgley, Christine; Maier, Tom; Machida, Curtis A.

2016-01-01

Background and objectives Acute apical abscesses are serious endodontic diseases resulting from pulpal infection with opportunistic oral microorganisms. The objective of this study was to identify and compare the oral microbiota in patients (N=18) exhibiting acute apical abscesses, originating from the demographic region in Portland, Oregon. The study hypothesis is that abscesses obtained from this demographic region may contain unique microorganisms not identified in specimens from other regions. Design Endodontic abscesses were sampled from patients at the Oregon Health & Science University (OHSU) School of Dentistry. DNA from abscess specimens was subjected to polymerase chain reaction amplification using 16S rRNA gene-specific primers and Cy3-dCTP labeling. Labeled DNA was then applied to microbial microarrays (280 species) generated by the Human Oral Microbial Identification Microarray Laboratory (Forsyth Institute, Cambridge, MA). Results The most prevalent microorganisms, found across multiple abscess specimens, include Fusobacterium nucleatum, Parvimonas micra, Megasphaera species clone CS025, Prevotella multisaccharivorax, Atopobium rimae, and Porphyromonas endodontalis. The most abundant microorganisms, found in highest numbers within individual abscesses, include F. nucleatum, P. micra, Streptococcus Cluster III, Solobacterium moorei, Streptococcus constellatus, and Porphyromonas endodontalis. Strong bacterial associations were identified between Prevotella multisaccharivorax, Acidaminococcaceae species clone DM071, Megasphaera species clone CS025, Actinomyces species clone EP053, and Streptococcus cristatus (all with Spearman coefficients >0.9). Conclusions Cultivable and uncultivable bacterial species have been identified in endodontic abscesses obtained from the Portland, Oregon demographic region, and taxa identifications correlated well with other published studies, with the exception of Treponema and Streptococcus cristae, which were not commonly identified in endodontic abscesses between the demographic region in Portland, Oregon and other regions. PMID:26983837

Effects of Hangeshashinto on Growth of Oral Microorganisms

PubMed Central

Fukamachi, Haruka; Matsumoto, Chinami; Omiya, Yuji; Arimoto, Takafumi; Kataoka, Hideo; Kadena, Miki; Funatsu, Takahiro; Fukutake, Masato; Kase, Yoshio; Kuwata, Hirotaka

2015-01-01

Oral mucositis (OM) in cancer patients induced by chemotherapy or radiotherapy has a significant impact on quality of life, and causes considerable morbidity. Oral microorganisms are likely to intensify the inflammatory process and aggravate the formation of ulcers. Hangeshashinto (HST), a Japanese kampo medicine, has been reported to be effective when used as a gargle for the treatment of OM. To clarify the effects of HST on oral microorganisms, we assessed its antimicrobial activity against 27 microbial species, including 19 oral bacteria and one fungus. HST extract inhibited the growth of Gram-negative bacteria, including Fusobacterium nucleatum, Porphyromonas gingivalis, Porphyromonas endodontalis, Prevotella intermedia, Prevotella melaninogenica, Tannerella forsythia, Treponema denticola, and Porphyromonas asaccharolytica, though inhibitory effects were less pronounced for Gram-positive bacteria and the fungal strain. We then investigated the effects of antibacterial activities on 15 purified ingredients of HST and determined that baicalein, berberine, coptisine, [6]-shogaol, and homogentisic acid actively inhibited the growth of these bacteria. These findings showed that HST inhibits the growth of specific Gram-negative periodontopathogenic bacteria, which are significant pathogens in OM, without disturbing the normal oral flora. Our data suggest that HST may be a useful treatment for OM in patients undergoing anticancer treatment. PMID:26170876

Microbial models with data-driven parameters predict stronger soil carbon responses to climate change.

PubMed

Hararuk, Oleksandra; Smith, Matthew J; Luo, Yiqi

2015-06-01

Long-term carbon (C) cycle feedbacks to climate depend on the future dynamics of soil organic carbon (SOC). Current models show low predictive accuracy at simulating contemporary SOC pools, which can be improved through parameter estimation. However, major uncertainty remains in global soil responses to climate change, particularly uncertainty in how the activity of soil microbial communities will respond. To date, the role of microbes in SOC dynamics has been implicitly described by decay rate constants in most conventional global carbon cycle models. Explicitly including microbial biomass dynamics into C cycle model formulations has shown potential to improve model predictive performance when assessed against global SOC databases. This study aimed to data-constrained parameters of two soil microbial models, evaluate the improvements in performance of those calibrated models in predicting contemporary carbon stocks, and compare the SOC responses to climate change and their uncertainties between microbial and conventional models. Microbial models with calibrated parameters explained 51% of variability in the observed total SOC, whereas a calibrated conventional model explained 41%. The microbial models, when forced with climate and soil carbon input predictions from the 5th Coupled Model Intercomparison Project (CMIP5), produced stronger soil C responses to 95 years of climate change than any of the 11 CMIP5 models. The calibrated microbial models predicted between 8% (2-pool model) and 11% (4-pool model) soil C losses compared with CMIP5 model projections which ranged from a 7% loss to a 22.6% gain. Lastly, we observed unrealistic oscillatory SOC dynamics in the 2-pool microbial model. The 4-pool model also produced oscillations, but they were less prominent and could be avoided, depending on the parameter values. © 2014 John Wiley & Sons Ltd.

From birth to ‘immuno-health’, allergies and enterocolitis

PubMed Central

Houghteling, Pearl D.; Walker, W. Allan

2015-01-01

Microbial signals stimulate development and maintenance of the neonatal immune system. The process begins in utero, with limited exposure to microbes in the intrauterine environment, as well as maternal immune signals priming the developing immune system. After birth and initial colonization, the immune system must be able to activate against pathogens, but also achieve oral tolerance of food and resident gut microbes. Through microbial signals and appropriate nutrition, the immune system is able to achieve homeostasis. Major challenges to successful colonization and immune system regulation include abnormal microbial inoculi (cesarean section, hygiene) and antibiotics. When normal colonization is interrupted, dysbiosis occurs. This imbalance of microbes and subsequently of the immune system can result in allergic diseases, asthma or necrotizing enterocolitis. Probiotics and probiotic-derived therapies represent an exciting avenue to replete the population of commensal microbes and to prevent the immune-mediated sequelae of dysbiosis. PMID:26447970

Identifying Low pH Active and Lactate-Utilizing Taxa within Oral Microbiome Communities from Healthy Children Using Stable Isotope Probing Techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLean, Jeffrey S.; Fansler, Sarah J.; Majors, Paul D.

Many human microbial infectious diseases including dental caries are polymicrobial in nature and how these complex multi-species communities evolve from a healthy to a diseased state is not well understood. Although many health- or disease-associated oral microbes have been characterized in vitro, their physiology in vivo in the presence of the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these oral species remain uncultivated to date and little is known except their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated microorganisms will remain enigmatic despite their apparent disease correlation.more » To start addressing these knowledge gaps, we applied a novel combination of in vivo Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for temporal monitoring of carbohydrate utilization, organic acid production and identification of metabolically active and inactive bacterial species.« less

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

PubMed Central

Adler, Christina J; Dobney, Keith; Weyrich, Laura S; Kaidonis, John; Walker, Alan W; Haak, Wolfgang; Bradshaw, Corey JA; Townsend, Grant; Sołtysiak, Arkadiusz; Alt, Kurt W; Parkhill, Julian; Cooper, Alan

2014-01-01

The importance of commensal microbes for human health is increasingly recognized1-5, yet the impacts of evolutionary changes in human diet and culture on commensal microbiota remain almost unknown. Two of the greatest dietary shifts in human evolution involved the adoption of carbohydrate-rich Neolithic (farming) diets6,7 (beginning ~10,000 years BP6,8), and the more recent advent of industrially processed flour and sugar (~1850)9. Here, we show that calcified dental plaque (dental calculus) on ancient teeth preserves a detailed genetic record throughout this period. Data from 34 early European skeletons indicate that the transition from hunter-gatherer to farming shifted the oral microbial community to a disease-associated configuration. The composition of oral microbiota remained surprisingly constant between Neolithic and Medieval times, after which (the now ubiquitous) cariogenic bacteria became dominant, apparently during the Industrial Revolution. Modern oral microbiota are markedly less diverse than historic populations, which might be contributing to chronic oral (and other) disease in post-industrial lifestyles. PMID:23416520

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

PubMed Central

Kim, Minsu; Or, Dani

2016-01-01

Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils. PMID:26807803

Genome-scale biological models for industrial microbial systems.

PubMed

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Cigarette smoking and the oral microbiome in a large study of American adults

PubMed Central

Wu, Jing; Peters, Brandilyn A; Dominianni, Christine; Zhang, Yilong; Pei, Zhiheng; Yang, Liying; Ma, Yingfei; Purdue, Mark P; Jacobs, Eric J; Gapstur, Susan M; Li, Huilin; Alekseyenko, Alexander V; Hayes, Richard B; Ahn, Jiyoung

2016-01-01

Oral microbiome dysbiosis is associated with oral disease and potentially with systemic diseases; however, the determinants of these microbial imbalances are largely unknown. In a study of 1204 US adults, we assessed the relationship of cigarette smoking with the oral microbiome. 16S rRNA gene sequencing was performed on DNA from oral wash samples, sequences were clustered into operational taxonomic units (OTUs) using QIIME and metagenomic content was inferred using PICRUSt. Overall oral microbiome composition differed between current and non-current (former and never) smokers (P<0.001). Current smokers had lower relative abundance of the phylum Proteobacteria (4.6%) compared with never smokers (11.7%) (false discovery rate q=5.2 × 10−7), with no difference between former and never smokers; the depletion of Proteobacteria in current smokers was also observed at class, genus and OTU levels. Taxa not belonging to Proteobacteria were also associated with smoking: the genera Capnocytophaga, Peptostreptococcus and Leptotrichia were depleted, while Atopobium and Streptococcus were enriched, in current compared with never smokers. Functional analysis from inferred metagenomes showed that bacterial genera depleted by smoking were related to carbohydrate and energy metabolism, and to xenobiotic metabolism. Our findings demonstrate that smoking alters the oral microbiome, potentially leading to shifts in functional pathways with implications for smoking-related diseases. PMID:27015003

Microbial Changes during Pregnancy, Birth, and Infancy

PubMed Central

Nuriel-Ohayon, Meital; Neuman, Hadar; Koren, Omry

2016-01-01

Several healthy developmental processes such as pregnancy, fetal development, and infant development include a multitude of physiological changes: weight gain, hormonal, and metabolic changes, as well as immune changes. In this review, we present an additional important factor which both influences and is affected by these physiological processes—the microbiome. We summarize the known changes in microbiota composition at a variety of body sites including gut, vagina, oral cavity, and placenta, throughout pregnancy, fetal development, and early childhood. There is still a lot to be discovered; yet several pieces of research point to the healthy desired microbial changes. Future research is likely to unravel precise roles and mechanisms of the microbiota in gestation; perhaps linking the metabolic, hormonal, and immune changes together. Although some research has started to link microbial dysbiosis and specific microbial populations with unhealthy pregnancy complications, it is important to first understand the context of the natural healthy microbial changes occurring. Until recently the placenta and developing fetus were considered to be germ free, containing no apparent microbiome. We present multiple study results showing distinct microbiota compositions in the placenta and meconium, alluding to early microbial colonization. These results may change dogmas and our overall understanding of the importance and roles of microbiota from the beginning of life. We further review the main factors shaping the infant microbiome—modes of delivery, feeding, weaning, and exposure to antibiotics. Taken together, we are starting to build a broader understanding of healthy vs. abnormal microbial alterations throughout major developmental time-points. PMID:27471494

Incorporating microbes into large-scale biogeochemical models

NASA Astrophysics Data System (ADS)

Allison, S. D.; Martiny, J. B.

2008-12-01

Micro-organisms, including Bacteria, Archaea, and Fungi, control major processes throughout the Earth system. Recent advances in microbial ecology and microbiology have revealed an astounding level of genetic and metabolic diversity in microbial communities. However, a framework for interpreting the meaning of this diversity has lagged behind the initial discoveries. Microbial communities have yet to be included explicitly in any major biogeochemical models in terrestrial ecosystems, and have only recently broken into ocean models. Although simplification of microbial communities is essential in complex systems, omission of community parameters may seriously compromise model predictions of biogeochemical processes. Two key questions arise from this tradeoff: 1) When and where must microbial community parameters be included in biogeochemical models? 2) If microbial communities are important, how should they be simplified, aggregated, and parameterized in models? To address these questions, we conducted a meta-analysis to determine if microbial communities are sensitive to four environmental disturbances that are associated with global change. In all cases, we found that community composition changed significantly following disturbance. However, the implications for ecosystem function were unclear in most of the published studies. Therefore, we developed a simple model framework to illustrate the situations in which microbial community changes would affect rates of biogeochemical processes. We found that these scenarios could be quite common, but powerful predictive models cannot be developed without much more information on the functions and disturbance responses of microbial taxa. Small-scale models that explicitly incorporate microbial communities also suggest that process rates strongly depend on microbial interactions and disturbance responses. The challenge is to scale up these models to make predictions at the ecosystem and global scales based on measurable parameters. We argue that meeting this challenge will require a coordinated effort to develop a series of nested models at scales ranging from the micron to the globe in order to optimize the tradeoff between model realism and feasibility.

Circadian oscillations of microbial and functional composition in the human salivary microbiome

PubMed Central

Takayasu, Lena; Suda, Wataru; Takanashi, Kageyasu; Iioka, Erica; Kurokawa, Rina; Shindo, Chie; Hattori, Yasue; Yamashita, Naoko; Nishijima, Suguru; Oshima, Kenshiro

2017-01-01

Abstract The human microbiomes across the body evidently interact with various signals in response to biogeographical physiological conditions. To understand such interactions in detail, we investigated how the salivary microbiome in the oral cavity would be regulated by host-related signals. Here, we show that the microbial abundance and gene participating in keeping the human salivary microbiome exhibit global circadian rhythm. Analysis of the 16S rRNA sequences of salivary microbial samples of six healthy adults collected at 4-h intervals for three days revealed that the microbial genera accounting for 68.4–89.6% of the total abundance were observed to significantly oscillate with the periodicity of ∼24 h. These oscillation patterns showed high variations amongst individuals, and the extent of circadian variations in individuals was generally lower than that of interindividual variations. Of the microbial categories oscillated, those classified by aerobic/anaerobic growth and Gram staining, Firmicutes including Streptococcus and Gemella, and Bacteroidetes including Prevotella showed high association with the circadian oscillation. The circadian oscillation was completely abolished by incubating the saliva in vitro, suggesting that host’s physiological changes mostly contributed to the microbial oscillation. Further metagenomic analysis showed that circadian oscillation enriched the functions of environmental responses such as various transporters and two-component regulatory systems in the evening, and those of metabolisms such as the biosynthesis of vitamins and fatty acids in the morning. PMID:28338745

Host-Microbiome Cross-talk in Oral Mucositis

PubMed Central

Vasconcelos, R.M.; Sanfilippo, N.; Paster, B.J.; Kerr, A.R.; Li, Y.; Ramalho, L.; Queiroz, E.L.; Smith, B.; Sonis, S.T.; Corby, P.M.

2016-01-01

Oral mucositis (OM) is among the most common, painful, and debilitating toxicities of cancer regimen–related treatment, resulting in the formation of ulcers, which are susceptible to increased colonization of microorganisms. Novel discoveries in OM have focused on understanding the host-microbial interactions, because current pathways have shown that major virulence factors from microorganisms have the potential to contribute to the development of OM and may even prolong the existence of already established ulcerations, affecting tissue healing. Additional comprehensive and disciplined clinical investigation is needed to carefully characterize the relationship between the clinical trajectory of OM, the local levels of inflammatory changes (both clinical and molecular), and the ebb and flow of the oral microbiota. Answering such questions will increase our knowledge of the mechanisms engaged by the oral immune system in response to mucositis, facilitating their translation into novel therapeutic approaches. In doing so, directed clinical strategies can be developed that specifically target those times and tissues that are most susceptible to intervention. PMID:27053118

Green tea: a novel functional food for the oral health of older adults.

PubMed

Gaur, Sumit; Agnihotri, Rupali

2014-04-01

Functional foods are foods with positive health effects that extend beyond their nutritional value. They affect the function of the body and help in the management of specific health conditions. Green tea, a time-honoured Chinese herb, might be regarded as a functional food because of its inherent anti-oxidant, anti-inflammatory, antimicrobial and antimutagenic properties. They are attributed to its reservoir of polyphenols, particularly the catechin, epigallocatechin-3-gallate. Owing to these beneficial actions, this traditional beverage was used in the management of chronic systemic diseases including cancer. Recently, it has been emphasized that the host immuno-inflammatory reactions destroy the oral tissues to a greater extent than the microbial activity alone. Green tea with its wide spectrum of activities could be a healthy alternative for controlling these damaging reactions seen in oral diseases, specifically, chronic periodontitis, dental caries and oral cancer, which are a common occurrence in the elderly population. © 2013 Japan Geriatrics Society.

Betel nut chewing, oral premalignant lesions, and the oral microbiome

PubMed Central

Hernandez, Brenda Y.; Zhu, Xuemei; Goodman, Marc T.; Gatewood, Robert; Mendiola, Paul; Quinata, Katrina; Paulino, Yvette C.

2017-01-01

Oral cancers are attributed to a number of causal agents including tobacco, alcohol, human papillomavirus (HPV), and areca (betel) nut. Although betel nut chewing has been established as an independent cause of oral cancer, the mechanisms of carcinogenesis are poorly understood. An investigation was undertaken to evaluate the influence of betel nut chewing on the oral microbiome and oral premalignant lesions. Study participants were recruited from a dental clinic in Guam. Structured interviews and oral examinations were performed. Oral swabbing and saliva samples were evaluated by 454 pyrosequencing of the V3- V5 region of the 16S rRNA bacterial gene and genotyped for HPV. One hundred twenty-two adults were enrolled including 64 current betel nut chewers, 37 former chewers, and 21 with no history of betel nut use. Oral premalignant lesions, including leukoplakia and submucous fibrosis, were observed in 10 chewers. Within-sample bacterial diversity was significantly lower in long-term (≥10 years) chewers vs. never chewers and in current chewers with oral lesions vs. individuals without lesions. Between-sample bacterial diversity based on Unifrac distances significantly differed by chewing status and oral lesion status. Current chewers had significantly elevated levels of Streptococcus infantis and higher and lower levels of distinct taxa of the Actinomyces and Streptococcus genera. Long-term chewers had reduced levels of Parascardovia and Streptococcus. Chewers with oral lesions had significantly elevated levels of Oribacterium, Actinomyces, and Streptococcus, including Streptococcus anginosus. In multivariate analyses, controlling for smoking, oral HPV, S.anginosus, and S. infantis levels, current betel nut chewing remained the only predictor of oral premalignant lesions. Our study provides evidence that betel nut chewing alters the oral bacterial microbiome including that of chewers who develop oral premalignant lesions. Nonetheless, whether microbial changes are involved in betel nut-induced oral carcinogenesis is only speculative. Further research is needed to discern the clinical significance of an altered oral microbiome and the mechanisms of oral cancer development in betel nut chewers. PMID:28225785

Betel nut chewing, oral premalignant lesions, and the oral microbiome.

PubMed

Hernandez, Brenda Y; Zhu, Xuemei; Goodman, Marc T; Gatewood, Robert; Mendiola, Paul; Quinata, Katrina; Paulino, Yvette C

2017-01-01

Oral cancers are attributed to a number of causal agents including tobacco, alcohol, human papillomavirus (HPV), and areca (betel) nut. Although betel nut chewing has been established as an independent cause of oral cancer, the mechanisms of carcinogenesis are poorly understood. An investigation was undertaken to evaluate the influence of betel nut chewing on the oral microbiome and oral premalignant lesions. Study participants were recruited from a dental clinic in Guam. Structured interviews and oral examinations were performed. Oral swabbing and saliva samples were evaluated by 454 pyrosequencing of the V3- V5 region of the 16S rRNA bacterial gene and genotyped for HPV. One hundred twenty-two adults were enrolled including 64 current betel nut chewers, 37 former chewers, and 21 with no history of betel nut use. Oral premalignant lesions, including leukoplakia and submucous fibrosis, were observed in 10 chewers. Within-sample bacterial diversity was significantly lower in long-term (≥10 years) chewers vs. never chewers and in current chewers with oral lesions vs. individuals without lesions. Between-sample bacterial diversity based on Unifrac distances significantly differed by chewing status and oral lesion status. Current chewers had significantly elevated levels of Streptococcus infantis and higher and lower levels of distinct taxa of the Actinomyces and Streptococcus genera. Long-term chewers had reduced levels of Parascardovia and Streptococcus. Chewers with oral lesions had significantly elevated levels of Oribacterium, Actinomyces, and Streptococcus, including Streptococcus anginosus. In multivariate analyses, controlling for smoking, oral HPV, S.anginosus, and S. infantis levels, current betel nut chewing remained the only predictor of oral premalignant lesions. Our study provides evidence that betel nut chewing alters the oral bacterial microbiome including that of chewers who develop oral premalignant lesions. Nonetheless, whether microbial changes are involved in betel nut-induced oral carcinogenesis is only speculative. Further research is needed to discern the clinical significance of an altered oral microbiome and the mechanisms of oral cancer development in betel nut chewers.

Relationship between Oral Malodor and the Global Composition of Indigenous Bacterial Populations in Saliva ▿

PubMed Central

Takeshita, Toru; Suzuki, Nao; Nakano, Yoshio; Shimazaki, Yoshihiro; Yoneda, Masahiro; Hirofuji, Takao; Yamashita, Yoshihisa

2010-01-01

Oral malodor develops mostly from the metabolic activities of indigenous bacterial populations within the oral cavity, but whether healthy or oral malodor-related patterns of the global bacterial composition exist remains unclear. In this study, the bacterial compositions in the saliva of 240 subjects complaining of oral malodor were divided into groups based on terminal-restriction fragment length polymorphism (T-RFLP) profiles using hierarchical cluster analysis, and the patterns of the microbial community composition of those exhibiting higher and lower malodor were explored. Four types of bacterial community compositions were detected (clusters I, II, III, and IV). Two parameters for measuring oral malodor intensity (the concentration of volatile sulfur compounds in mouth air and the organoleptic score) were noticeably lower in cluster I than in the other clusters. Using multivariate analysis, the differences in the levels of oral malodor were significant after adjustment for potential confounding factors such as total bacterial count, mean periodontal pocket depth, and tongue coating score (P < 0.001). Among the four clusters with different proportions of indigenous members, the T-RFLP profiles of cluster I were implicated as the bacterial populations with higher proportions of Streptococcus, Granulicatella, Rothia, and Treponema species than those of the other clusters. These results clearly correlate the global composition of indigenous bacterial populations with the severity of oral malodor. PMID:20228112

Optimal Antibiotic Dosage for Chronic Kidney Disease Patient: A Pharmacological Manual for Oral Clinicians.

PubMed

Chidambaram, Ramasamy

2015-01-01

Chronic kidney disease, (CKD) a gradual and inevitable deterioration in renal function, is the disease with the most associations in dentistry. Dosage adjustment is one amongst the vital elements to be familiar with during their oral care. CKD patients take extended duration to filter out medications, therefore dosage must always be tailored under the supervision of nephrologist. The relished benefits from antibiotic could transform as anti-microbial resistance on their abuse and nephrotoxic when contraindicated drugs are encouraged. New patented drug belonging to oxazoliodine group has driven the researchers to handle the emerging AMR. The present communication discusses the pharmacological factors influencing in prescribing the antibiotics for CKD patient from the dentist's point of view. The formulas destined for calculating the optimal dosage of antibiotics have been documented to aid oral physicians.

Introduction to Clinical Microbiology for the General Dentist.

PubMed

Rams, Thomas E; van Winkelhoff, Arie J

2017-04-01

Clinical oral microbiology may help dental professionals identify infecting pathogenic species and evaluate their in vitro antimicrobial susceptibility. Saliva, dental plaque biofilms, mucosal smears, abscess aspirates, and soft tissue biopsies are sources of microorganisms for laboratory testing. Microbial-based treatment end points may help clinicians better identify patients in need of additional or altered dental therapies before the onset of clinical treatment failure, and help improve patient oral health outcomes. Microbiological testing appears particularly helpful in periodontal disease treatment planning. Further research and technological advances are likely to increase the availability and clinical utility of microbiological analysis in modern dental practice. Copyright © 2016 Elsevier Inc. All rights reserved.

Concepts and tools for predictive modeling of microbial dynamics.

PubMed

Bernaerts, Kristel; Dens, Els; Vereecken, Karen; Geeraerd, Annemie H; Standaert, Arnout R; Devlieghere, Frank; Debevere, Johan; Van Impe, Jan F

2004-09-01

Description of microbial cell (population) behavior as influenced by dynamically changing environmental conditions intrinsically needs dynamic mathematical models. In the past, major effort has been put into the modeling of microbial growth and inactivation within a constant environment (static models). In the early 1990s, differential equation models (dynamic models) were introduced in the field of predictive microbiology. Here, we present a general dynamic model-building concept describing microbial evolution under dynamic conditions. Starting from an elementary model building block, the model structure can be gradually complexified to incorporate increasing numbers of influencing factors. Based on two case studies, the fundamentals of both macroscopic (population) and microscopic (individual) modeling approaches are revisited. These illustrations deal with the modeling of (i) microbial lag under variable temperature conditions and (ii) interspecies microbial interactions mediated by lactic acid production (product inhibition). Current and future research trends should address the need for (i) more specific measurements at the cell and/or population level, (ii) measurements under dynamic conditions, and (iii) more comprehensive (mechanistically inspired) model structures. In the context of quantitative microbial risk assessment, complexity of the mathematical model must be kept under control. An important challenge for the future is determination of a satisfactory trade-off between predictive power and manageability of predictive microbiology models.

Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Yujie; Yang, Jinyan; Zhuang, Qianlai

Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here in this study we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbialmore » dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO 2 efflux (R H) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil R H (7.5 ± 2.4 PgCyr -1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4-0.6) in the simulated spatial pattern of soil R H with both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = -0.43 to -0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.« less

Density-dependent microbial turnover improves soil carbon model predictions of long-term litter manipulations

NASA Astrophysics Data System (ADS)

Georgiou, Katerina; Abramoff, Rose; Harte, John; Riley, William; Torn, Margaret

2017-04-01

Climatic, atmospheric, and land-use changes all have the potential to alter soil microbial activity via abiotic effects on soil or mediated by changes in plant inputs. Recently, many promising microbial models of soil organic carbon (SOC) decomposition have been proposed to advance understanding and prediction of climate and carbon (C) feedbacks. Most of these models, however, exhibit unrealistic oscillatory behavior and SOC insensitivity to long-term changes in C inputs. Here we diagnose the sources of instability in four models that span the range of complexity of these recent microbial models, by sequentially adding complexity to a simple model to include microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We propose a formulation that introduces density-dependence of microbial turnover, which acts to limit population sizes and reduce oscillations. We compare these models to results from 24 long-term C-input field manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that widely used first-order models and microbial models without density-dependence cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures. The proposed formulation improves predictions of long-term C-input changes, and implies greater SOC storage associated with CO2-fertilization-driven increases in C inputs over the coming century compared to common microbial models. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in Earth System Models.

Inhibition of Streptococcus mutans biofilm formation, extracellular polysaccharide production, and virulence by an oxazole derivative.

PubMed

Chen, Lulu; Ren, Zhi; Zhou, Xuedong; Zeng, Jumei; Zou, Jing; Li, Yuqing

2016-01-01

Dental caries, a biofilm-related oral disease, is a result of disruption of the microbial ecological balance in the oral environment. Streptococcus mutans, which is one of the primary cariogenic bacteria, produces glucosyltransferases (Gtfs) that synthesize extracellular polysaccharides (EPSs). The EPSs, especially water-insoluble glucans, contribute to the formation of dental plaque, biofilm stability, and structural integrity, by allowing bacteria to adhere to tooth surfaces and supplying the bacteria with protection against noxious stimuli and other environmental attacks. The identification of novel alternatives that selectively inhibit cariogenic organisms without suppressing oral microbial residents is required. The goal of the current study is to investigate the influence of an oxazole derivative on S. mutans biofilm formation and the development of dental caries in rats, given that oxazole and its derivatives often exhibit extensive and pharmacologically important biological activities. Our data shows that one particular oxazole derivative, named 5H6, inhibited the formation of S. mutans biofilms and prevented synthesis of extracellular polysaccharides by antagonizing Gtfs in vitro, without affecting the growth of the bacteria. In addition, topical applications with the inhibitor resulted in diminished incidence and severity of both smooth and sulcal surface caries in vivo with a lower percentage of S. mutans in the animals' dental plaque compared to the control group (P < 0.05). Our results showed that this oxazole derivative has the capacity to inhibit biofilm formation and cariogenicity of S. mutans.

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

PubMed Central

Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

2016-01-01

We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can be used to analyze complex “omics” data and to infer and optimize metabolic processes. Thereby, SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, microalgae blooms methanogenic fermentation, and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations. PMID:27242701

Salivary microbial profiles in relation to age, periodontal, and systemic diseases

PubMed Central

Lira-Junior, Ronaldo; Åkerman, Sigvard; Klinge, Björn

2018-01-01

Background Analysis of saliva is emerging as a promising tool to diagnose and monitor diseases which makes determination of the salivary microbial profile in different scenarios essential. Objective To evaluate the effects of age, periodontal disease, sex, smoking, and medical conditions on the salivary microbial profile. Design A randomly selected sample of 441 individuals was enrolled (51% women; mean age 48.5±16.8). Participants answered a health questionnaire and underwent an oral examination. Stimulated saliva was collected and the counts of 41 bacteria were determined by checkerboard DNA-DNA hybridization. Results Elderly participants (> 64 years old) presented a significant increase in 24 out of 41 bacterial species compared to adults (≤ 64 years old). Eubacterium nodatum, Porphyromonas gingivalis, and Tannerella forsythia were significantly higher in participants with generalized bone loss compared to without. Males and non-smokers had higher bacteria counts in saliva. Individuals having mental disorders or muscle and joint diseases showed significantly altered microbial profiles whereas small or no differences were found for subjects with high blood pressure, heart disease, previous heart surgery, bowel disease, tumors, or diabetes. Conclusion Age, periodontal status, sex, smoking, and certain medical conditions namely, mental disorders and muscle and joint diseases, might affect the microbial profile in saliva. PMID:29538390

Microbial cross-contamination by airborne dispersion and contagion during defeathering of poultry.

PubMed

Allen, V M; Hinton, M H; Tinker, D B; Gibson, C; Mead, G C; Wathes, C M

2003-09-01

1. A readily identifiable strain of Escherichia coli K12 was used as a 'marker' organism to determine the sources, routes and patterns of microbial cross-contamination during mechanical defeathering of broiler chicken carcases. 2. Inoculation of scald water with the marker organism led to a relatively even pattern of carcase contamination during subsequent defeathering. Microbial cross-contamination was greater by this route of inoculation than by either surface inoculation of a 'seeder' carcase or oral inoculation of a live bird one day before slaughter. 3. Dispersal of the marker organism was strongly influenced by the mechanical action of the defeathering machines. Forward transmission of the marker occurred by aerosol or large airborne droplets and particulates such as feathers. Moving carcases through the defeathering machines when these were non-operational clearly reduced backward transmission of the marker. 4. Although microbial dispersal was unaffected by increasing the spacing between individual carcases or installing a water curtain at the entry and exit of the defeathering machines, shielding of carcases with aluminium baffles reduced counts of the marker organism from contaminated carcases by > 90%. 5. The results imply that microbial cross-contamination of broiler chicken carcases during defeathering occurs mainly via the airborne route, which could be contained by physical means.

Measures of Microbial Biomass for Soil Carbon Decomposition Models

NASA Astrophysics Data System (ADS)

Mayes, M. A.; Dabbs, J.; Steinweg, J. M.; Schadt, C. W.; Kluber, L. A.; Wang, G.; Jagadamma, S.

2014-12-01

Explicit parameterization of the decomposition of plant inputs and soil organic matter by microbes is becoming more widely accepted in models of various complexity, ranging from detailed process models to global-scale earth system models. While there are multiple ways to measure microbial biomass, chloroform fumigation-extraction (CFE) is commonly used to parameterize models.. However CFE is labor- and time-intensive, requires toxic chemicals, and it provides no specific information about the composition or function of the microbial community. We investigated correlations between measures of: CFE; DNA extraction yield; QPCR base-gene copy numbers for Bacteria, Fungi and Archaea; phospholipid fatty acid analysis; and direct cell counts to determine the potential for use as proxies for microbial biomass. As our ultimate goal is to develop a reliable, more informative, and faster methods to predict microbial biomass for use in models, we also examined basic soil physiochemical characteristics including texture, organic matter content, pH, etc. to identify multi-factor predictive correlations with one or more measures of the microbial community. Our work will have application to both microbial ecology studies and the next generation of process and earth system models.

[The influence of alcohol on the oral cavity, salivary glands and saliva].

PubMed

Waszkiewicz, Napoleon; Zalewska, Anna; Szulc, Agata; Kepka, Alina; Konarzewska, Beata; Zalewska-Szajda, Beata; Chojnowska, Sylwia; Waszkiel, Danuta; Zwierz, Krzysztof

2011-01-01

Ethanol diffuses rapidly into saliva during the drinking, and immediately after its salivary concentration is temporarily much higher than in plasma. Within 30 minutes, salivary ethanol concentration equilibrates with the plasma level, thus suggesting that ethanol easily penetrates the whole body, including oral cavity tissues and salivary glands. After alcohol intake, the level of acetaldehyde in saliva strikingly exceeds the level in systemic blood. From saliva, acetaldehyde and ethanol easily reach all local tissues. Damage to the oral tissues seems to be ascribed mostly to the action of acetaldehyde, although some acute effects depend on a direct action of ethanol and formation of reactive oxygen species (ROS) and fatty acid ethyl esters (FAEEs). It is known that the oral mucosal surface is the home of numerous normal flora microorganisms and is the portal of entry for the majority of pathogens. The oral cavity and salivary antimicrobial immune defense systems eliminate pathogens and prevent massive overgrowth of microorganisms. An oral defense system participate in the protection of not only oral tissues, but also in the protection of upper digestive and respiratory tracts, against a number of microbial pathogens. Saliva plays the role in the oral cavity lubrication, maintenance of mucosal and tooth integrity, esophageal physiology, digestion and gastric cytoprotection. As alcohol abuse affects the structure and function of oral cavity mucosa, salivary glands and saliva, the maintenance of oral and general health under normal conditions is seriously impaired during the drinking. The severe tissue damage occurs in particular when alcohol abuse coincides with smoking.

Licochalcone A induces apoptosis in KB human oral cancer cells via a caspase-dependent FasL signaling pathway

PubMed Central

KIM, JAE-SUNG; PARK, MI-RA; LEE, SOOK-YOUNG; KIM, DO KYOUNG; MOON, SUNG-MIN; KIM, CHUN SUNG; CHO, SEUNG SIK; YOON, GOO; IM, HEE-JEONG; YOU, JAE-SEEK; OH, JI-SU; KIM, SU-GWAN

2014-01-01

Licochalcone A (Lico-A) is a natural phenol licorice compound with multiple bioactivities, including anti-inflammatory, anti-microbial, anti-fungal and osteogenesis-inducing properties. In the present study, we investigated the Lico-A-induced apoptotic effects and examined the associated apoptosis pathway in KB human oral cancer cells. Lico-A decreased the number of viable KB oral cancer cells. However, Lico-A did not have an effect on primary normal human oral keratinocytes. In addition, the IC50 value of Lico-A was determined to be ~50 μM following dose-dependent stimulation. KB oral cancer cells stimulated with Lico-A for 24 h showed chromatin condensation by DAPI staining, genomic DNA fragmentation by agarose gel electrophoresis and a gradually increased apoptotic cell population by FACS analysis. These data suggest that Lico-A induces apoptosis in KB oral cancer cells. Additionally, Lico-A-induced apoptosis in KB oral cancer cells was mediated by the expression of factor associated suicide ligand (FasL) and activated caspase-8 and −3 and poly(ADP-ribose) polymerase (PARP). Furthermore, in the KB oral cancer cells co-stimulation with a caspase inhibitor (Z-VAD-fmk) and Lico-A significantly abolished the apoptotic phenomena. Our findings demonstrated that Lico-A-induced apoptosis in KB oral cancer cells involves the extrinsic apoptotic signaling pathway, which involves a caspase-dependent FasL-mediated death receptor pathway. Our data suggest that Lico-A be developed as a chemotherapeutic agent for the management of oral cancer. PMID:24337492

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.

PubMed

Cardona, Cesar; Lax, Simon; Larsen, Peter; Stephens, Brent; Hampton-Marcell, Jarrad; Edwardson, Christian F; Henry, Chris; Van Bonn, Bill; Gilbert, Jack A

2018-01-01

Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and respiratory tract-associated microbiota in four aquarium-housed dolphins daily over a period of 6 weeks, including administration of a probiotic during weeks 4 to 6. The environmental bacterial sources were also characterized, including the animals' human handlers, the aquarium air and water, and the dolphins' food supply. Continuous microbial exposure occurred between all sites, yet each environment maintained a characteristic microbiota, suggesting that the majority of exposure events do not result in colonization. Small changes in water physicochemistry had a significant but weak correlation with change in dolphin-associated bacterial richness but had no influence on phylogenetic diversity. Food and air microbiota were the richest and had the largest conditional influence on other microbiota in the absence of probiotics, but during probiotic administration, food alone had the largest influence on the stability of the dolphin microbiota. Our results suggest that respiratory tract and gastrointestinal epithelium interactions with air- and food-associated microbes had the biggest influence on host-microbiota dynamics, while other interactions, such as skin transmission, played only a minor role. Finally, direct oral stimulation with a foreign exogenous microbial source can have a profound effect on microbial stability. IMPORTANCE These results provide valuable insights into the ecological influence of exogenous microbial exposure, as well as laying the foundation for improving aquarium management practices. By comparing data for dolphins from aquaria that use natural versus artificial seawater, we demonstrate the potential influence of aquarium water disinfection procedures on dolphin microbial dynamics.

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

PubMed Central

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J.; Waghorn, Garry C.; Janssen, Peter H.

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided. PMID:24040342

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

PubMed

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J; Waghorn, Garry C; Janssen, Peter H

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

DOE PAGES

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; ...

2017-09-28

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

NASA Astrophysics Data System (ADS)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; Zhou, Xiaolu; Wang, Meng; Zhang, Kerou; Wang, Gangsheng

2017-10-01

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195 Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated by Xu et al. (2014). We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC), and mineral-associated organic carbon (MOC). However, our work represents the first step toward a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Identification of Microbial Pathogens in Periodontal disease and Diabetic patients of South Indian Population

PubMed Central

Chiranjeevi, Tikka; Prasad, Osuru Hari; Prasad, Uppu Venkateswara; Kumar, Avula Kishor; Chakravarthi, Veeraraghavulu Praveen; Rao, Paramala Balaji; Sarma, Potuguchi Venkata Gurunadha Krishna; Reddy, Nagi reddy Raveendra; Bhaskar, Matcha

2014-01-01

Periodontitis have been referred to as the sixth complication of diabetes found in high prevalence among diabetic patients than among healthy controls. The aim of the present study was to examine the periodontal disease status among collected dental plaque samples. Chromosomal DNA was isolated and amplified by universal primers. The DNA was sequenced for bacterial confirmation and phylogenetic analysis performed for the evolutionary relationship with other known pathogens. No amplification products were observed in groups labeled non periodontal and non Diabetes (NP&ND) and non Periodontal and Diabetes (NP&D). But in the case of Periodontal and non Diabetes (P&ND) groups 22 amplified products were observed. In case of Periodontal and Diabetes (P&D), 32 amplified products were positive for microbes. Among the four microbial groups, Treponemadenticola, and Tannerella forsythia were found to be prevalent in P&D. The phylogenetic analysis of 16s rRNA of Treponemadenticola showed the relationship with other Treponema oral pathogen species and with the Spirochaetazuelaera. Tannerella forsythia shows its evolutionary relationship only with four oral pathogens (Macellibacteroidesfermentans, Porphyromadaceae bacterium, Parabacteroidesmeredae and Bacillus fosythus). Prevotellaintermedia also showed its evolutionary relationship only with Prevotella Spcs while Fusobacterium revealed close evolutionary relationship only with Porpiromonasgingivalis. PMID:24966528

Role of Vancomycin as a Component of Oral Nonabsorbable Antibiotics for Microbial Suppression in Leukemic Patients

PubMed Central

Bender, John F.; Schimpff, Stephen C.; Young, Viola Mae; Fortner, Clarence L.; Brouillet, Mary D.; Love, Lillian J.; Wiernik, Peter H.

1979-01-01

A total of 38 adult patients with acute leukemia who were undergoing remission induction chemotherapy in regular patient rooms were randomly allocated to one of two oral nonabsorbable antibiotic regimens for infection prophylaxis (gentamicin, vancomycin, and nystatin [GVN] or gentamicin and nystatin [GN]) to evaluate whether vancomycin was a necessary component. The patient population in both groups were comparable. Tolerance to GVN was less than GN but compliance was approximately equal (>85% in both groups). Patients receiving vancomycin demonstrated greater overall alimentary tract microbial suppression; however, acquisition of potential pathogens was approximately equal in both groups. The incidence of bacteremia, as well as the overall incidence of infection as related to the number of days at various granulocyte levels, was also approximately equal in both groups. Group D Streptococcus species were poorly suppressed by GN compared with GVN, although no patient developed an infection with these organisms. Colonization by newly acquired gram-negative bacilli was significantly less in the GN group (GN, 3 colonizations; GVN, 13 colonizations; P < 0.01). It is concluded that vancomycin may be safely eliminated from the GVN regimen provided microbiological data is monitored to detect resistant organisms. PMID:464573

A Theoretical Reassessment of Microbial Maintenance and Implications for Microbial Ecology Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Gangsheng; Post, Wilfred M

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a critical reassessment. We provided a rigorous proof that the true growth yield coefficient (YG) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert ( max,H) is higher than those in the other twomore » models ( max,P and max,C), and the difference is the physiological maintenance factor (mq = a); and (3) the overall maintenance coefficient (mT) is more sensitive to mq than to the specific growth rate ( G) and YG. Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.« less

Modeling the Response of Soil Organic Matter Decomposition to Warming: Effects of Dynamical Enzyme Productivity and Nuanced Representation of Respiration.

NASA Astrophysics Data System (ADS)

Sihi, D.; Gerber, S.; Inglett, K. S.; Inglett, P.

2014-12-01

Recent development in modeling soil organic carbon (SOC) decomposition includes the explicit incorporation of enzyme and microbial dynamics. A characteristic of these models is a feedback between substrate and consumers which is absent in traditional first order decay models. Second, microbial decomposition models incorporate carbon use efficiency (CUE) as a function of temperature which proved to be critical to prediction of SOC with warming. Our main goal is to explore microbial decomposition models with respect to responses of microbes to enzyme activity, costs to enzyme production, and to incorporation of growth vs. maintenance respiration. In order to simplify the modeling setup we assumed quick adjustment of enzyme activity and depolymerized carbon to microbial and SOC pools. Enzyme activity plays an important role to decomposition if its production is scaled to microbial biomass. In fact if microbes are allowed to optimize enzyme productivity the microbial enzyme model becomes unstable. Thus if the assumption of enzyme productivity is relaxed, other limiting factors must come into play. To stabilize the model, we account for two feedbacks that include cost of enzyme production and diminishing return of depolymerization with increasing enzyme concentration and activity. These feedback mechanisms caused the model to behave in a similar way to traditional, first order decay models. Most importantly, we found, that under warming, the changes in SOC carbon were more severe in enzyme synthesis is costly. In turn, carbon use efficiency (CUE) and its dynamical response to temperature is mainly determined by 1) the rate of turnover of microbes 2) the partitioning of dead microbial matter into different quality pools, and 3) and whether growth, maintenance respiration and microbial death rate have distinct responses to changes in temperature. Abbreviations: p: decay of enzyme, g: coefficient for growth respiration, : fraction of material from microbial turnover that enters the DOC pool, loss of C scaled to microbial mass, half saturation constant.

Resistance of chemokine receptor 6-deficient mice to Yersinia enterocolitica infection: evidence of defective M-cell formation in vivo.

PubMed

Westphal, Sabine; Lügering, Andreas; von Wedel, Julia; von Eiff, Christof; Maaser, Christian; Spahn, Thomas; Heusipp, Gerhard; Schmidt, M Alexander; Herbst, Hermann; Williams, Ifor R; Domschke, Wolfram; Kucharzik, Torsten

2008-03-01

M cells, specialized cells within Peyer's patches (PPs), are reduced in number in chemokine receptor 6 (CCR6)-deficient mice. The pathogenic microorganism Yersinia enterocolitica exploits M cells for the purpose of mucosal tissue invasion exclusively through PPs. The aim of this study was to evaluate the course of yersiniosis in CCR6-deficient mice and to investigate whether these mice might be used as an in vivo model to determine M-cell function. After oral challenge with Y. enterocolitica, control mice suffered from lethal septic infection whereas CCR6-deficient mice showed very limited symptoms of infection. Immunohistochemical analysis demonstrated PP invasion by Y. enterocolitica in control mice whereas no bacteria could be found in CCR6-deficient mice. In addition, a significant induction of proinflammatory cytokines could be found in control mice whereas proinflammatory cytokine levels in CCR6-deficient mice remained unchanged. In contrast, intraperitoneal infection resulted in severe systemic yersiniosis in both mouse groups. Abrogated oral Y. enterocolitica infection in CCR6-deficient mice demonstrates the importance of CCR6 expression in the physiological and pathological immune responses generated within PPs by influencing M-cell differentiation, underscoring the important role of M cells in the process of microbial uptake. CCR6-deficient mice may therefore represent a suitable model for the study of M-cell function in vivo.

Effects of frequent oral hygiene instructions on microbial levels and salivary buffer capacity in orthodontic patients and their parents.

PubMed

Katz-Sagi, Hadas; Redlich, Meir; Shapira, Joseph; Peretz, Benjamin; Steinberg, Doron

2008-01-01

To assess whether parental involvement can improve children's oral health as a strategiy to reduce caries risk in children undergoing orthodontic treatment. The study population consisted of 40 healthy children aged 7 to 15 years (mean 10.93 ± 2.78) and their accompanying parents (mother or father). Oral hygiene instructions were given simultaneously to all children and accompanying parents every 6 weeks at their regular orthodontic appointments. Levels of Streptococcus mutans and salivary buffer capacity were assessed for both children and parents before and 9 months into orthodontic treatment. The majority of children (74%) and parents (92%) expressed unchanged levels of Streptococcus mutans and stable salivary buffer capacity throughout the study. When analyzing child-parent pairs with respect to Streptococcus mutans and salivary buffer capacity, no significant differences were found prior to treatment. Nine months into treatment, 57% of the children and parents still showed similar Streptococcus mutans counts and buffer capacity. The child-parent approach succeeded in preventing deterioration of children's oral hygiene. Parental involvement has an essential part in maintaining children's oral health. Oral health care professionals should partner with parents when implementing any kind of health behavior. COPYRIGHT © 2008 BY QUINTESSENCE PUBLISHING CO, INC.

Activity-based mass spectrometric characterization of proteases and inhibitors in human saliva

PubMed Central

Sun, Xiuli; Salih, Erdjan; Oppenheim, Frank G.; Helmerhorst, Eva J.

2009-01-01

Proteases present in oral fluid effectively modulate the structure and function of some salivary proteins and have been implicated in tissue destruction in oral disease. To identify the proteases operating in the oral environment, proteins in pooled whole saliva supernatant were separated by anion-exchange chromatography and individual fractions were analyzed for proteolytic activity by zymography using salivary histatins as the enzyme substrates. Protein bands displaying proteolytic activity were particularly prominent in the 50–75 kDa region. Individual bands were excised, in-gel trypsinized and subjected to LC/ESI-MS/MS. The data obtained were searched against human, oral microbial and protease databases. A total of 13 proteases were identified all of which were of mammalian origin. Proteases detected in multiple fractions with cleavage specificities toward arginine and lysine residues, were lactotransferrin, kallikrein-1, and human airway trypsin-like protease. Unexpectedly, ten protease inhibitors were co-identified suggesting they were associated with the proteases in the same fractions. The inhibitors found most frequently were alpha-2-macroglobulin-like protein 1, alpha-1-antitrypsin, and leukocyte elastase inhibitor. Regulation of oral fluid proteolysis is highly important given that an inbalance in such activities has been correlated to a variety of pathological conditions including oral cancer. PMID:20011683

Relationship between acetaldehyde concentration in mouth air and tongue coating volume.

PubMed

Yokoi, Aya; Maruyama, Takayuki; Yamanaka, Reiko; Ekuni, Daisuke; Tomofuji, Takaaki; Kashiwazaki, Haruhiko; Yamazaki, Yutaka; Morita, Manabu

2015-01-01

Acetaldehyde is the first metabolite of ethanol and is produced in the epithelium by mucosal ALDH, while higher levels are derived from microbial oxidation of ethanol by oral microflora such as Candida species. However, it is uncertain whether acetaldehyde concentration in human breath is related to oral condition or local production of acetaldehyde by oral microflora. The aim of this pilot study was to investigate the relationship between physiological acetaldehyde concentration and oral condition in healthy volunteers. Sixty-five volunteers (51 males and 14 females, aged from 20 to 87 years old) participated in the present study. Acetaldehyde concentration in mouth air was measured using a portable monitor. Oral examination, detection of oral Candida species and assessment of alcohol sensitivity were performed. Acetaldehyde concentration [median (25%, 75%)] in mouth air was 170.7 (73.5, 306.3) ppb. Acetaldehyde concentration in participants with a tongue coating status score of 3 was significantly higher than in those with a score of 1 (p<0.017). After removing tongue coating, acetaldehyde concentration decreased significantly (p<0.05). Acetaldehyde concentration was not correlated with other clinical parameters, presence of Candida species, smoking status or alcohol sensitivity. Physiological acetaldehyde concentration in mouth air was associated with tongue coating volume.

Relationship between acetaldehyde concentration in mouth air and tongue coating volume

PubMed Central

YOKOI, Aya; MARUYAMA, Takayuki; YAMANAKA, Reiko; EKUNI, Daisuke; TOMOFUJI, Takaaki; KASHIWAZAKI, Haruhiko; YAMAZAKI, Yutaka; MORITA, Manabu

2015-01-01

Objective Acetaldehyde is the first metabolite of ethanol and is produced in the epithelium by mucosal ALDH, while higher levels are derived from microbial oxidation of ethanol by oral microflora such as Candida species. However, it is uncertain whether acetaldehyde concentration in human breath is related to oral condition or local production of acetaldehyde by oral microflora. The aim of this pilot study was to investigate the relationship between physiological acetaldehyde concentration and oral condition in healthy volunteers. Material and Methods Sixty-five volunteers (51 males and 14 females, aged from 20 to 87 years old) participated in the present study. Acetaldehyde concentration in mouth air was measured using a portable monitor. Oral examination, detection of oral Candida species and assessment of alcohol sensitivity were performed. Results Acetaldehyde concentration [median (25%, 75%)] in mouth air was 170.7 (73.5, 306.3) ppb. Acetaldehyde concentration in participants with a tongue coating status score of 3 was significantly higher than in those with a score of 1 (p<0.017). After removing tongue coating, acetaldehyde concentration decreased significantly (p<0.05). Acetaldehyde concentration was not correlated with other clinical parameters, presence of Candida species, smoking status or alcohol sensitivity. Conclusion Physiological acetaldehyde concentration in mouth air was associated with tongue coating volume. PMID:25760268

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE PAGES

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; ...

2016-02-24

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed Central

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

2016-01-01

Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed

Graham, Emily B; Knelman, Joseph E; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J M; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C; Glanville, Helen C; Jones, Davey L; Angel, Roey; Salminen, Janne; Newton, Ryan J; Bürgmann, Helmut; Ingram, Lachlan J; Hamer, Ute; Siljanen, Henri M P; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C; Lopes, Ana R; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S; Basiliko, Nathan; Nemergut, Diana R

2016-01-01

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Health-Associated Niche Inhabitants as Oral Probiotics: The Case of Streptococcus dentisani

PubMed Central

López-López, Arantxa; Camelo-Castillo, Anny; Ferrer, María D.; Simon-Soro, Áurea; Mira, Alex

2017-01-01

Oral diseases, including dental caries and periodontitis, are among the most prevalent diseases worldwide and develop as a consequence of a microbial dysbiosis. Several bacterial strains are being tested as potential oral health-promoting organisms, but usually they are species isolated from niches other than the site where they must exert its probiotic action, typically from fecal samples. We hypothesize that oral inhabitants associated to health conditions will be more effective than traditional, gut-associated probiotic species in key aspects such as colonization of the oral site where disease takes place or the possession of oral health promoting functions, as well as more practical issues like safety and toxicity, and establishing proper doses for administration. As an example of these active colonizers, we describe the case of Streptococcus dentisani, a new streptococcal species isolated from dental plaque of caries-free individuals. We have detected it in 98% of dental plaque samples from healthy individuals and, as expected, it does not produce any toxic secondary metabolite and does not survive a simulated stomach digestion, preventing potential secondary effects. Besides, this species has a double probiotic action, as it inhibits the growth of major oral pathogens through the production of bacteriocins, and also buffers acidic pH (the primary cause of dental caries) through an arginolytic pathway. We propose the use of S. dentisani as a promising probiotic against tooth decay. PMID:28344574

Pseudomembranous Type of Oral Candidiasis is Associated with Decreased Salivary Flow Rate and Secretory Immunoglobulin A Levels.

PubMed

Mahajan, Bela; Bagul, Neeta; Desai, Rajiv; Reddy, Mamatha; Mahajan, Amit; Shete, Ashwini; Risbud, Arun; Mane, Arati

2015-08-01

Saliva plays an important role in maintaining microbial homeostasis in the oral cavity, while salivary gland hypofunction predisposes the oral mucosa to pathologic alteration and increases the risk for oral candidiasis. This study sought to determine the salivary flow rate (SFR) and secretory immunoglobulin A (SIgA) levels in HIV-positive and HIV-negative individuals and evaluate their relationship with the determinants of oral candidiasis. Sixty HIV-positive (30 with and 30 without oral candidiasis) and 30 healthy HIV-negative individuals were enrolled. Cotton pellet was weighed pre- and post-saliva collection for the assessment of SFR, while SIgA levels were estimated by commercial ELISA (Diametra, Italy) kit. The mean ± SD, SFR and SIgA levels in HIV-positive individuals with candidiasis, without candidiasis and HIV-negative controls were 0.396 ± 0.290, 0.546 ± 0.355 and 0.534 ± 0.214 ml/min and 115.891 ± 37.621, 136.024 ± 51.075 and 149.418 ± 31.765 µg/ml, respectively. A positive correlation between low CD4 counts (indicator of immunodeficiency) and SIgA was observed in HIV-positive individuals with candidiasis (r = 0.373, p = 0.045). We also report here for the first time the significant decrease in SFR and SIgA levels in individuals presenting with pseudomembranous type of oral candidiasis and Candida albicans infection.

Anti-inflammatory and protective effects of 2-methacryloyloxyethyl phosphorylcholine polymer on oral epithelial cells.

PubMed

Yumoto, Hiromichi; Hirota, Katsuhiko; Hirao, Kouji; Miyazaki, Tsuyoshi; Yamamoto, Nobuyuki; Miyamoto, Koji; Murakami, Keiji; Fujiwara, Natsumi; Matsuo, Takashi; Miyake, Yoichiro

2015-02-01

Periodontitis is a chronic inflammatory disease initiated by a microbial biofilm formed in the periodontal pocket. Gingival epithelium plays important roles as the first physical barrier to bacterial invasion and in orchestrating the innate immune reaction via toll-like receptors (TLRs), which recognize various bacterial products, and maintaining its function. Newly developed oral care products to inhibit bacterial adherence, subsequent inflammatory reaction and protect the gingival epithelium are expected. We previously reported that 2-methacryloyloxyethyl phosphorylcholine (MPC)-polymer coating decreased bacterial adhesion to human oral keratinocytes, RT-7, and mouth-rinsing with MPC-polymer inhibited the increase of oral bacteria. In this study, regarding the possibility of MPC-polymer application for preventing the adherence of periodontal pathogen, subsequent inflammatory reaction and protection of gingival epithelium, we examined the effects of MPC-polymer on the adherence of Porphyromonas gingivalis, major periodontitis-related pathogen, and TLR2 ligand to RT-7 and subsequent interleukin (IL)-8 production. MPC-polymer treatment significantly reduced P. gingivalis adherence by 44% and TLR2-mediated IL-8 production by blocking the binding of its specific-ligand in a concentration-dependent manner. Furthermore, MPC-polymer pretreatment protected RT-7 from injury by chemical irritants, cetylpyridinium chloride. These findings suggest that MPC-polymer is potentially useful for oral care to prevent oral infection and to maintain oral epithelial function. © 2014 Wiley Periodicals, Inc.

Nanotechnology in dentistry: drug delivery systems for the control of biofilm-dependent oral diseases.

PubMed

de Sousa, Francisco Fabio Oliveira; Ferraz, Camila; Rodrigues, Lidiany K Arla de Azevedo; Nojosa, Jacqueline de Santiago; Yamauti, Monica

2014-01-01

Dental disorders, such as caries, periodontal and endodontic diseases are major public health issues worldwide. In common, they are biofilm-dependent oral diseases, and the specific conditions of oral cavity may develop infectious foci that could affect other physiological systems. Efforts have been made to develop new treatment routes for the treatment of oral diseases, and therefore, for the prevention of some systemic illnesses. New drugs and materials have been challenged to prevent and treat these conditions, especially by means of bacteria elimination. "Recent progresses in understanding the etiology, epidemiology and microbiology of the microbial flora in those circumstances have given insight and motivated the innovation on new therapeutic approaches for the management of the oral diseases progression". Some of the greatest advances in the medical field have been based in nanosized systems, ranging from the drug release with designed nanoparticles to tissue scaffolds based on nanotechnology. These systems offer new possibilities for specific and efficient therapies, been assayed successfully in preventive/curative therapies to the oral cavity, opening new challenges and opportunities to overcome common diseases based on bacterial biofilm development. The aim of this review is to summarize the recent nanotechnological developments in the drug delivery field related to the prevention and treatment of the major biofilm-dependent oral diseases and to identify those systems, which may have higher potential for clinical use.

Liaison between micro-organisms and oral cancer

PubMed Central

Srinivasprasad, Vijayan; Dineshshankar, Janardhanam; Sathiyajeeva, J.; Karthikeyan, M.; Sunitha, J.; Ragunathan, Ramachandran

2015-01-01

Oral cancer which is a subtype of head and neck, cancer is any neoplastic tissue growth in the oral cavity. It comprises an abnormal mass of cells that foists genetic mutation and impedes the normal cell cycle, resulting in its unrestrained growth. Various studies on the plausible link between oral microbial flora and cancer notwithstanding, our understanding of their link remains obscure and inadequate. The multitude of mechanisms by which the microflora initiate or spur Carcinogenesis are still under study and scrutiny. As is widely known, the oral cavity is an abode to a wide assortment of microbes, each present in contrasting amounts. It is observed that increased growth of the microflora is concomitant with known clinical risk factors for oral cancer. Manifold bacterial species have been found to interfere directly with eukaryotic cellular signaling, adopting a style typical of tumor promoters. Bacteria are also known to impede apoptosis thereby potentially promoting carcinogenesis. The viral role in carcinogenesis (by annulling of p53 tumor suppressor gene and other cellular proteins with subsequent alteration in host genome function) is well documented. Furthermore, the changes occurring in the commensal microflora in accompaniment with cancer development could possibly be used as a diagnostic indicator for early cancer detection. The intention of this review is to obtain a better understanding of the “role” that micro-organisms play in oral cancer etiology. PMID:26538877

Oral and intraperitoneal administration of phosphorothioate oligodeoxynucleotides leads to control of Cryptosporidium parvum infection in neonatal mice.

PubMed

Barrier, Mathieu; Lacroix-Lamandé, Sonia; Mancassola, Roselyne; Auray, Gaël; Bernardet, Nelly; Chaussé, Anne-Marie; Uematsu, Satoshi; Akira, Shizuo; Laurent, Fabrice

2006-05-15

Neonates are particularly vulnerable to infections, in part because of the incomplete development of their immune system. Recent advances in immunostimulatory treatments based on conserved microbial components led us to assess the potential of oligodeoxynucleotides (ODNs) for decreasing the sensitivity of neonates to Cryptosporidium parvum infection. Neonate mice were treated orally or intraperitoneally (ip) with CpG ODNs or non-CpG ODNs 24 h before C. parvum infection, and parasite load and cytokine up-regulation were evaluated. CpG ODN 1668 and non-CpG ODN 1668 administered orally, as well as CpG ODN 1668 administered ip, induced an 80%-95% decrease in intestinal parasite load 6 days after infection. Intraperitoneal and oral pretreatment with CpG ODN 1668 led to a strong initial up-regulation of cytokines and CD69 messenger RNA in the intestine and a decrease in parasite load by a Toll-like receptor 9 (TLR9)-dependent mechanism. By contrast, oral administration of non-CpG ODN 1668 decreased parasite load by a TLR9-independent mechanism. The control of neonatal C. parvum infection by ip or oral administration of ODNs is feasible by 2 different mechanisms: (1) the well-known interaction involving CpG/TLR9, leading to the production of cytokines and lymphocyte activation, and (2) a new unknown mechanism that is independent of TLR9 and effective orally.

Towards a paradigm shift in the modeling of soil organic carbon decomposition for earth system models

NASA Astrophysics Data System (ADS)

He, Yujie

Soils are the largest terrestrial carbon pools and contain approximately 2200 Pg of carbon. Thus, the dynamics of soil carbon plays an important role in the global carbon cycle and climate system. Earth System Models are used to project future interactions between terrestrial ecosystem carbon dynamics and climate. However, these models often predict a wide range of soil carbon responses and their formulations have lagged behind recent soil science advances, omitting key biogeochemical mechanisms. In contrast, recent mechanistically-based biogeochemical models that explicitly account for microbial biomass pools and enzyme kinetics that catalyze soil carbon decomposition produce notably different results and provide a closer match to recent observations. However, a systematic evaluation of the advantages and disadvantages of the microbial models and how they differ from empirical, first-order formulations in soil decomposition models for soil organic carbon is still needed. This dissertation consists of a series of model sensitivity and uncertainty analyses and identifies dominant decomposition processes in determining soil organic carbon dynamics. Poorly constrained processes or parameters that require more experimental data integration are also identified. This dissertation also demonstrates the critical role of microbial life-history traits (e.g. microbial dormancy) in the modeling of microbial activity in soil organic matter decomposition models. Finally, this study surveys and synthesizes a number of recently published microbial models and provides suggestions for future microbial model developments.

Different Mechanisms of Soil Microbial Response to Global Change Result in Different Outcomes in the MIMICS-CN Model

NASA Astrophysics Data System (ADS)

Kyker-Snowman, E.; Wieder, W. R.; Grandy, S.

2017-12-01

Microbial-explicit models of soil carbon (C) and nitrogen (N) cycling have improved upon simulations of C and N stocks and flows at site-to-global scales relative to traditional first-order linear models. However, the response of microbial-explicit soil models to global change factors depends upon which parameters and processes in a model are altered by those factors. We used the MIcrobial-MIneral Carbon Stabilization Model with coupled N cycling (MIMICS-CN) to compare modeled responses to changes in temperature and plant inputs at two previously-modeled sites (Harvard Forest and Kellogg Biological Station). We spun the model up to equilibrium, applied each perturbation, and evaluated 15 years of post-perturbation C and N pools and fluxes. To model the effect of increasing temperatures, we independently examined the impact of decreasing microbial C use efficiency (CUE), increasing the rate of microbial turnover, and increasing Michaelis-Menten kinetic rates of litter decomposition, plus several combinations of the three. For plant inputs, we ran simulations with stepwise increases in metabolic litter, structural litter, whole litter (structural and metabolic), or labile soil C. The cumulative change in soil C or N varied in both sign and magnitude across simulations. For example, increasing kinetic rates of litter decomposition resulted in net releases of both C and N from soil pools, while decreasing CUE produced short-term increases in respiration but long-term accumulation of C in litter pools and shifts in soil C:N as microbial demand for C increased and biomass declined. Given that soil N cycling constrains the response of plant productivity to global change and that soils generate a large amount of uncertainty in current earth system models, microbial-explicit models are a critical opportunity to advance the modeled representation of soils. However, microbial-explicit models must be improved by experiments to isolate the physiological and stoichiometric parameters of soil microbes that shift under global change.

The effects of family, dentition, and dental caries on the salivary microbiome.

PubMed

Foxman, Betsy; Luo, Ting; Srinivasan, Usha; Ramadugu, Kirtana; Wen, Ai; Goldberg, Deborah; Shedden, Kerby; Crout, Richard; McNeil, Daniel W; Weyant, Robert; Marazita, Mary L

2016-05-01

Family members share genes, environment, and microbial communities. If there is a strong effect of family on the salivary microbiota, controlling for family will enhance identification of microbial communities associated with cariogenesis. The present study was designed to assess the similarity of the salivary microbiome among families and the association between the salivary microbiome and dental decay taking age into account. We selected families (n = 49) participating in the cohort study of oral health conducted by the Center for Oral Health Research in Appalachia. All families where at least two children and at least one parent gave a saliva sample (n = 173) were included. Saliva samples were collected at least 1 hour after eating or drinking. After DNA extraction, the V6 region of the 16s rRNA gene was sequenced. Paired ends were joined using fast length adjustment of short reads, sequences were demultiplexed and filtered using Quantitative Insights Into Microbial Ecology 1.9.0, and taxonomy was assigned using the Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) classifier and sequences aligned with the CORE database using PyNAST. The salivary microbiome changed with age and was more similar within families than between families. There was no difference in the diversity of the salivary microbiome by dental decay. After taking into account age and family, signals of dental decay were weak in the saliva, whether examined at the phyla, genus, or operational taxonomic level. The salivary microbiome does not appear to be a good indicator of dental caries. Copyright © 2016 Elsevier Inc. All rights reserved.

The antimicrobial efficacy of commercial dentifrices.

PubMed

Haraszthy, Violet I; Zambon, Joseph J; Sreenivasan, Prem K

2010-01-01

This investigation compared the effects of a fluoride dentifrice and toothpastes formulated with antimicrobial ingredients (stannous fluoride and triclosan/copolymer) on oral micro-organisms, including those found in samples taken from the human oral cavity. Microbiological techniques determined the minimum inhibitory concentrations (MICs) of each dentifrice necessary to inhibit the growth of bacterial strains from the healthy oral cavity, as well as those found in dental caries, periodontal disease, and halitosis. Ex vivo studies utilized oral rinse samples and supragingival plaque from adults to determine antimicrobial effects on the entire microbial diversity of these samples, including biofilm-derived micro-organisms. The triclosan/copolymer dentifrice demonstrated the lowest MICs and significantly inhibited Gram-positive and Gram-negative bacteria (including the periodontal pathogens Aggregatibacter actinomycetemcomitans, Eikenella corrodens, and Fusobacterium nucleatum). In the ex vivo tests, the triclosan/copolymer dentifrice demonstrated substantial inhibition in the oral rinse samples over each treatment period (p > 0.0005) as compared to either the fluoride or stannous fluoride dentifrices. Similarly, the triclosan/copolymer dentifrice demonstrated the highest inhibition of micro-organisms in the supragingival plaque biofilm (p < 0.0005). No significant differences were observed between the fluoride and stannous fluoride dentifrices (p > 0.5).

Oral microbiota in youth with perinatally acquired HIV infection.

PubMed

Starr, Jacqueline R; Huang, Yanmei; Lee, Kyu Ha; Murphy, C M; Moscicki, Anna-Barbara; Shiboski, Caroline H; Ryder, Mark I; Yao, Tzy-Jyun; Faller, Lina L; Van Dyke, Russell B; Paster, Bruce J

2018-05-31

Microbially mediated oral diseases can signal underlying HIV/AIDS progression in HIV-infected adults. The role of the oral microbiota in HIV-infected youth is not known. The Adolescent Master Protocol of the Pediatric HIV/AIDS Cohort Study is a longitudinal study of perinatally HIV-infected (PHIV) and HIV-exposed, uninfected (PHEU) youth. We compared oral microbiome levels and associations with caries or periodontitis in 154 PHIV and 100 PHEU youth. Species richness and alpha diversity differed little between PHIV and PHEU youth. Group differences in average counts met the significance threshold for six taxa; two Corynebacterium species were lower in PHIV and met thresholds for noteworthiness. Several known periodontitis-associated organisms (Prevotella nigrescens, Tannerella forsythia, Aggregatibacter actinomycetemcomitans, and Filifactor alocis) exhibited expected associations with periodontitis in PHEU youth, associations not observed in PHIV youth. In both groups, odds of caries increased with counts of taxa in four genera, Streptococcus, Scardovia, Bifidobacterium, and Lactobacillus. The microbiomes of PHIV and PHEU youth were similar, although PHIV youth seemed to have fewer "health"-associated taxa such as Corynebacterium species. These results are consistent with the hypothesis that HIV infection, or its treatment, may contribute to oral dysbiosis.

Contemporary perspective on plaque control.

PubMed

Marsh, P D

2012-06-22

The aim of this review article is to provide a scientific platform that will enable the dental team to develop a rational approach to plaque control based on the latest knowledge of the role of the oral microflora in health and disease. The resident oral microflora is natural and forms spatially-organised, interactive, multi-species biofilms on mucosal and dental surfaces in the mouth. These resident oral microbial communities play a key function in the normal development of the physiology of the host and are important in preventing colonisation by exogenous and often undesirable microbes. A dynamic balance exists between the resident microflora and the host in health, and disease results from a breakdown of this delicate relationship. Patients should be taught effective plaque control techniques that maintain dental biofilms at levels compatible with oral health so as to retain the beneficial properties of the resident microflora while reducing the risk of dental disease from excessive plaque accumulation. Antimicrobial and antiplaque agents in oral care products can augment mechanical plaque control by several direct and indirect mechanisms that not only involve reducing or removing dental biofilms but also include inhibiting bacterial metabolism when the agents are still present at sub-lethal concentrations.

Non-conventional therapeutics for oral infections

PubMed Central

Allaker, Robert P; Ian Douglas, CW

2015-01-01

As our knowledge of host-microbial interactions within the oral cavity increases, future treatments are likely to be more targeted. For example, efforts to target a single species or key virulence factors that they produce, while maintaining the natural balance of the resident oral microbiota that acts to modulate the host immune response would be an advantage. Targeted approaches may be directed at the black-pigmented anaerobes, Porphyromonas gingivalis and Prevotella intermedia, associated with periodontitis. Such pigments provide an opportunity for targeted phototherapy with high-intensity monochromatic light. Functional inhibition approaches, including the use of enzyme inhibitors, are also being explored to control periodontitis. More general disruption of dental plaque through the use of enzymes and detergents, alone and in combination, shows much promise. The use of probiotics and prebiotics to improve gastrointestinal health has now led to an interest in using these approaches to control oral disease. More recently the potential of antimicrobial peptides and nanotechnology, through the application of nanoparticles with biocidal, anti-adhesive and delivery capabilities, has been explored. The aim of this review is to consider the current status as regards non-conventional treatment approaches for oral infections with particular emphasis on the plaque-related diseases. PMID:25668296

Autophagy and its implication in human oral diseases.

PubMed

Tan, Ya-Qin; Zhang, Jing; Zhou, Gang

2017-02-01

Macroautophagy/autophagy is a conserved lysosomal degradation process essential for cell physiology and human health. By regulating apoptosis, inflammation, pathogen clearance, immune response and other cellular processes, autophagy acts as a modulator of pathogenesis and is a potential therapeutic target in diverse diseases. With regard to oral disease, autophagy can be problematic either when it is activated or impaired, because this process is involved in diverse functions, depending on the specific disease and its level of progression. In particular, activated autophagy functions as a cytoprotective mechanism under environmental stress conditions, which regulates tumor growth and mediates resistance to anticancer treatment in established tumors. During infections and inflammation, activated autophagy selectively delivers microbial antigens to the immune systems, and is therefore connected to the elimination of intracellular pathogens. Impaired autophagy contributes to oxidative stress, genomic instability, chronic tissue damage, inflammation and tumorigenesis, and is involved in aberrant bacterial clearance and immune priming. Hence, substantial progress in the study of autophagy provides new insights into the pathogenesis of oral diseases. This review outlines the mechanisms of autophagy, and highlights the emerging roles of this process in oral cancer, periapical lesions, periodontal diseases, and oral candidiasis.

The Negative Effects of Volatile Sulphur Compounds.

PubMed

Milella, Lisa

2015-01-01

Oral malodor has been studied extensively in humans but not necessarily to the same degree in our veterinary patients where malodor constitutes a significant problem. Breath malodor may originate from the mouth, or from an extra oral source, originating from other organ systems such as gastrointestinal, respiratory, or even systemic disease. Oral malodor is a result of microbial metabolism of exogenous and endogenous proteinaceous substrates leading to the production of compounds such as indole, skatole, tyramine, cadaverine, puterescine, mercaptans, and sulphides. Volatile sulphur compounds have been shown to be the main cause of oral malodor. Although most clients perceive oral malodor to be primarily a cosmetic problem, there is an increasing volume of evidence in human dental literature demonstrating that volatile sulphur compounds produced by bacteria, even at low concentrations, are toxic to tissues and play a role in the pathogenesis of periodontitis. This article reviews the current available literature in human dentistry looking at these negative effects. No veterinary studies have been conducted looking at the negative effects of volatile sulphur compounds specifically, but as this article highlights, we should be aware of the potential negative effects of volatile sulphur compounds and consider this an area of future research.

Oral microbiota in patients with atherosclerosis.

PubMed

Fåk, Frida; Tremaroli, Valentina; Bergström, Göran; Bäckhed, Fredrik

2015-12-01

Recent evidence suggests that the microbiota may be considered as an environmental factor that contributes to the development of atherosclerosis. Periodontal disease has been associated with cardio- and cerebrovascular events, and inflammation in the periodontium is suggested to increase the systemic inflammatory level of the host, which may in turn influence plaque composition and rupture. We previously showed that bacteria from the oral cavity and the gut could be found in atherosclerotic plaques. To elucidate whether the oral microbiota composition differed between patients with asymptomatic and symptomatic atherosclerosis we performed pyrosequencing of the oral microbiota of 92 individuals including patients with asymptomatic and symptomatic atherosclerosis and control individuals without carotid plaques or previous stroke or myocardial infarction. The overall microbial structure was similar in controls and atherosclerosis patients, but patients with symptomatic atherosclerosis had higher relative abundance of Anaeroglobus (mean 0.040% (SD 0.049)) than the control group (0.010% (SD 0.028)) (P = 0.03). Using linear regression analysis, we found that Parvimonas associated positively with uCRP and Capnocytophaga, Catonella and Lactobacillus associated with blood lipid markers. In conclusion, abundance of Anaeroglobus in the oral cavity could be associated with symptomatic atherosclerosis. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Autophagy and its implication in human oral diseases

PubMed Central

Tan, Ya-Qin; Zhang, Jing; Zhou, Gang

2017-01-01

ABSTRACT Macroautophagy/autophagy is a conserved lysosomal degradation process essential for cell physiology and human health. By regulating apoptosis, inflammation, pathogen clearance, immune response and other cellular processes, autophagy acts as a modulator of pathogenesis and is a potential therapeutic target in diverse diseases. With regard to oral disease, autophagy can be problematic either when it is activated or impaired, because this process is involved in diverse functions, depending on the specific disease and its level of progression. In particular, activated autophagy functions as a cytoprotective mechanism under environmental stress conditions, which regulates tumor growth and mediates resistance to anticancer treatment in established tumors. During infections and inflammation, activated autophagy selectively delivers microbial antigens to the immune systems, and is therefore connected to the elimination of intracellular pathogens. Impaired autophagy contributes to oxidative stress, genomic instability, chronic tissue damage, inflammation and tumorigenesis, and is involved in aberrant bacterial clearance and immune priming. Hence, substantial progress in the study of autophagy provides new insights into the pathogenesis of oral diseases. This review outlines the mechanisms of autophagy, and highlights the emerging roles of this process in oral cancer, periapical lesions, periodontal diseases, and oral candidiasis. PMID:27764582

A Spatially Continuous Model of Carbohydrate Digestion and Transport Processes in the Colon

PubMed Central

Moorthy, Arun S.; Brooks, Stephen P. J.; Kalmokoff, Martin; Eberl, Hermann J.

2015-01-01

A spatially continuous mathematical model of transport processes, anaerobic digestion and microbial complexity as would be expected in the human colon is presented. The model is a system of first-order partial differential equations with context determined number of dependent variables, and stiff, non-linear source terms. Numerical simulation of the model is used to elucidate information about the colon-microbiota complex. It is found that the composition of materials on outflow of the model does not well-describe the composition of material in other model locations, and inferences using outflow data varies according to model reactor representation. Additionally, increased microbial complexity allows the total microbial community to withstand major system perturbations in diet and community structure. However, distribution of strains and functional groups within the microbial community can be modified depending on perturbation length and microbial kinetic parameters. Preliminary model extensions and potential investigative opportunities using the computational model are discussed. PMID:26680208

(A)biotic processes control soil carbon dynamics: quantitative assessment of model complexity, stability and response to perturbations for improving ESMs

NASA Astrophysics Data System (ADS)

Georgiou, K.; Abramoff, R. Z.; Harte, J.; Riley, W. J.; Torn, M. S.

2016-12-01

As global temperatures and atmospheric CO2 concentrations continue to increase, soil microbial activity and decomposition of soil organic matter (SOM) are expected to follow suit, potentially limiting soil carbon storage. Traditional global- and ecosystem-scale models simulate SOM decomposition using linear kinetics, which are inherently unable to reproduce carbon-concentration feedbacks, such as priming of native SOM at elevated CO2 concentrations. Recent studies using nonlinear microbial models of SOM decomposition seek to capture these interactions, and several groups are currently integrating these microbial models into Earth System Models (ESMs). However, despite their widespread ability to exhibit nonlinear responses, these models vary tremendously in complexity and, consequently, dynamics. In this study, we explore, both analytically and numerically, the emergent oscillatory behavior and insensitivity of SOM stocks to carbon inputs that have been deemed `unrealistic' in recent microbial models. We discuss the sources of instability in four models of varying complexity, by sequentially reducing complexity of a detailed model that includes microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We also present an alternative representation of microbial turnover that limits population sizes and, thus, reduces oscillations. We compare these models to several long-term carbon input manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that traditional linear and nonlinear models cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures, and that modifying microbial turnover results in more realistic predictions. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in ESMs.

The oral microbiota in patients with pancreatic cancer, patients with IPMNs, and controls: a pilot study.

PubMed

Olson, Sara H; Satagopan, Jaya; Xu, Youming; Ling, Lilan; Leong, Siok; Orlow, Irene; Saldia, Amethyst; Li, Peter; Nunes, Pamela; Madonia, Vincent; Allen, Peter J; O'Reilly, Eileen; Pamer, Eric; Kurtz, Robert C

2017-09-01

Poor oral health appears to be a risk factor for pancreatic cancer, possibly implicating the oral microbiota. In this pilot study, we evaluated the characteristics of the oral microbiota in patients with pancreatic ductal adenocarcinoma (PDAC), intraductal papillary mucinous neoplasms (IPMN), and healthy controls. Forty newly diagnosed PDAC patients, 39 IPMN patients, and 58 controls, excluding current smokers and users of antibiotics, provided saliva samples. Common oral bacterial species were comprehensively surveyed by sequencing of the 16S rRNA microbial genes. We obtained measures of diversity and the mean relative proportions of individual taxa. We explored the degree to which these measures differed according to respondent characteristics based on individual interviews. PDAC cases did not differ in diversity measures from either controls or IPMN cases. PDAC cases had higher mean relative proportions of Firmicutes and related taxa, while controls had higher mean relative proportions of Proteobacteria and related taxa. Results were generally similar when comparing PDAC to IPMN cases. Among IPMNs and controls combined, younger individuals had higher levels of several taxa within the Proteobacteria. The only other variable consistently related to mean relative proportions was mouthwash use, with taxa within Firmicutes more common among users. While there were no differences in diversity of the oral microbiota among these groups, there were differences in the mean relative proportions of some taxa. Characteristics of the oral microbiota are not associated with most measures of oral health.

Application of a neutral community model to assess structuring of the human lung microbiome.

PubMed

Venkataraman, Arvind; Bassis, Christine M; Beck, James M; Young, Vincent B; Curtis, Jeffrey L; Huffnagle, Gary B; Schmidt, Thomas M

2015-01-20

DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples. Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health. Copyright © 2015 Venkataraman et al.

Bacteria and Candida yeasts in inflammations of the oral mucosa in children with secondary immunodeficiency.

PubMed

Olczak-Kowalczyk, Dorota; Daszkiewicz, Marta; Krasuska-Sławińska; Dembowska-Bagińska, Bozena; Gozdowski, Dariusz; Daszkiewicz, Paweł; Fronc, Beata; Semczuk, Katarzyna

2012-08-01

Oral microbial flora and a damaged oral mucosa may increase the risk of bacteriemia, fungemia and complications in immunocompromised patients. Assessment of presence: bacteria and Candida spp. in different oral lesions, and the incidence of bacteremia in the case of a damaged mucosa in transplant recipients and patients receiving anti-tumour chemotherapy. Forty-five patients – 18 months to 18 years of life, were included (20 – organ recipients, 14– anti-tumour chemotherapy, 11 – control group). Clinical, oral mucosa examination focused on the type, severity and site of lesions, and microbiology assessed the presence of bacteria and fungi in the material from lesions. Blood cultures were performed in ten immunocompromised patients with manifestations of systemic infection. The control material consisted of blood cultures made prior to the onset of oral lesions and after 4–6 weeks following their remission in a diagnosed bacteremia. The statistical analysis was performed. In the subjects with secondary immunodeficiency, among other coagulase-negative Staphylococcus (CoNS), Candidia spp. were more frequent. In cancer patients, mucositis was associated with Candida spp., Streptococcus spp. Organ recipients with stomatitis exhibited the presence of CoNS, Streptococcus viridians and other. Oral lesions in the control group contained Haemophilus parainfluenzae, Neisseria spp. and Staphylococcus aureus. In 30% of immunocompromised patients, oral lesions were accompanied by bacteremia. A correlation has been found between oral lesions and the presence of S. aureus in patients without secondary immunodeficiency, and of CoNS, Enterococcus spp., Candida spp. in immunocompromised patients.

Cognitive Impairment by Antibiotic-Induced Gut Dysbiosis: Analysis of Gut Microbiota-Brain Communication

PubMed Central

Fröhlich, Esther E.; Farzi, Aitak; Mayerhofer, Raphaela; Reichmann, Florian; Jačan, Angela; Wagner, Bernhard; Zinser, Erwin; Bordag, Natalie; Magnes, Christoph; Fröhlich, Eleonore; Kashofer, Karl; Gorkiewicz, Gregor; Holzer, Peter

2016-01-01

Emerging evidence indicates that disruption of the gut microbial community (dysbiosis) impairs mental health. Germ-free mice and antibiotic-induced gut dysbiosis are two approaches to establish causality in gut microbiota-brain relationships. However, both models have limitations, as germ-free mice display alterations in blood-brain barrier and brain ultrastructure and antibiotics may act directly on the brain. We hypothesized that the concerns related to antibiotic-induced gut dysbiosis can only adequately be addressed if the effect of intragastric treatment of adult mice with multiple antibiotics on (i) gut microbial community, (ii) metabolite profile in the colon, (iii) circulating metabolites, (iv) expression of neuronal signaling molecules in distinct brain areas and (v) cognitive behavior is systematically investigated. Of the antibiotics used (ampicillin, bacitracin, meropenem, neomycin, vancomycin), ampicillin had some oral bioavailability but did not enter the brain. 16S rDNA sequencing confirmed antibiotic-induced microbial community disruption, and metabolomics revealed that gut dysbiosis was associated with depletion of bacteria-derived metabolites in the colon and alterations of lipid species and converted microbe-derived molecules in the plasma. Importantly, novel object recognition, but not spatial, memory was impaired in antibiotic-treated mice. This cognitive deficit was associated with brain region-specific changes in the expression of cognition-relevant signaling molecules, notably brain-derived neurotrophic factor, N-methyl-D-aspartate receptor subunit 2B, serotonin transporter and neuropeptide Y system. We conclude that circulating metabolites and the cerebral neuropeptide Y system play an important role in the cognitive impairment and dysregulation of cerebral signaling molecules due to antibiotic-induced gut dysbiosis. PMID:26923630

Production of bioactive substances by intestinal bacteria as a basis for explaining probiotic mechanisms: bacteriocins and conjugated linoleic acid.

PubMed

O'Shea, Eileen F; Cotter, Paul D; Stanton, Catherine; Ross, R Paul; Hill, Colin

2012-01-16

The mechanisms by which intestinal bacteria achieve their associated health benefits can be complex and multifaceted. In this respect, the diverse microbial composition of the human gastrointestinal tract (GIT) provides an almost unlimited potential source of bioactive substances (pharmabiotics) which can directly or indirectly affect human health. Bacteriocins and fatty acids are just two examples of pharmabiotic substances which may contribute to probiotic functionality within the mammalian GIT. Bacteriocin production is believed to confer producing strains with a competitive advantage within complex microbial environments as a consequence of their associated antimicrobial activity. This has the potential to enable the establishment and prevalence of producing strains as well as directly inhibiting pathogens within the GIT. Consequently, these antimicrobial peptides and the associated intestinal producing strains may be exploited to beneficially influence microbial populations. Intestinal bacteria are also known to produce a diverse array of health-promoting fatty acids. Indeed, certain strains of intestinal bifidobacteria have been shown to produce conjugated linoleic acid (CLA), a fatty acid which has been associated with a variety of systemic health-promoting effects. Recently, the ability to modulate the fatty acid composition of the liver and adipose tissue of the host upon oral administration of CLA-producing bifidobacteria and lactobacilli was demonstrated in a murine model. Importantly, this implies a potential therapeutic role for probiotics in the treatment of certain metabolic and immunoinflammatory disorders. Such examples serve to highlight the potential contribution of pharmabiotic production to probiotic functionality in relation to human health maintenance. Copyright © 2011 Elsevier B.V. All rights reserved.

A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling.

PubMed

Wang, Gangsheng; Post, Wilfred M

2012-09-01

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models. © This article is a US government work and is in the public domain in the USA.

Development and application of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

NASA Astrophysics Data System (ADS)

Hong, E.; Park, Y.; Muirhead, R.; Jeong, J.; Pachepsky, Y. A.

2017-12-01

Pathogenic microorganisms in recreational and irrigation waters remain the subject of concern. Water quality models are used to estimate microbial quality of water sources, to evaluate microbial contamination-related risks, to guide the microbial water quality monitoring, and to evaluate the effect of agricultural management on the microbial water quality. The Agricultural Policy/Environmental eXtender (APEX) is the watershed-scale water quality model that includes highly detailed representation of agricultural management. The APEX currently does not have microbial fate and transport simulation capabilities. The objective of this work was to develop the first APEX microbial fate and transport module that could use the APEX conceptual model of manure removal together with recently introduced conceptualizations of the in-stream microbial fate and transport. The module utilizes manure erosion rates found in the APEX. Bacteria survival in soil-manure mixing layer was simulated with the two-stage survival model. Individual survival patterns were simulated for each manure application date. Simulated in-stream microbial fate and transport processes included the reach-scale passive release of bacteria with resuspended bottom sediment during high flow events, the transport of bacteria from bottom sediment due to the hyporheic exchange during low flow periods, the deposition with settling sediment, and the two-stage survival. Default parameter values were available from recently published databases. The APEX model with the newly developed microbial fate and transport module was applied to simulate seven years of monitoring data for the Toenepi watershed in New Zealand. Based on calibration and testing results, the APEX with the microbe module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water under various agricultural practices, evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations.

A mathematical model of microbial enhanced oil recovery (MEOR) method for mixed type rock

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sitnikov, A.A.; Eremin, N.A.; Ibattulin, R.R.

1994-12-31

This paper deals with the microbial enhanced oil recovery method. It covers: (1) Mechanism of microbial influence on the reservoir was analyzed; (2) The main groups of metabolites affected by the hydrodynamic characteristics of the reservoir were determined; (3) The criterions of use of microbial influence method on the reservoir are defined. The mathematical model of microbial influence on the reservoir was made on this basis. The injection of molasse water solution with Clostridium bacterias into the mixed type of rock was used in this model. And the results of calculations were compared with experimental data.

Dental plaque - associated infections and antibacterial oral hygiene products.

PubMed

Verran, J

1991-02-01

Synopsis Dental plaque accumulates on hard non-shedding surfaces such as teeth, dentures and orthodontic appliances. This accumulation is facilitated by the absence of adequate oral hygiene procedures. The term 'plaque' describes a mass of microorganisms embedded in an organic matrix of host and microbial origin. In addition to the aesthetic desirability of 'clean teeth, healthy gums and fresh breath' associated with the absence of plaque, obvious consequences of the presence of plaque include tooth decay (dental caries), gingivitis and periodontal (gum) disease and denture associated problems. Thus the prevention of plaque formation, the reduction of plaque accumulation and the effective removal of plaque are considerations of the cosmetic and health professions alike. There are many oral hygiene products available to the general public - toothpastes, mouthwashes, denture cleaners, and, more recently, chewing gums and novel mouthwashes. Several of these products have antimicrobial components. This paper reviews the microbiology of plaque and plaque associated problems, and surveys the type of products currently available for maintenance of good oral hygiene. Potential areas for future development are also explored.

Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico

PubMed Central

Narganes-Storde, Yvonne; Toranzos, Gary A.; Cano, Raul J.

2017-01-01

Background The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production. Fruits, as well as small marine and terrestrial animals were also part of the Saladoid diet. Methods Dental calculi samples were recovered from the archaeological site of Sorcé, in the municipal island of Vieques, Puerto Rico, characterized using 16S rRNA gene high-throughput sequencing, and compared to the microbiome of previously characterized coprolites of the same culture, as well modern plaque, saliva and stool microbiomes available from the Human Microbiome Project. Results Actinobacteria, Proteobacteria and Firmicutes comprised the majority of the Saladoid dental calculi microbiome. The Saladoid dental calculi microbiome was distinct when compared to those of modern saliva and dental plaque, but showed the presence of common inhabitants of modern oral cavities including Streptococcus sp., Veillonella dispar and Rothia mucilaginosa. Cell motility, signal transduction and biosynthesis of other secondary metabolites may be unique features of the Saladoid microbiome. Discussion Results suggest that the Saladoid dental calculi microbiome structure and function may possibly reflect a horticulturalist lifestyle and distinct dietary habits. Results also open the opportunity to further elucidate oral disease states in extinct Caribbean cultures and extinct indigenous cultures with similar lifestyles. PMID:28480145

Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico.

PubMed

Santiago-Rodriguez, Tasha M; Narganes-Storde, Yvonne; Chanlatte-Baik, Luis; Toranzos, Gary A; Cano, Raul J

2017-01-01

The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production. Fruits, as well as small marine and terrestrial animals were also part of the Saladoid diet. Dental calculi samples were recovered from the archaeological site of Sorcé, in the municipal island of Vieques, Puerto Rico, characterized using 16S rRNA gene high-throughput sequencing, and compared to the microbiome of previously characterized coprolites of the same culture, as well modern plaque, saliva and stool microbiomes available from the Human Microbiome Project. Actinobacteria, Proteobacteria and Firmicutes comprised the majority of the Saladoid dental calculi microbiome. The Saladoid dental calculi microbiome was distinct when compared to those of modern saliva and dental plaque, but showed the presence of common inhabitants of modern oral cavities including Streptococcus sp., Veillonella dispar and Rothia mucilaginosa . Cell motility, signal transduction and biosynthesis of other secondary metabolites may be unique features of the Saladoid microbiome. Results suggest that the Saladoid dental calculi microbiome structure and function may possibly reflect a horticulturalist lifestyle and distinct dietary habits. Results also open the opportunity to further elucidate oral disease states in extinct Caribbean cultures and extinct indigenous cultures with similar lifestyles.

Development of a program to fit data to a new logistic model for microbial growth.

PubMed

Fujikawa, Hiroshi; Kano, Yoshihiro

2009-06-01

Recently we developed a mathematical model for microbial growth in food. The model successfully predicted microbial growth at various patterns of temperature. In this study, we developed a program to fit data to the model with a spread sheet program, Microsoft Excel. Users can instantly get curves fitted to the model by inputting growth data and choosing the slope portion of a curve. The program also could estimate growth parameters including the rate constant of growth and the lag period. This program would be a useful tool for analyzing growth data and further predicting microbial growth.

Quantitative analysis of microbial biomass yield in aerobic bioreactor.

PubMed

Watanabe, Osamu; Isoda, Satoru

2013-12-01

We have studied the integrated model of reaction rate equations with thermal energy balance in aerobic bioreactor for food waste decomposition and showed that the integrated model has the capability both of monitoring microbial activity in real time and of analyzing biodegradation kinetics and thermal-hydrodynamic properties. On the other hand, concerning microbial metabolism, it was known that balancing catabolic reactions with anabolic reactions in terms of energy and electron flow provides stoichiometric metabolic reactions and enables the estimation of microbial biomass yield (stoichiometric reaction model). We have studied a method for estimating real-time microbial biomass yield in the bioreactor during food waste decomposition by combining the integrated model with the stoichiometric reaction model. As a result, it was found that the time course of microbial biomass yield in the bioreactor during decomposition can be evaluated using the operational data of the bioreactor (weight of input food waste and bed temperature) by the combined model. The combined model can be applied to manage a food waste decomposition not only for controlling system operation to keep microbial activity stable, but also for producing value-added products such as compost on optimum condition. Copyright © 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Stoichiometry constrains microbial response to root exudation - insights from a model and a field experiment in a temperate forest

NASA Astrophysics Data System (ADS)

Drake, J. E.; Darby, B. A.; Giasson, M.-A.; Kramer, M. A.; Phillips, R. P.; Finzi, A. C.

2012-06-01

Healthy plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exo-enzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The causal role of exudation, however, is difficult to isolate with in-situ observations, given the complex nature of the rhizosphere environment. We investigated the potential effects of root exudation on microbial and exo-enzyme activity using a theoretical model of decomposition and a field experiment, with a specific focus on the stoichiometric constraint of nitrogen (N) availability. The field experiment isolated the effect of exudation by pumping solutions of exudate mimics through microlysimeter "root simulators" into intact forest soils over two 50-day periods. Using a combined model-experiment approach, we tested two hypotheses: (1) exudation alone is sufficient to stimulate microbial and exo-enzyme activity in rhizosphere soils, and (2) microbial response to C-exudates (carbohydrates and organic acids) is constrained by N-limitation. Experimental delivery of exudate mimics containing C and N significantly increased microbial respiration, microbial biomass, and the activity of exo-enzymes that decompose labile components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exo-enzymes that degrade recalcitrant SOM (e.g., polyphenols, lignin). However, delivery of C-only exudates had no effect on microbial biomass or overall exo-enzyme activity, and only increased microbial respiration. The theoretical decomposition model produced complementary results; the modeled microbial response to C-only exudates was constrained by limited N supply to support the synthesis of N-rich microbial biomass and exo-enzymes, while exuding C and N together elicited an increase in modeled microbial biomass, exo-enzyme activity, and decomposition. Thus, hypothesis (2) was supported, while hypothesis (1) was only supported when C and N compounds were exuded together. This study supports a cause-and-effect relationship between root exudation and enhanced microbial activity, and suggests that exudate stoichiometry is an important and underappreciated driver of microbial activity in rhizosphere soils.

Modeling the impact of the indigenous microbial population on the maximum population density of Salmonella on alfalfa.

PubMed

Rijgersberg, Hajo; Franz, Eelco; Nierop Groot, Masja; Tromp, Seth-Oscar

2013-07-01

Within a microbial risk assessment framework, modeling the maximum population density (MPD) of a pathogenic microorganism is important but often not considered. This paper describes a model predicting the MPD of Salmonella on alfalfa as a function of the initial contamination level, the total count of the indigenous microbial population, the maximum pathogen growth rate and the maximum population density of the indigenous microbial population. The model is parameterized by experimental data describing growth of Salmonella on sprouting alfalfa seeds at inoculum size, native microbial load and Pseudomonas fluorescens 2-79. The obtained model fits well to the experimental data, with standard errors less than ten percent of the fitted average values. The results show that the MPD of Salmonella is not only dictated by performance characteristics of Salmonella but depends on the characteristics of the indigenous microbial population like total number of cells and its growth rate. The model can improve the predictions of microbiological growth in quantitative microbial risk assessments. Using this model, the effects of preventive measures to reduce pathogenic load and a concurrent effect on the background population can be better evaluated. If competing microorganisms are more sensitive to a particular decontamination method, a pathogenic microorganism may grow faster and reach a higher level. More knowledge regarding the effect of the indigenous microbial population (size, diversity, composition) of food products on pathogen dynamics is needed in order to make adequate predictions of pathogen dynamics on various food products.

Lactoferrin: Balancing Ups and Downs of Inflammation Due to Microbial Infections.

PubMed

Drago-Serrano, Maria Elisa; Campos-Rodríguez, Rafael; Carrero, Julio César; de la Garza, Mireya

2017-03-01

Lactoferrin (Lf) is a glycoprotein of the primary innate immune-defense system of mammals present in milk and other mucosal secretions. This protein of the transferrin family has broad antimicrobial properties by depriving pathogens from iron, or disrupting their plasma membranes through its highly cationic charge. Noteworthy, Lf also exhibits immunomodulatory activities performing up- and down-regulation of innate and adaptive immune cells, contributing to the homeostasis in mucosal surfaces exposed to myriad of microbial agents, such as the gastrointestinal and respiratory tracts. Although the inflammatory process is essential for the control of invasive infectious agents, the development of an exacerbated or chronic inflammation results in tissue damage with life-threatening consequences. In this review, we highlight recent findings in in vitro and in vivo models of the gut, lung, oral cavity, mammary gland, and liver infections that provide experimental evidence supporting the therapeutic role of human and bovine Lf in promoting some parameters of inflammation and protecting against the deleterious effects of bacterial, viral, fungal and protozoan-associated inflammation. Thus, this new knowledge of Lf immunomodulation paves the way to more effective design of treatments that include native or synthetic Lf derivatives, which may be useful to reduce immune-mediated tissue damage in infectious diseases.

Tracking of Engineered Bacteria In Vivo Using Nonstandard Amino Acid Incorporation.

PubMed

Praveschotinunt, Pichet; Dorval Courchesne, Noémie-Manuelle; den Hartog, Ilona; Lu, Chaochen; Kim, Jessica J; Nguyen, Peter Q; Joshi, Neel S

2018-06-15

The rapidly growing field of microbiome research presents a need for better methods of monitoring gut microbes in vivo with high spatial and temporal resolution. We report a method of tracking microbes in vivo within the gastrointestinal tract by programming them to incorporate nonstandard amino acids (NSAA) and labeling them via click chemistry. Using established machinery constituting an orthogonal translation system (OTS), we engineered Escherichia coli to incorporate p-azido-l-phenylalanine (pAzF) in place of the UAG (amber) stop codon. We also introduced a mutant gene encoding for a cell surface protein (CsgA) that was altered to contain an in-frame UAG codon. After pAzF incorporation and extracellular display, the engineered strains could be covalently labeled via copper-free click reaction with a Cy5 dye conjugated to the dibenzocyclooctyl (DBCO) group. We confirmed the functionality of the labeling strategy in vivo using a murine model. Labeling of the engineered strain could be observed using oral administration of the dye to mice several days after colonization of the gastrointestinal tract. This work sets the foundation for the development of in vivo tracking microbial strategies that may be compatible with noninvasive imaging modalities and are capable of longitudinal spatiotemporal monitoring of specific microbial populations.

Lactoferrin: Balancing Ups and Downs of Inflammation Due to Microbial Infections

PubMed Central

Drago-Serrano, Maria Elisa; Campos-Rodríguez, Rafael; Carrero, Julio César; de la Garza, Mireya

2017-01-01

Lactoferrin (Lf) is a glycoprotein of the primary innate immune-defense system of mammals present in milk and other mucosal secretions. This protein of the transferrin family has broad antimicrobial properties by depriving pathogens from iron, or disrupting their plasma membranes through its highly cationic charge. Noteworthy, Lf also exhibits immunomodulatory activities performing up- and down-regulation of innate and adaptive immune cells, contributing to the homeostasis in mucosal surfaces exposed to myriad of microbial agents, such as the gastrointestinal and respiratory tracts. Although the inflammatory process is essential for the control of invasive infectious agents, the development of an exacerbated or chronic inflammation results in tissue damage with life-threatening consequences. In this review, we highlight recent findings in in vitro and in vivo models of the gut, lung, oral cavity, mammary gland, and liver infections that provide experimental evidence supporting the therapeutic role of human and bovine Lf in promoting some parameters of inflammation and protecting against the deleterious effects of bacterial, viral, fungal and protozoan-associated inflammation. Thus, this new knowledge of Lf immunomodulation paves the way to more effective design of treatments that include native or synthetic Lf derivatives, which may be useful to reduce immune-mediated tissue damage in infectious diseases. PMID:28257033

Diflerent formulations of microbial respiratory losses and microbial efficiency have pronounced short and long term consequences for soil C dynamics and soil respiration

NASA Astrophysics Data System (ADS)

Ballantyne, F.; Billings, S. A.

2016-12-01

Much of the variability in projections of Earth's future C balance derives from uncertainty in how to formulate and parameterize models of biologically mediated transformations of soil organic C (SOC). Over the past decade, models of belowground decomposition have incorporated more realism, namely microbial biomass and exoenzyme pools, but it remains unclear whether microbially mediated decomposition is accurately formulated. Different models and different assumptions about how microbial efficiency, defined in terms of respiratory losses, varies with temperature exert great influence on SOC and CO2 flux projections for the future. Here, we incorporate a physiologically realistic formulation of CO2 loss from microbes, distinct from extant formulations and logically consistent with microbial C uptake and losses, into belowground dynamics and contrast its projections for SOC pools and CO2 flux from soils to those from the phenomenological formulations of efficiency in current models. We quantitatively describe how short and long term SOC dynamics are influenced by different mathematical formulations of efficiency, and that our lack of knowledge regarding loss rates from SOC and microbial biomass pools, specific respiration rate and maximum substrate uptake rate severely constrains our ability to confidently parameterize microbial SOC modules in Earth System Models. Both steady-state SOC and microbial biomass C pools, as well as transient responses to perturbations, can differ substantially depending on how microbial efficiency is derived. In particular, the discrepancy between SOC stocks for different formulations of efficiency varies from negligible to more than two orders of magnitude, depending on the relative values of respiratory versus non-respiratory losses from microbial biomass. Mass-specific respiration and proportional loss rates from soil microbes emerge as key determinants of the consequences of different formulations of efficiency for C flux in soils.

Modeling the unmeasurable: scaling soil physiology from microns to meters and seconds to centuries (Invited)

NASA Astrophysics Data System (ADS)

Schimel, J.; Xu, X.; Lawrence, C. R.

2013-12-01

Models are essential tools for linking microbial dynamics to their manifestations at large scales. Yet, developing mechanistically accurate models requires data that we often don't have and may not be able to get, such as the functional life-span of an extracellular enzyme. Yet there are approaches to condense complex microbial dynamics into 'workable' models. One example is in describing soil responses to moisture pulses. We developed a family of five separate models to capture microbial dynamics through dry/wet cycles. The simplest was a straight multi-pool, 1st-order decomposition model, with versions adding levels of microbial mechanism, culminating in one that included exoenzyme-breakdown of detritus. However, this identified the critical mechanism, not as exoenzymes, but as the production of a bioavailable C pool that accumulates in dry soil and is rapidly metabolized on rewetting. A final version of the model therefore stripped out explicit enzymes but retained separate polymer breakdown and substrate use; this model was the most robust. A second pervasive question in soil biology has been what controls the size of the microbial biomass across biomes? We approached this through a physiological model that regulated microbial C assimilation into biomass by two processes: initial assimilation followed by ongoing maintenance. Assimilation is a function of substrate quality, while maintenance is regulated by climate--notably the period of the year during which microbes are active. This model was tested against a global dataset of microbial biomass. It explains why, for example, deserts and tundra have relatively high proportions of their organic matter in microbial biomass, while the low substrate quality and long active periods common in temperate conifer forests lead to low biomass levels.

Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

NASA Astrophysics Data System (ADS)

Wang, G.; Mayes, M. A.; Gu, L.; Schadt, C. W.

2013-12-01

Experimental observations and modeling efforts have shown that dormancy is likely a common strategy for microorganisms to contend with environmental stress. We review the state-of-the-art in modeling approaches for microbial dormancy and discuss the rationales of these models. We proved that the physiological state index model is not appropriate for describing transformation between active and dormant states. Based on the generally accepted assumptions summarized from ten existing models, we postulated a new synthetic microbial physiology component within the Microbial-ENzyme-mediated Decomposition (MEND) model. Both the steady state active fraction (rss) and substrate saturation level (Øss) positively depend on two physiological indices: α and β. The index α = mR /(μG+ mR), where μG and mR represent the maximum specific growth and maintenance rates, respectively, for active microbes. β denotes the ratio of dormant to active maintenance rate. The rss equals to Øss only under the condition of β→0, and they are identical to α. When substrate availability is the only limiting factor, the maximum rss is ca. 0.5 with α≤0.5 and β ≤0.01. This threshold value (0.5) of rss (not dynamic r) can explain the low active microbial fractions observed in undisturbed soils. The applications of the improved model to a 14C-labeled glucose induced respiration dataset and a batch experimental dataset show satisfactory model performance. We found that the exponential growth respiration rates can only be used to determine μG and initial active microbial biomass (Ba0), thus we suggest using respiration data representing both exponential growth and non-accelerating phases to robustly determine other important parameters such as initial total live microbial biomass (B0), initial active fraction (r0), μG, α, and the half-saturation constant (Ks). Similar improved representations of microbial physiology should be incorporated into existing ecosystem models in order to account for the significance of dormancy in microbially-mediated processes.

Development of the Human Mycobiome over the First Month of Life and across Body Sites.

PubMed

Ward, Tonya L; Dominguez-Bello, Maria Gloria; Heisel, Tim; Al-Ghalith, Gabriel; Knights, Dan; Gale, Cheryl A

2018-01-01

With the advent of next-generation sequencing and microbial community characterization, we are beginning to understand the key factors that shape early-life microbial colonization and associated health outcomes. Studies characterizing infant microbial colonization have focused mostly on bacteria in the microbiome and have largely neglected fungi (the mycobiome), despite their relevance to mucosal infections in healthy infants. In this pilot study, we characterized the skin, oral, and anal mycobiomes of infants over the first month of life ( n = 17) and the anal and vaginal mycobiomes of mothers ( n = 16) by internal transcribed spacer 2 (ITS2) amplicon sequencing. We found that infant mycobiomes differed by body site, with the infant mycobiomes at the anal sites being different from those at the skin and oral sites. The relative abundances of body site-specific taxa differed by birth mode, with significantly more Candida albicans fungi present on the skin of vaginally born infants on day 30 and significantly more Candida orthopsilosis fungi present in the oral cavity of caesarean section-born infants throughout the first month of life. We found the mycobiomes within individual infants to be variable over the first month of life, and vaginal birth did not result in infant mycobiomes that were more similar to the mother's vaginal mycobiome. Therefore, although vertical transmission of specific fungal isolates from mother to infant has been reported, it is likely that other sources (environment, other caregivers) also contribute to early-life mycobiome establishment. Thus, future longitudinal studies of mycobiome and bacterial microbiome codevelopment, with dense sampling from birth to beyond the first month of life, are warranted. IMPORTANCE Humans are colonized by diverse fungi (mycobiome), which have received much less study to date than colonizing bacteria. We know very little about the succession of fungal colonization in early life and whether it may relate to long-term health. To better understand fungal colonization and its sources, we studied the skin, oral, and anal mycobiomes of healthy term infants and the vaginal and anal mycobiomes of their mothers. Generally, infants were colonized by few fungal taxa, and fungal alpha diversity did not increase over the first month of life. There was no clear community maturation over the first month of life, regardless of body site. Key body-site-specific taxa, but not overall fungal community structures, were impacted by birth mode. Thus, additional studies to characterize mycobiome acquisition and succession throughout early life are needed to form a foundation for research into the relationship between mycobiome development and human disease.

Integrated Environmental Modeling: Quantitative Microbial Risk Assessment

EPA Science Inventory

The presentation discusses the need for microbial assessments and presents a road map associated with quantitative microbial risk assessments, through an integrated environmental modeling approach. A brief introduction and the strengths of the current knowledge are illustrated. W...

Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders.

PubMed

Hsiao, Elaine Y; McBride, Sara W; Hsien, Sophia; Sharon, Gil; Hyde, Embriette R; McCue, Tyler; Codelli, Julian A; Chow, Janet; Reisman, Sarah E; Petrosino, Joseph F; Patterson, Paul H; Mazmanian, Sarkis K

2013-12-19

Neurodevelopmental disorders, including autism spectrum disorder (ASD), are defined by core behavioral impairments; however, subsets of individuals display a spectrum of gastrointestinal (GI) abnormalities. We demonstrate GI barrier defects and microbiota alterations in the maternal immune activation (MIA) mouse model that is known to display features of ASD. Oral treatment of MIA offspring with the human commensal Bacteroides fragilis corrects gut permeability, alters microbial composition, and ameliorates defects in communicative, stereotypic, anxiety-like and sensorimotor behaviors. MIA offspring display an altered serum metabolomic profile, and B. fragilis modulates levels of several metabolites. Treating naive mice with a metabolite that is increased by MIA and restored by B. fragilis causes certain behavioral abnormalities, suggesting that gut bacterial effects on the host metabolome impact behavior. Taken together, these findings support a gut-microbiome-brain connection in a mouse model of ASD and identify a potential probiotic therapy for GI and particular behavioral symptoms in human neurodevelopmental disorders. Copyright © 2013 Elsevier Inc. All rights reserved.

Biofilm community succession: a neutral perspective.

PubMed

Woodcock, Stephen; Sloan, William T

2017-05-22

Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested. Here, we further develop spatially resolved neutral community models and demonstrate that these can also explain these patterns and offer alternative explanations of microbial succession. The success of neutral models suggests that stochastic effects alone may have a much greater influence on microbial community succession than previously acknowledged. Furthermore, such models are much more readily parameterised and can be used as the foundation of more complex and realistic models of microbial community succession.

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

PubMed

Ebrahimi, Ali; Or, Dani

2016-09-01

Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

A Workflow to Model Microbial Loadings in Watersheds ...

EPA Pesticide Factsheets

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated with 1) land-applied manure on undeveloped areas from domestic animals; 2) direct shedding on undeveloped lands by domestic animals and wildlife; 3) urban or engineered areas; and 4) point sources that directly discharge to streams from septic systems and shedding by domestic animals. A microbial source module, which houses these formulations, is linked within a workflow containing eight models and a set of databases that form a loosely configured modeling infrastructure which supports watershed-scale microbial source-to-receptor modeling by focusing on animal-impacted catchments. A hypothetical example application – accessing, retrieving, and using real-world data – demonstrates the ability of the infrastructure to automate many of the manual steps associated with a standard watershed assessment, culminating with calibrated flow and microbial densities at the pour point of a watershed. Presented at 2016 Biennial Conference, International Environmental Modelling & Software Society.

In vitro Increased Respiratory Activity of Selected Oral Bacteria May Explain Competitive and Collaborative Interactions in the Oral Microbiome

PubMed Central

Hernandez-Sanabria, Emma; Slomka, Vera; Herrero, Esteban R.; Kerckhof, Frederiek-Maarten; Zaidel, Lynette; Teughels, Wim; Boon, Nico

2017-01-01

Understanding the driving forces behind the shifts in the ecological balance of the oral microbiota will become essential for the future management and treatment of periodontitis. As the use of competitive approaches for modulating bacterial outgrowth is unexplored in the oral ecosystem, our study aimed to investigate both the associations among groups of functional compounds and the impact of individual substrates on selected members of the oral microbiome. We employed the Phenotype Microarray high-throughput technology to analyse the microbial cellular phenotypes of 15 oral bacteria. Multivariate statistical analysis was used to detect respiratory activity triggers and to assess similar metabolic activities. Carbon and nitrogen were relevant for the respiration of health-associated bacteria, explaining competitive interactions when grown in biofilms. Carbon, nitrogen, and peptides tended to decrease the respiratory activity of all pathobionts, but not significantly. None of the evaluated compounds significantly increased activity of pathobionts at both 24 and 48 h. Additionally, metabolite requirements of pathobionts were dissimilar, suggesting that collective modulation of their respiratory activity may be challenging. Flow cytometry indicated that the metabolic activity detected in the Biolog plates may not be a direct result of the number of bacterial cells. In addition, damage to the cell membrane may not influence overall respiratory activity. Our methodology confirmed previously reported competitive and collaborative interactions among bacterial groups, which could be used either as marker of health status or as targets for modulation of the oral environment. PMID:28638806

Longitudinal research on the oral environment of elderly wearing fixed or removable prostheses.

PubMed

Tanaka, Junko; Tanaka, Masahiro; Kawazoe, Takayoshi

2009-04-01

The purpose of this study was to investigate oral environmental risk factors involved in caries incidence in the elderly. We investigated the relationship between the oral environment factors of the elderly with both fixed prostheses and removable prostheses at baseline and at follow-up and examined time-course changes of each oral environmental factor by prosthesis type. The subject group consisted 11 elderly patients with fixed prostheses and 11 who wore removable prostheses. We examined oral environmental factors by saliva tests. Five oral environmental factors were examined: the stimulated salivary flow rate, buffering capacity, and the counts of mutans streptococci (SM), lactobacilli (LB), and Candida (CA). We compared these factors for subjects with fixed prostheses and those wearing removable prostheses at baseline and at follow-up. Furthermore, 3-year changes in the factors of each oral environment were compared and evaluated. Significant differences were observed between the two groups in the salivary microbial counts of SM and LB at baseline and at follow-up. The LB counts increased in the Denture group during the 3-year period and significant differences were noted. We found that fixed prostheses are less cariogenic, and removable prostheses cause an increase in the cariogenic bacterial count. Regarding time-course changes by the type of prosthesis, the LB count tended to increase in the subjects with removable prostheses. The risk of caries due to a fixed prosthesis may be lower than that of removable prostheses.

Composition and development of oral bacterial communities.

PubMed

Palmer, Robert J

2014-02-01

The oral bacterial microbiome encompasses approximately 700 commonly occurring phylotypes, approximately half of which can be present at any time in any individual. These bacteria are largely indigenous to the oral cavity; this limited habitat range suggests that interactions between the various phylotypes, and between the phylotypes and their environment, are crucial for their existence. Molecular cataloging has confirmed many basic observations on the composition of the oral microbiome that were formulated well before ribosomal RNA-based systematics, but the power and the scope of molecular taxonomy have resulted in the discovery of new phylotypes and, more importantly, have made possible a level of bacterial community analysis that was unachievable with classical methods. Bacterial community structure varies with location within the mouth, and changes in community structure are related to disease initiation and disease progression. Factors that influence the formation and the evolution of communities include selective adherence to epithelial or tooth surfaces, specific cell-to-cell binding as a driver of early community composition, and interorganismal interaction leading to alteration of the local environment, which represents the first step on the road to oral disease. A comprehensive understanding of how these factors interact to drive changes in the composition of the oral microbial community can lead to new strategies for the inhibition of periodontal diseases and dental caries. Published 2013. This article is a US Government work and is in the public domain in the USA.

Microbial Ecology along the Gastrointestinal Tract

PubMed Central

Hillman, Ethan T.; Lu, Hang; Yao, Tianming; Nakatsu, Cindy H.

2017-01-01

The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem. Furthermore, due to the challenges associated with collecting samples directly from the inside of humans, many studies are still exploratory, with a primary focus on the composition of microbiomes. Thus, mechanistic studies to investigate functions are conducted using animal models. However, differences in physiology and microbiomes need to be clarified in order to aid in the translation of animal model findings into the context of humans. This review will highlight Bacteria, Archaea, Fungi, and Viruses, discuss differences along the GI tract of healthy humans, and perform comparisons with three common animal models: rats, mice, and pigs. PMID:29129876

Plasma treatment of onychomycosis

NASA Astrophysics Data System (ADS)

Xiong, Zilan; Roe, Jeff; Grammer, Tim; Him, Yeon-Ho; Graves, David B.

2015-09-01

Onychomycosis or fungal infection of the toenail or fingernail is a common affliction. Approximately 10% of the world's adult population is estimated to suffer from onychomycosis. Current treatment options such as topical creams, oral drugs, or laser treatments are generally limited by a variety of problems. We present results for an alternative onychomycosis treatment scheme using atmospheric pressure cold air plasmas. Using thinned cow hoof as a model nail material, we tested the ability of various plasma sources to act through the model nail to eradicate either bacteria or fungus deposited on the opposite side. Following 20 minute exposure to a surface microdischarge (SMD) device operating in room air, we observed a ~ 2 log reduction of E. coli. A similar result was obtained against T. rubrum after 45 min plasma treatment. NOx species concentration penetrating through the model nail as well as uptake into the nail were measured as a function of nail thickness. We propose that these plasma-generated species, or perhaps their reaction products, are responsible for at least part of the observed anti-microbial effect. We also explore the use of ultraviolet light acting in synergy with plasma-generated chemical species.

Treatment modalities and evaluation models for periodontitis

PubMed Central

Tariq, Mohammad; Iqbal, Zeenat; Ali, Javed; Baboota, Sanjula; Talegaonkar, Sushama; Ahmad, Zulfiqar; Sahni, Jasjeet K

2012-01-01

Periodontitis is the most common localized dental inflammatory disease related with several pathological conditions like inflammation of gums (gingivitis), degeneration of periodontal ligament, dental cementum and alveolar bone loss. In this perspective, the various preventive and treatment modalities, including oral hygiene, gingival irrigations, mechanical instrumentation, full mouth disinfection, host modulation and antimicrobial therapy, which are used either as adjunctive treatments or as stand-alone therapies in the non-surgical management of periodontal infections, have been discussed. Intra-pocket, sustained release systems have emerged as a novel paradigm for the future research. In this article, special consideration is given to different locally delivered anti-microbial and anti inflammatory medications which are either commercially available or are currently under consideration for Food and Drug Administration (FDA) approval. The various in vitro dissolution models and microbiological strain investigated to impersonate the infected and inflamed periodontal cavity and to predict the in vivo performance of treatment modalities have also been thrashed out. Animal models that have been employed to explore the pathology at the different stages of periodontitis and to evaluate its treatment modalities are enlightened in this proposed review. PMID:23373002

Natural Antimicrobials and Oral Microorganisms: A Systematic Review on Herbal Interventions for the Eradication of Multispecies Oral Biofilms

PubMed Central

Karygianni, Lamprini; Al-Ahmad, Ali; Argyropoulou, Aikaterini; Hellwig, Elmar; Anderson, Annette C.; Skaltsounis, Alexios L.

2016-01-01

Oral diseases such as caries and periodontitis are mainly caused by microbial biofilms. Antibiotic therapy has reached its limits with regard to antimicrobial resistance, and new therapeutic measures utilizing natural phytochemicals are currently a focus of research. Hence, this systematic review provides a critical presentation of the antimicrobial effects of various medicinal herbs against in vitro, ex vivo, and in situ formed multispecies oral biofilms. Searches were performed in three English databases (PubMed, EMBASE, CAMbase) and the electronic archives of five German journals from the times of their establishment until October 10th, 2014, with the search terms “(plant extracts OR herbal extracts OR plant OR herb) AND (oral biofilm OR dental biofilm OR dental plaque OR oral disease OR dental disease).” The pooled data were assessed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA). Initially, 1848 articles were identified, out of which 585 full-text articles were screened, 149 articles were reevaluated for eligibility and finally, 14 articles met all inclusion criteria. The data of 14 reports disclosed enhanced antiadhesive and antibiofilm activity by the plant extracts obtained from Vitis vinifera, Pinus spp., Coffea canephora, Camellia sinensis, Vaccinium macrocarpon, Galla chinensis, Caesalpinia ferrea Martius, Psidium cattleianum, representative Brazilian plants and manuka honey. Overall, a positive correlation was revealed between herb-based therapies and elimination rates of all types of multispecies oral biofilms. In that context, integrating or even replacing conventional dental therapy protocols with herbal-inspired treatments can allow effective antimicrobial control of oral biofilms and thus, dental diseases. PMID:26834707

Natural Antimicrobials and Oral Microorganisms: A Systematic Review on Herbal Interventions for the Eradication of Multispecies Oral Biofilms.

PubMed

Karygianni, Lamprini; Al-Ahmad, Ali; Argyropoulou, Aikaterini; Hellwig, Elmar; Anderson, Annette C; Skaltsounis, Alexios L

2015-01-01

Oral diseases such as caries and periodontitis are mainly caused by microbial biofilms. Antibiotic therapy has reached its limits with regard to antimicrobial resistance, and new therapeutic measures utilizing natural phytochemicals are currently a focus of research. Hence, this systematic review provides a critical presentation of the antimicrobial effects of various medicinal herbs against in vitro, ex vivo, and in situ formed multispecies oral biofilms. Searches were performed in three English databases (PubMed, EMBASE, CAMbase) and the electronic archives of five German journals from the times of their establishment until October 10th, 2014, with the search terms "(plant extracts OR herbal extracts OR plant OR herb) AND (oral biofilm OR dental biofilm OR dental plaque OR oral disease OR dental disease)." The pooled data were assessed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA). Initially, 1848 articles were identified, out of which 585 full-text articles were screened, 149 articles were reevaluated for eligibility and finally, 14 articles met all inclusion criteria. The data of 14 reports disclosed enhanced antiadhesive and antibiofilm activity by the plant extracts obtained from Vitis vinifera, Pinus spp., Coffea canephora, Camellia sinensis, Vaccinium macrocarpon, Galla chinensis, Caesalpinia ferrea Martius, Psidium cattleianum, representative Brazilian plants and manuka honey. Overall, a positive correlation was revealed between herb-based therapies and elimination rates of all types of multispecies oral biofilms. In that context, integrating or even replacing conventional dental therapy protocols with herbal-inspired treatments can allow effective antimicrobial control of oral biofilms and thus, dental diseases.

In-Drift Microbial Communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

D. Jolley

2000-11-09

As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999).more » This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.« less

Exploring a microbial ecosystem approach to modeling deep ocean biogeochemical cycles

NASA Astrophysics Data System (ADS)

Zakem, E.; Follows, M. J.

2014-12-01

Though microbial respiration of organic matter in the deep ocean governs ocean and atmosphere biogeochemistry, it is not represented mechanistically in current global biogeochemical models. We seek approaches that are feasible for a global resolution, yet still reflect the enormous biodiversity of the deep microbial community and its associated metabolic pathways. We present a modeling framework grounded in thermodynamics and redox reaction stoichiometry that represents diverse microbial metabolisms explicitly. We describe a bacterial/archaeal functional type with two parameters: a growth efficiency representing the chemistry underlying a bacterial metabolism, and a rate limitation given by the rate of uptake of each of the necessary substrates for that metabolism. We then apply this approach to answer questions about microbial ecology. As a start, we resolve two dominant heterotrophic respiratory pathways- reduction of oxygen and nitrate- and associated microbial functional types. We combine these into an ecological model and a two-dimensional ocean circulation model to explore the organization, biogeochemistry, and ecology of oxygen minimum zones. Intensified upwelling and lateral transport conspire to produce an oxygen minimum at mid-depth, populated by anaerobic denitrifiers. This modeling approach should ultimately allow for the emergence of bacterial biogeography from competition of metabolisms and for the incorporation of microbial feedbacks to the climate system.

Integrating microbial diversity in soil carbon dynamic models parameters

NASA Astrophysics Data System (ADS)

Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

2015-04-01

Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten sampling time in order to follow the dynamic of residue and soil organic matter mineralization. Diversity, structure and composition of microbial communities have been characterized before incubation time. The dynamic of carbon fluxes through CO2 emissions has been modelled through a simple model. Using statistical tools, relations between parameters of the model and microbial diversity indexes and/or pedological characteristics have been developed and integrated to the model. First results show that global diversity has an impact on the models parameters. Moreover, larger fungi diversity seems to lead to larger parameters representing decomposition rates and/or carbon use efficiencies than bacterial diversity. Classically, pedological factors such as soil pH and texture must also be taken into account.

Effect of 12-month weekly professional oral hygiene care on the composition of the oral flora in dentate, dependent elderly residents: A prospective study.

PubMed

Wikström, Maude; Kareem, Kawa L; Almståhl, Annica; Palmgren, Erika; Lingström, Peter; Wårdh, Inger

2017-06-01

To study the effect of weekly professional oral hygiene care on the proportion of micro-organisms associated with good oral health, caries, and periodontal and soft tissue diseases in oral biofilms in dentate, dependent elderly residents. Assisted oral hygiene care reduces the plaque score and number of micro-organisms in the oral biofilms in elderly residents. Less is known about the effect on the quality/composition of the remaining oral flora. Participants comprised 33 residents in the study and 35 in the control group. Dental status (≥10 natural teeth and no removable dentures to be included), plaque score, salivary secretion rate and prescription medicines were recorded. Duplicate samples, collected from supragingival plaque and tongue, were analysed using cultivation technique. Differences between and within groups were analysed using one-way and two-way ANOVA, respectively. At the baseline, the number of teeth in the participants (mean age, 83.7 ± 7.4 years) was 22.0 ± 4.5. The number of prescription medicines was 9.4 ± 4.5. Seventy-six per cent had low salivary secretion rate. Fifty per cent had "visible thick" supragingival plaque. At the 12-month registration, "no visible" or "visible but thin" plaque was recorded in 92% in the study group. The proportions of bacteria associated with good oral health and periodontal diseases were decreased over time, while the frequency and proportions of micro-organisms associated with caries and soft tissue infection were unaffected or increased. The results indicate that assisted oral hygiene care alone is not sufficient to regain an oral microbial flora associated with good oral health in dentate, dependent elderly residents. © 2016 John Wiley & Sons A/S and The Gerodontology Association. Published by John Wiley & Sons Ltd.

Identification of Rothia Bacteria as Gluten-Degrading Natural Colonizers of the Upper Gastro-Intestinal Tract

PubMed Central

Zamakhchari, Maram; Wei, Guoxian; Dewhirst, Floyd; Lee, Jaeseop; Schuppan, Detlef; Oppenheim, Frank G.; Helmerhorst, Eva J.

2011-01-01

Background Gluten proteins, prominent constituents of barley, wheat and rye, cause celiac disease in genetically predisposed subjects. Gluten is notoriously difficult to digest by mammalian proteolytic enzymes and the protease-resistant domains contain multiple immunogenic epitopes. The aim of this study was to identify novel sources of gluten-digesting microbial enzymes from the upper gastro-intestinal tract with the potential to neutralize gluten epitopes. Methodology/Principal Findings Oral microorganisms with gluten-degrading capacity were obtained by a selective plating strategy using gluten agar. Microbial speciations were carried out by 16S rDNA gene sequencing. Enzyme activities were assessed using gliadin-derived enzymatic substrates, gliadins in solution, gliadin zymography, and 33-mer α-gliadin and 26-mer γ-gliadin immunogenic peptides. Fragments of the gliadin peptides were separated by RP-HPLC and structurally characterized by mass spectrometry. Strains with high activity towards gluten were typed as Rothia mucilaginosa and Rothia aeria. Gliadins (250 µg/ml) added to Rothia cell suspensions (OD620 1.2) were degraded by 50% after ∼30 min of incubation. Importantly, the 33-mer and 26-mer immunogenic peptides were also cleaved, primarily C-terminal to Xaa-Pro-Gln (XPQ) and Xaa-Pro-Tyr (XPY). The major gliadin-degrading enzymes produced by the Rothia strains were ∼70–75 kDa in size, and the enzyme expressed by Rothia aeria was active over a wide pH range (pH 3–10). Conclusion/Significance While the human digestive enzyme system lacks the capacity to cleave immunogenic gluten, such activities are naturally present in the oral microbial enzyme repertoire. The identified bacteria may be exploited for physiologic degradation of harmful gluten peptides. PMID:21957450

Identification of Rothia bacteria as gluten-degrading natural colonizers of the upper gastro-intestinal tract.

PubMed

Zamakhchari, Maram; Wei, Guoxian; Dewhirst, Floyd; Lee, Jaeseop; Schuppan, Detlef; Oppenheim, Frank G; Helmerhorst, Eva J

2011-01-01

Gluten proteins, prominent constituents of barley, wheat and rye, cause celiac disease in genetically predisposed subjects. Gluten is notoriously difficult to digest by mammalian proteolytic enzymes and the protease-resistant domains contain multiple immunogenic epitopes. The aim of this study was to identify novel sources of gluten-digesting microbial enzymes from the upper gastro-intestinal tract with the potential to neutralize gluten epitopes. Oral microorganisms with gluten-degrading capacity were obtained by a selective plating strategy using gluten agar. Microbial speciations were carried out by 16S rDNA gene sequencing. Enzyme activities were assessed using gliadin-derived enzymatic substrates, gliadins in solution, gliadin zymography, and 33-mer α-gliadin and 26-mer γ-gliadin immunogenic peptides. Fragments of the gliadin peptides were separated by RP-HPLC and structurally characterized by mass spectrometry. Strains with high activity towards gluten were typed as Rothia mucilaginosa and Rothia aeria. Gliadins (250 µg/ml) added to Rothia cell suspensions (OD(620) 1.2) were degraded by 50% after ∼30 min of incubation. Importantly, the 33-mer and 26-mer immunogenic peptides were also cleaved, primarily C-terminal to Xaa-Pro-Gln (XPQ) and Xaa-Pro-Tyr (XPY). The major gliadin-degrading enzymes produced by the Rothia strains were ∼70-75 kDa in size, and the enzyme expressed by Rothia aeria was active over a wide pH range (pH 3-10). While the human digestive enzyme system lacks the capacity to cleave immunogenic gluten, such activities are naturally present in the oral microbial enzyme repertoire. The identified bacteria may be exploited for physiologic degradation of harmful gluten peptides.

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces

PubMed Central

Brandt, Bernd W.; Teixeira de Mattos, M. Joost; Buijs, Mark J.; Caspers, Martien P. M.; Rashid, Mamun-Ur; Weintraub, Andrej; Nord, Carl Erik; Savell, Ann; Hu, Yanmin; Coates, Antony R.; Hubank, Mike; Spratt, David A.; Wilson, Michael; Keijser, Bart J. F.; Crielaard, Wim

2015-01-01

ABSTRACT Due to the spread of resistance, antibiotic exposure receives increasing attention. Ecological consequences for the different niches of individual microbiomes are, however, largely ignored. Here, we report the effects of widely used antibiotics (clindamycin, ciprofloxacin, amoxicillin, and minocycline) with different modes of action on the ecology of both the gut and the oral microbiomes in 66 healthy adults from the United Kingdom and Sweden in a two-center randomized placebo-controlled clinical trial. Feces and saliva were collected at baseline, immediately after exposure, and 1, 2, 4, and 12 months after administration of antibiotics or placebo. Sequences of 16S rRNA gene amplicons from all samples and metagenomic shotgun sequences from selected baseline and post-antibiotic-treatment sample pairs were analyzed. Additionally, metagenomic predictions based on 16S rRNA gene amplicon data were performed using PICRUSt. The salivary microbiome was found to be significantly more robust, whereas the antibiotics negatively affected the fecal microbiome: in particular, health-associated butyrate-producing species became strongly underrepresented. Additionally, exposure to different antibiotics enriched genes associated with antibiotic resistance. In conclusion, healthy individuals, exposed to a single antibiotic treatment, undergo considerable microbial shifts and enrichment in antibiotic resistance in their feces, while their salivary microbiome composition remains unexpectedly stable. The health-related consequences for the gut microbiome should increase the awareness of the individual risks involved with antibiotic use, especially in a (diseased) population with an already dysregulated microbiome. On the other hand, understanding the mechanisms behind the resilience of the oral microbiome toward ecological collapse might prove useful in combating microbial dysbiosis elsewhere in the body. PMID:26556275

Nano-graphene oxide incorporated into PMMA resin to prevent microbial adhesion.

PubMed

Lee, Jung-Hwan; Jo, Jeong-Ki; Kim, Dong-Ae; Patel, Kapil Dev; Kim, Hae-Won; Lee, Hae-Hyoung

2018-04-01

Although polymethyl methacrylate (PMMA) is widely used as a dental material, a major challenge of using this substance is its poor antimicrobial (anti-adhesion) effects, which increase oral infections. Here, graphene-oxide nanosheets (nGO) were incorporated into PMMA to introduce sustained antimicrobial-adhesive effects by increasing the hydrophilicity of PMMA. After characterizing nGO and nGO-incorporated PMMA (up to 2wt%) in terms of morphology and surface characteristics, 3-point flexural strength and hardness were evaluated. The anti-adhesive effects were determined for 4 different microbial species with experimental specimens and the underlying anti-adhesive mechanism was investigated by a non-thermal oxygen plasma treatment. Sustained antimicrobial-adhesive effects were characterized with incubation in artificial saliva for up to 28 days. The typical nanosheet morphology was observed for nGO. Incorporating nGO into PMMA roughened its surface and increased its hydrophilicity without compromising flexural strength or surface hardness. An anti-adhesive effect after 1h of exposure to microbial species in artificial saliva was observed in nGO-incorporated specimens, which accelerated with increasing levels of nGO without significant cytotoxicity to oral keratinocytes. Plasma treatment of native PMMA demonstrated that the antimicrobial-adhesive effects of nGO incorporation were at least partially due to increased hydrophilicity, not changes in the surface roughness. A sustained antimicrobial-adhesive property against Candida albicans was observed in 2% nGO for up to 28 days. The presence of sustained anti-adhesion properties in nGO-incorporated PMMA without loading any antimicrobial drugs suggests the potential usefulness of this compound as a promising antimicrobial dental material for dentures, orthodontic devices and provisional restorative materials. Copyright © 2018 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

A Workflow to Model Microbial Loadings in Watersheds

EPA Science Inventory

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

Why fruit rots: theoretical support for Janzen's theory of microbe-macrobe competition.

PubMed

Ruxton, Graeme D; Wilkinson, David M; Schaefer, H Martin; Sherratt, Thomas N

2014-05-07

We present a formal model of Janzen's influential theory that competition for resources between microbes and vertebrates causes microbes to be selected to make these resources unpalatable to vertebrates. That is, fruit rots, seeds mould and meat spoils, in part, because microbes gain a selective advantage if they can alter the properties of these resources to avoid losing the resources to vertebrate consumers. A previous model had failed to find circumstances in which such a costly spoilage trait could flourish; here, we present a simple analytic model of a general situation where costly microbial spoilage is selected and persists. We argue that the key difference between the two models lies in their treatments of microbial dispersal. If microbial dispersal is sufficiently spatially constrained that different resource items can have differing microbial communities, then spoilage will be selected; however, if microbial dispersal has a strong homogenizing effect on the microbial community then spoilage will not be selected. We suspect that both regimes will exist in the natural world, and suggest how future empirical studies could explore the influence of microbial dispersal on spoilage.

Modelling the competition of planktonic and sessile aerobic heterotrophs for complementary nutrients in biofilm reactor.

PubMed

Lu, T; Saikaly, P E; Oerther, D B

2007-01-01

A comprehensive, simplified microbial biofilm model was developed to evaluate the impact of bioreactor operating parameters on changes in microbial population abundance. Biofilm simulations were conducted using three special cases: fully penetrated, internal mass transfer resistance and external mass transfer resistance. The results of model simulations showed that for certain operating conditions, competition for growth limiting nutrients generated oscillations in the abundance of planktonic and sessile microbial populations. These oscillations resulted in the violation of the competitive exclusion principle where the number of microbial populations was greater than the number of growth limiting nutrients. However, the operating conditions which impacted microbial community diversity were different for the three special cases. Comparing the results of model simulations for dispersed-growth, biofilms and bioflocs showed that oscillations and microbial community diversity were a function of competition as well as other key features of the ecosystem. The significance of the current study is that it is the first to examine competition as a mechanism for controlling microbial community diversity in biofilm reactors.

A Workflow to Model Microbial Loadings in Watersheds ...

EPA Pesticide Factsheets

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated with 1) land-applied manure on undeveloped areas from domestic animals; 2) direct shedding on undeveloped lands by domestic animals and wildlife; 3) urban or engineered areas; and 4) point sources that directly discharge to streams from septic systems and shedding by domestic animals. A microbial source module, which houses these formulations, is linked within a workflow containing eight models and a set of databases that form a loosely configured modeling infrastructure which supports watershed-scale microbial source-to-receptor modeling by focusing on animal-impacted catchments. A hypothetical example application – accessing, retrieving, and using real-world data – demonstrates the ability of the infrastructure to automate many of the manual steps associated with a standard watershed assessment, culminating with calibrated flow and microbial densities at the pour point of a watershed. In the Proceedings of the International Environmental Modelling and Software Society (iEMSs), 8th International Congress on Environmental Modelling and Software, Toulouse, France

Mineral solubility and free energy controls on microbial reaction kinetics: Application to contaminant transport in the subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taillefert, Martial; Van Cappellen, Philippe

Recent developments in the theoretical treatment of geomicrobial reaction processes have resulted in the formulation of kinetic models that directly link the rates of microbial respiration and growth to the corresponding thermodynamic driving forces. The overall objective of this project was to verify and calibrate these kinetic models for the microbial reduction of uranium(VI) in geochemical conditions that mimic as much as possible field conditions. The approach combined modeling of bacterial processes using new bioenergetic rate laws, laboratory experiments to determine the bioavailability of uranium during uranium bioreduction, evaluation of microbial growth yield under energy-limited conditions using bioreactor experiments, competitionmore » experiments between metabolic processes in environmentally relevant conditions, and model applications at the field scale. The new kinetic descriptions of microbial U(VI) and Fe(III) reduction should replace those currently used in reactive transport models that couple catabolic energy generation and growth of microbial populations to the rates of biogeochemical redox processes. The above work was carried out in collaboration between the groups of Taillefert (batch reactor experiments and reaction modeling) at Georgia Tech and Van Cappellen (retentostat experiments and reactive transport modeling) at University of Waterloo (Canada).« less

Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

NASA Astrophysics Data System (ADS)

Masum, Shakil A.; Thomas, Hywel R.

2018-06-01

To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

DOE PAGES

Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart

2016-11-28

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes producemore » chemically diverse, stable SOM. As a result, we show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.« less

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes producemore » chemically diverse, stable SOM. As a result, we show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.« less

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

NASA Astrophysics Data System (ADS)

Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart

2016-11-01

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls.

PubMed

Kallenbach, Cynthia M; Frey, Serita D; Grandy, A Stuart

2016-11-28

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.

Effects of short-term xylitol gum chewing on the oral microbiome.

PubMed

Söderling, Eva; ElSalhy, Mohamed; Honkala, Eino; Fontana, Margherita; Flannagan, Susan; Eckert, George; Kokaras, Alexis; Paster, Bruce; Tolvanen, Mimmi; Honkala, Sisko

2015-03-01

The aim of this study was to determine the effects of short-term xylitol gum chewing on the salivary microbiota of children. The study was a randomised, controlled, double-blind trial. Healthy children used xylitol chewing gum (xylitol group, n = 35) or sorbitol chewing gum (control group, n = 38) for 5 weeks. The daily dose of xylitol/sorbitol was approximately 6 g/day. At baseline and at the end of the test period, unstimulated and paraffin-stimulated saliva were collected. The microbial composition of the saliva was assessed using human oral microbe identification microarray (HOMIM). Mutans streptococci (MS) were plate cultured. As judged by HOMIM results, no xylitol-induced changes in the salivary microbiota took place in the xylitol group. In the control group, Veillonella atypica showed a significant decrease (p = 0.0001). The xylitol gum chewing decreased viable counts of MS in both stimulated (p = 0.006) and unstimulated (p = 0.002) saliva, but similar effects were also seen in the control group. The use of xylitol gum decreased MS, in general, but did not change the salivary microbial composition. Short-term consumption of xylitol had no impact on the composition of the salivary microbiota, but resulted in a decrease in the levels of MS.

Stunting Persists despite Optimal Feeding: Are Toilets Part of the Solution?

PubMed

Prendergast, Andrew J; Humphrey, Jean H

2015-01-01

Children in developing countries have an average length-for-age that is already below the World Health Organization standard at birth and show a further decline in linear growth over the first 24 months of life; however, complementary feeding interventions have only a modest impact on growth. Children living in conditions of poor sanitation and hygiene are frequently exposed to pathogenic microbes through feco-oral transmission. Acute diarrhea represents only the tip of the 'enteric disease iceberg', with a substantial underlying burden of chronic, subclinical enteropathy. Environmental enteric dysfunction (EED) is characterized by disturbance in small intestinal structure and impaired gut barrier function, enabling microbial translocation and chronic systemic inflammation, which may impair growth. Gut damage appears to arise early in infancy and markers of intestinal inflammation, intestinal permeability and systemic immune activation are inversely associated with linear growth. Reducing feco-oral microbial transmission by improving water, sanitation and hygiene (WASH) may theoretically prevent or ameliorate EED and improve linear growth; ongoing trials are exploring this hypothesis. Given the complex interplay of factors leading to stunting, multisectoral interventions are likely required. Improving WASH in addition to infant feeding may be one approach to improve the growth and developmental potential of infants in developing countries. © 2015 Nestec Ltd., Vevey/S. Karger AG, Basel.

Comparative effects of direct-fed microbials alone or with a trace minerals supplements on the productive performance, blood metabolites, and antioxidant status in grazing Awassi lambs.

PubMed

Alhidary, I A; Abdelrahman, M M; Khan, R U

2016-12-01

Twenty Awassi lambs were used to find the effects of direct-fed microbials (DFM) and long-acting trace minerals rumen bolus (TMB) supplements on performance, blood biochemical variables, and antioxidant status of the lambs under grazing conditions. The lambs were randomly distributed into four groups as follows: (1) untreated, (2) oral dose of 5 mL DFM, (3) TMB, or (4) oral dose of 5 mL DFM and TMB. The treatments were carried out for 90 days. Supplementation with TMB significantly increased (P < 0.05) average daily gain (ADG) and feed efficiency compared with the control. A significant (P < 0.05) increase in blood albumin in the DFM and a significant (P < 0.05) decrease in aspartate aminotrasferase were found in the lambs supplemented with TMB alone or in combination with DFM. Supplementing lambs with TMB resulted in higher glutathione peroxidase, total antioxidant capacity (P < 0.001) and activity of superoxide dismutase (P < 0.05) compared with no supplementation and supplementation with DFM only. In conclusion, TMB supplementation had a positive impact on performance traits and the antioxidant system of the lambs under grazing condition.

Health-based ingestion exposure guidelines for Vibrio cholerae: Technical basis for water reuse applications.

PubMed

Watson, Annetta P; Armstrong, Anthony Q; White, George H; Thran, Brandolyn H

2018-02-01

U.S. military and allied contingency operations are increasingly occurring in locations with limited, unstable or compromised fresh water supplies. Non-potable graywater reuse is currently under assessment as a viable means to increase mission sustainability while significantly reducing the resources, logistics and attack vulnerabilities posed by transport of fresh water. Development of health-based (non-potable) exposure guidelines for the potential microbial components of graywater would provide a logical and consistent human-health basis for water reuse strategies. Such health-based strategies will support not only improved water security for contingency operations, but also sustainable military operations. Dose-response assessment of Vibrio cholerae based on adult human oral exposure data were coupled with operational water exposure scenario parameters common to numerous military activities, and then used to derive health risk-based water concentrations. The microbial risk assessment approach utilized oral human exposure V. cholerae dose studies in open literature. Selected studies focused on gastrointestinal illness associated with experimental infection by specific V. cholerae serogroups most often associated with epidemics and pandemics (O1 and O139). Nonlinear dose-response model analyses estimated V. cholerae effective doses (EDs) aligned with gastrointestinal illness severity categories characterized by diarrheal purge volume. The EDs and water exposure assumptions were used to derive Risk-Based Water Concentrations (CFU/100mL) for mission-critical illness severity levels over a range of water use activities common to military operations. Human dose-response studies, data and analyses indicate that ingestion exposures at the estimated ED 1 (50CFU) are unlikely to be associated with diarrheal illness while ingestion exposures at the lower limit (200CFU) of the estimated ED 10 are not expected to result in a level of diarrheal illness associated with degraded individual capability. The current analysis indicates that the estimated ED 20 (approximately 1000CFU) represents initiation of a more advanced stage of diarrheal illness associated with clinical care. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

[Relationship of consequences of anastomotic insufficiency and bacterial flora of oral cavity in patients with esophageal and cardia cancer].

PubMed

Balázs, Ákos; Winkler, Beáta; Kristóf, Katalin; Harsányi, László; Bokor, Lívia

2017-01-01

In the course of anastomotic insufficiency following resection of esophageal cancers the bacterial compound of the esophageal substance has a remarkable, presumable role in the outcome of complications. The purpose of this study is to compare the consequences of the anastomotic leak with the bacterial flora of patients' oral cavity. In this prospective study a total of 131 patients were investigated directly before the surgical intervention taking a bacterial sample. Bacterial flora of patients' oral cavity was analysed; and the correlation between the consequences of the anastomotic leak and the content of the bacterial flora was examined. Pathogenic bacteria in the oral microflora in 50 cases (38.2%) was found. Statistically significant, moderate correlation was found between the severity of the complication and the incidence of pathogenic bacteria (r s = 0.553; p≤0.05). Pathogenic agent in the microbial flora might induce higher risk and more severe outcome in case of anastomotic leakage and it might be evaluated as a determinative factor. Consideration of the bacterial flora of the oral cavity requires more attention in the preoperative preparation than before and it demands the change of the current practice. Orv. Hetil., 2017, 158(1), 25-30.

In vitro gastric survival of commercially available probiotic strains and oral dosage forms.

PubMed

Caillard, Romain; Lapointe, Nicolas

2017-03-15

Although the intestinal microbial community is still incompletely understood, there is strong evidence of the benefits of using probiotics to address some medical states or conditions. As a result, the probiotics oral supplements market has exploded during the last few years. However, while their sensitivity to gastric juices, acidic pH and bile is well known, most of these oral forms would not guarantee any survival of the strains in such conditions. In this work, we have studied the resistance to simulated gastric juices of several commercially available probiotics products. These included sixteen strains and ten oral forms such as enteric/non-enteric capsules/tablets and microencapsulated strains. Results demonstrated that all tested strains showed high sensitivity to acidic conditions and suggested that most of these microorganisms would not show any viability when immersed in the stomach at fasting. Most probiotics oral forms did not provide any protection to strains, unless these forms presented strong enteric protection. Consequently, the efficacy of non-enteric products to fully provide to the patient the benefits related to the consumption of probiotics supplement would be strongly questionable. This study underlines the chasm between the current opinion about probiotics protection needs and the products proposed by many companies in the dietary supplements area. Copyright © 2017 Elsevier B.V. All rights reserved.

A Workflow to Model Microbial Loadings in Watersheds (proceedings)

EPA Science Inventory

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

Microbiota-dependent crosstalk between macrophages and ILC3 promotes intestinal homeostasis.

PubMed

Mortha, Arthur; Chudnovskiy, Aleksey; Hashimoto, Daigo; Bogunovic, Milena; Spencer, Sean P; Belkaid, Yasmine; Merad, Miriam

2014-03-28

The intestinal microbiota and tissue-resident myeloid cells promote immune responses that maintain intestinal homeostasis in the host. However, the cellular cues that translate microbial signals into intestinal homeostasis remain unclear. Here, we show that deficient granulocyte-macrophage colony-stimulating factor (GM-CSF) production altered mononuclear phagocyte effector functions and led to reduced regulatory T cell (T(reg)) numbers and impaired oral tolerance. We observed that RORγt(+) innate lymphoid cells (ILCs) are the primary source of GM-CSF in the gut and that ILC-driven GM-CSF production was dependent on the ability of macrophages to sense microbial signals and produce interleukin-1β. Our findings reveal that commensal microbes promote a crosstalk between innate myeloid and lymphoid cells that leads to immune homeostasis in the intestine.

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

Calibration and analysis of genome-based models for microbial ecology.

PubMed

Louca, Stilianos; Doebeli, Michael

2015-10-16

Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.

Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism.

PubMed

Hoek, Milan J A van; Merks, Roeland M H

2017-05-16

The human gut contains approximately 10 14 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short chain fatty acids and additional metabolites, e.g., vitamin K. Microbial diversity is important for colonic health: Changes in the composition of the microbiota have been associated with inflammatory bowel disease, diabetes, obesity and Crohn's disease, and make the microbiota more vulnerable to infestation by harmful species, e.g., Clostridium difficile. To get a grip on the controlling factors of microbial diversity in the gut, we here propose a multi-scale, spatiotemporal dynamic flux-balance analysis model to study the emergence of metabolic diversity in a spatial gut-like, tubular environment. The model features genome-scale metabolic models (GEM) of microbial populations, resource sharing via extracellular metabolites, and spatial population dynamics and evolution. In this model, cross-feeding interactions emerge readily, despite the species' ability to metabolize sugars autonomously. Interestingly, the community requires cross-feeding for producing a realistic set of short-chain fatty acids from an input of glucose, If we let the composition of the microbial subpopulations change during invasion of adjacent space, a complex and stratified microbiota evolves, with subspecies specializing on cross-feeding interactions via a mechanism of compensated trait loss. The microbial diversity and stratification collapse if the flux through the gut is enhanced to mimic diarrhea. In conclusion, this in silico model is a helpful tool in systems biology to predict and explain the controlling factors of microbial diversity in the gut. It can be extended to include, e.g., complex nutrient sources, and host-microbiota interactions via the intestinal wall.

Development and evaluation of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

NASA Astrophysics Data System (ADS)

Hong, Eun-Mi; Park, Yongeun; Muirhead, Richard; Pachepsky, Yakov

2017-04-01

Pathogenic microorganisms in recreational and irrigation waters remain the subject of concern. Water quality models are used to estimate microbial quality of water sources, to evaluate microbial contamination-related risks, to guide the microbial water quality monitoring, and to evaluate the effect of agricultural management on the microbial water quality. The Agricultural Policy/Environmental eXtender (APEX) is the watershed-scale water quality model that includes highly detailed representation of agricultural management. The APEX currently does not have microbial fate and transport simulation capabilities. The objective of this work was to develop the first APEX microbial fate and transport module that could use the APEX conceptual model of manure removal together with recently introduced conceptualizations of the in-stream microbial fate and transport. The module utilizes manure erosion rates found in the APEX. The total number of removed bacteria was set to the concentrations of bacteria in soil-manure mixing layer and eroded manure amount. Bacteria survival in soil-manure mixing layer was simulated with the two-stage survival model. Individual survival patterns were simulated for each manure application date. Simulated in-stream microbial fate and transport processes included the reach-scale passive release of bacteria with resuspended bottom sediment during high flow events, the transport of bacteria from bottom sediment due to the hyporheic exchange during low flow periods, the deposition with settling sediment, and the two-stage survival. Default parameter values were available from recently published databases. The APEX model with the newly developed microbial fate and transport module was applied to simulate seven years of monitoring data for the Toenepi watershed in New Zealand. The stream network of the watershed ran through grazing lands with the daily bovine waste deposition. Based on calibration and testing results, the APEX with the microbe module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water under various agricultural practices (grazing, cropping, and manure application), evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations. Future development should include modeling contributions of wildlife, manure weathering, and weather effects on manure-borne microorganism survival and release.

Mouse Models for Studying Oral Cancer: Impact in the Era of Cancer Immunotherapy.

PubMed

Luo, J J; Young, C D; Zhou, H M; Wang, X J

2018-04-01

Model systems for oral cancer research have progressed from tumor epithelial cell cultures to in vivo systems that mimic oral cancer genetics, pathological characteristics, and tumor-stroma interactions of oral cancer patients. In the era of cancer immunotherapy, it is imperative to use model systems to test oral cancer prevention and therapeutic interventions in the presence of an immune system and to discover mechanisms of stromal contributions to oral cancer carcinogenesis. Here, we review in vivo mouse model systems commonly used for studying oral cancer and discuss the impact these models are having in advancing basic mechanisms, chemoprevention, and therapeutic intervention of oral cancer while highlighting recent discoveries concerning the role of immune cells in oral cancer. Improvements to in vivo model systems that highly recapitulate human oral cancer hold the key to identifying features of oral cancer initiation, progression, and invasion as well as molecular and cellular targets for prevention, therapeutic response, and immunotherapy development.

Quantitative Microbial Risk Assessment Tutorial: Installation of Software for Watershed Modeling in Support of QMRA

EPA Science Inventory

This tutorial provides instructions for accessing, retrieving, and downloading the following software to install on a host computer in support of Quantitative Microbial Risk Assessment (QMRA) modeling:• SDMProjectBuilder (which includes the Microbial Source Module as part...

Evaluation of tissue engineered models of the oral mucosa to investigate oral candidiasis.

PubMed

Yadev, Nishant P; Murdoch, Craig; Saville, Stephen P; Thornhill, Martin H

2011-06-01

Candida albicans is a commensal organism that can be isolated from the majority of healthy individuals. However, in certain susceptible individuals C. albicans can become pathogenic leading to the mucocutaneous infection; oral candidiasis. Murine models and in vitro monolayer cultures have generated some data on the likely virulence and host factors that contribute to oral candidiasis but these models have limitations. Recently, tissue engineered oral mucosal models have been developed to mimic the normal oral mucosa but little information is available on their true representation. In this study, we assessed the histological features of three different tissue engineered oral mucosal models compared to the normal oral mucosa and analysed both cell damage and cytokine release following infection with C. albicans. Models comprised of normal oral keratinocytes and a fibroblast-containing matrix displayed more similar immunohistological and proliferation characteristics to normal mucosa, compared to models composed of an oral carcinoma cell line. Although all models were invaded and damaged by C. albicans in a similar manner, the cytokine response was much more pronounced in models containing normal keratinocytes. These data suggest that models based on normal keratinocytes atop a fibroblast-containing connective tissue will significantly aid in dissecting the molecular pathogenesis of oral candidiasis. Copyright © 2011 Elsevier Ltd. All rights reserved.

Synergism between Trichuris suis and the microbial flora of the large intestine causing dysentery in pigs.

PubMed

Rutter, J M; Beer, R J

1975-02-01

The role of the microbial flora of the large intestine in experimental Trichuris suis infection was studied by comparing the clinical syndrome in conventionally reared (CR) pigs, specific pathogen-free pigs, and gnotobiotic pigs. Thedisease in CR pigs was characterized by a severe mucohemorrhagic enteritis; in contrast, a mild catarrhal enteritis was observed in specific pathogen-free and gnotobiotic pigs. Spirochaetes and vibrio-like organisms were observed only in CR pigs and increased during the clinical phase of the disease. The clinical syndrome was not transmitted by oral administration of intestinal or fecal material from infected CR pigs to CR pigs free of T. suis. Smaller numbers of T. suis produced diarrhea in CR pigs and significantly reduced the growth rates of infected animals; clinical signs and the reduction in growth rate was prevented by incorporating an antibacterial substance (dimetridazole) in the food. Although clinical trichuriasis closely resembles swin dysentery, the two syndromes seem to be distinct. The present results suggest that a microbial component acts synergistically with T. suis to produce the severe clinical syndrome in CR pigs, but identification of the microbial component and the mechanism by which clinical signs are produced await further studies of the bacterial flora of the large intestine of pigs.

Priming effect and microbial diversity in ecosystem functioning and response to global change: a modeling approach using the SYMPHONY model.

PubMed

Perveen, Nazia; Barot, Sébastien; Alvarez, Gaël; Klumpp, Katja; Martin, Raphael; Rapaport, Alain; Herfurth, Damien; Louault, Frédérique; Fontaine, Sébastien

2014-04-01

Integration of the priming effect (PE) in ecosystem models is crucial to better predict the consequences of global change on ecosystem carbon (C) dynamics and its feedbacks on climate. Over the last decade, many attempts have been made to model PE in soil. However, PE has not yet been incorporated into any ecosystem models. Here, we build plant/soil models to explore how PE and microbial diversity influence soil/plant interactions and ecosystem C and nitrogen (N) dynamics in response to global change (elevated CO2 and atmospheric N depositions). Our results show that plant persistence, soil organic matter (SOM) accumulation, and low N leaching in undisturbed ecosystems relies on a fine adjustment of microbial N mineralization to plant N uptake. This adjustment can be modeled in the SYMPHONY model by considering the destruction of SOM through PE, and the interactions between two microbial functional groups: SOM decomposers and SOM builders. After estimation of parameters, SYMPHONY provided realistic predictions on forage production, soil C storage and N leaching for a permanent grassland. Consistent with recent observations, SYMPHONY predicted a CO2 -induced modification of soil microbial communities leading to an intensification of SOM mineralization and a decrease in the soil C stock. SYMPHONY also indicated that atmospheric N deposition may promote SOM accumulation via changes in the structure and metabolic activities of microbial communities. Collectively, these results suggest that the PE and functional role of microbial diversity may be incorporated in ecosystem models with a few additional parameters, improving accuracy of predictions. © 2013 John Wiley & Sons Ltd.

Clonality of bacterial consortia in root canals and subjacent gingival crevices.

PubMed

Parahitiyawa, Nipuna B; Chu, Frederick C S; Leung, Wai K; Yam, Wing C; Jin, Li Jian; Samaranayake, Lakshman P

2015-02-01

No oral niche can be considered to be segregated from the subjacent milieu because of the complex community behavior and nature of the oral biofilms. The aim of this study was to address the paucity of information on how these species are clonally related to the subjacent gingival crevice bacteria. We utilized a metagenomic approach of amplifying 16S rDNA from genomic DNA, cloning, sequencing and analysis using LIBSHUFF software to assess the genetic homogeneity of the bacterial species from two infected root canals and subjacent gingival crevices. The four niches studied yielded 186 clones representing 54 phylotypes. Clone library comparisons using LIBSHUFF software indicated that each niche was inhabited by a unique flora. Further, 42% of the clones were of hitherto unknown phylotypes indicating the extent of bacterial diversity, especially in infected root canals and subjacent gingival crevices. We believe data generated through this novel analytical tool shed new light on understanding oral microbial ecosystems. © 2014 Wiley Publishing Asia Pty Ltd.

Bioadhesive, rheological, lubricant and other aspects of an oral gel formulation intended for the treatment of xerostomia.

PubMed

Kelly, H M; Deasy, P B; Busquet, M; Torrance, A A

2004-07-08

Xerostomia is commonly known as 'dry mouth' and is characterised by a reduction or loss in salivary production. A bioadhesive gel for its localised treatment was formulated to help enhance the residence time of the product, based on the polymer Carbopol 974P. The bioadhesion of various formulations was evaluated on different mucosal substrates, as simulations of the oral mucosa of xerostomic patients. Depending on the type of model substrate used, the mechanism of bioadhesion could alter. When the rheology of various formulations was examined, changes in bioadhesion were more easily interpreted, as the presence of other excipients caused an alteration in the rheological profile, with a change from a fully expanded and partially cross-linked system to an entangled system. Improving the lubricity of the product was considered important, with optimum incorporation of vegetable oil causing a desirable lowering of the observed friction of the product. The final complex formulation developed also contained salivary levels of electrolytes to help remineralisation of teeth, fluoride to prevent caries, zinc to enhance taste sensation, triclosan as the main anti-microbial/anti-inflammatory agent and non-cariogenic sweeteners with lemon flavour to increase the palatability of the product while stimulating any residual salivary function.

Quantifying oral inflammatory load: oral neutrophil counts in periodontal health and disease.

PubMed

Landzberg, M; Doering, H; Aboodi, G M; Tenenbaum, H C; Glogauer, M

2015-06-01

Neutrophils are the primary white blood cells that are recruited to fight the initial phases of microbial infections. While healthy norms have been determined for circulating blood neutrophil counts in order to identify patients with suspected systemic infections, the levels of oral neutrophils (oPMNs) in oral health and in the presence of periodontal diseases have not been described. It is important to address this deficiency in our knowledge as neutrophils are the primary immune cell present in the crevicular fluid and oral environment and previous work has suggested that they may be good indicators of overall oral inflammation and periodontal disease severity. The objective of this study was to measure oPMN counts obtained in a standardized oral rinse from healthy patients and from those with chronic periodontal disease in order to determine if oPMN levels have clinical relevance as markers of periodontal inflammation. A parallel goal of this investigation was to introduce the concept of 'oral inflammatory load', which constitutes the inflammatory burden experienced by the body as a consequence of oral inflammatory disease. Periodontal examinations of patients with a healthy periodontium and chronic periodontal disease were performed (n = 124). Two standardized consecutive saline rinses of 30 s each were collected before patient examination and instrumentation. Neutrophils were quantified in the rinse samples and correlated with the clinical parameters and periodontal diagnosis. Average oPMN counts were determined for healthy patients and for those with mild, moderate and severe chronic periodontal diseases. A statistically significant correlation was found between oPMN counts and deep periodontal probing, sites with bleeding on probing and overall severity of periodontal disease. oPMN counts obtained through a 30-s oral rinse are a good marker of oral inflammatory load and correlate with measures of periodontal disease severity. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

PubMed

Budinich, Marko; Bourdon, Jérémie; Larhlimi, Abdelhalim; Eveillard, Damien

2017-01-01

Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.

Using DGGE and 16S rRNA gene sequence analysis to evaluate changes in oral bacterial composition.

PubMed

Chen, Zhou; Trivedi, Harsh M; Chhun, Nok; Barnes, Virginia M; Saxena, Deepak; Xu, Tao; Li, Yihong

2011-01-01

To investigate whether a standard dental prophylaxis followed by tooth brushing with an antibacterial dentifrice will affect the oral bacterial community, as determined by denaturing gradient gel electrophoresis (DGGE) combined with 16S rRNA gene sequence analysis. Twenty-four healthy adults were instructed to brush their teeth using commercial dentifrice for 1 week during a washout period. An initial set of pooled supragingival plaque samples was collected from each participant at baseline (0 h) before prophylaxis treatment. The subjects were given a clinical examination and dental prophylaxis and asked to brush for 1 min with a dentifrice containing 0.3% triclosan, 2.0% PVM/MA copolymer and 0.243% sodium fluoride (Colgate Total). On the following day, a second set of pooled supragingival plaque samples (24 h) was collected. Total bacterial genomic DNA was isolated from the samples. Differences in the microbial composition before and after the prophylactic procedure and tooth brushing were assessed by comparing the DGGE profiles and 16S rRNA gene segments sequence analysis. Two distinct clusters of DGGE profiles were found, suggesting that a shift in the microbial composition had occurred 24 h after the prophylaxis and brushing. A detailed sequencing analysis of 16S rRNA gene segments further identified 6 phyla and 29 genera, including known and unknown bacterial species. Importantly, an increase in bacterial diversity was observed after 24 h, including members of the Streptococcaceae family, Prevotella, Corynebacterium, TM7 and other commensal bacteria. The results suggest that the use of a standard prophylaxis followed by the use of the dentifrice containing 0.3% triclosan, 2.0% PVM/MA copolymer and 0.243% sodium fluoride may promote a healthier composition within the oral bacterial community.

Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus.

PubMed

Wang, Jinfeng; Zheng, Jiayong; Shi, Wenyu; Du, Nan; Xu, Xiaomin; Zhang, Yanming; Ji, Peifeng; Zhang, Fengyi; Jia, Zhen; Wang, Yeping; Zheng, Zhi; Zhang, Hongping; Zhao, Fangqing

2018-05-14

The initial colonisation of the human microbiota and the impact of maternal health on neonatal microbiota at birth remain largely unknown. The aim of our study is to investigate the possible dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus (GDM) and to estimate the potential risks of the microbial shift to neonates. Pregnant women and neonates suffering from GDM were enrolled and 581 maternal (oral, intestinal and vaginal) and 248 neonatal (oral, pharyngeal, meconium and amniotic fluid) samples were collected. To avoid vaginal bacteria contaminations, the included neonates were predominantly delivered by C-section, with their samples collected within seconds of delivery. Numerous and diverse bacterial taxa were identified from the neonatal samples, and the samples from different neonatal body sites were grouped into distinct clusters. The microbiota of pregnant women and neonates was remarkably altered in GDM, with a strong correlation between certain discriminatory bacteria and the oral glucose tolerance test. Microbes varying by the same trend across the maternal and neonatal microbiota were observed, revealing the intergenerational concordance of microbial variation associated with GDM. Furthermore, lower evenness but more depletion of KEGG orthologues and higher abundance of some viruses (eg, herpesvirus and mastadenovirus) were observed in the meconium microbiota of neonates associated with GDM. GDM can alter the microbiota of both pregnant women and neonates at birth, which sheds light on another form of inheritance and highlights the importance of understanding the formation of early-life microbiome. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Stability of Cyclophosphamide in Extemporaneous Oral Suspensions

PubMed Central

Kennedy, Rachel; Groepper, Daniel; Tagen, Michael; Christensen, Robbin; Navid, Fariba; Gajjar, Amar; Stewart, Clinton F.

2010-01-01

Background Cyclophosphamide, an alkylating agent, is widely used for the treatment of many adult and pediatric malignancies. The stability of cyclophosphamide in aqueous- and methylcellulose-based oral suspending vehicles is currently unknown. Objectives The goals of this study were (1) to develop and validate a stability-indicating HPLC method to measure cyclophosphamide concentrations in simple syrup and Ora-Plus, and (2) to assess the 56-day chemical stability and physical appearance of cyclophosphamide in these suspensions at both room temperature and 4°C. Methods The i.v. formulation of cyclophosphamide was diluted to 20 mg/mL in normal saline, compounded 1:1 with either suspending vehicle, and stored in the dark in 3mL amber polypropylene oral syringes at 4°C and 22°C. Aliquots from each syringe were obtained on days 0, 3, 7, 14, 21, 28, 35, 42, 49, and 56 and assayed using the validated stability-indicating HPLC-UV method. A C18 analytical column was used to separate cyclophosphamide from the internal standard, ifosfamide, with a mobile phase of 21% acetonitrile in 79% sodium phosphate buffer. The suspension was examined for odor change, visually examined under normal fluorescent light for color change, and examined under a light microscope for evidence of microbial growth. Results Samples of cyclophosphamide in both simple syrup and Ora-Plus were stable when kept at 4°C for at least 56 days. At room temperature, cyclophosphamide in simple syrup and Ora-Plus had a shelf life of 8 and 3 days, respectively. No changes in color or odor or evidence of microbial growth were observed. Conclusion Cyclophosphamide can be extemporaneously prepared in simple syrup or Ora-Plus and stored at least 2 months under refrigeration without significant degradation. PMID:20103616

Stability of cyclophosphamide in extemporaneous oral suspensions.

PubMed

Kennedy, Rachel; Groepper, Daniel; Tagen, Michael; Christensen, Robbin; Navid, Fariba; Gajjar, Amar; Stewart, Clinton F

2010-02-01

Cyclophosphamide, an alkylating agent, is widely used for the treatment of many adult and pediatric malignancies. The stability of cyclophosphamide in aqueous- and methylcellulose-based oral suspending vehicles is currently unknown. To develop and validate a stability-indicating high-performance liquid chromatography (HPLC) method to measure cyclophosphamide concentrations in simple syrup and Ora-Plus, and assess the 56-day chemical stability and physical appearance of cyclophosphamide in these suspensions at both room temperature (22 degrees C) and 4 degrees C. The intravenous formulation of cyclophosphamide was diluted to 20 mg/mL in NaCl 0.9%, compounded 1:1 with either suspending vehicle, and stored in the dark in 3-mL amber polypropylene oral syringes at 4 degrees C and 22 degrees C. Aliquots from each syringe were obtained on days 0, 3, 7, 14, 21, 28, 35, 42, 49, and 56 and assayed using the validated stability-indicating HPLC-UV method. A C18 analytical column was used to separate cyclophosphamide from the internal standard, ifosfamide, with a mobile phase of 21% acetonitrile in 79% sodium phosphate buffer. The suspension was examined for odor change, visually examined under normal fluorescent light for color change, and examined under a light microscope for evidence of microbial growth. Samples of cyclophosphamide in both simple syrup and Ora-Plus were stable when kept at 4 degrees C for at least 56 days. At room temperature, cyclophosphamide in simple syrup and Ora-Plus had a shelf life of 8 and 3 days, respectively. No changes in color or odor or evidence of microbial growth were observed. Cyclophosphamide can be extemporaneously prepared in simple syrup or Ora-Plus and stored for at least 2 months under refrigeration without significant degradation.

Prevalence of dental caries among school children of Bharatpur city, India.

PubMed

Ingle, Navin Anand; Dubey, Harsh Vardhan; Kaur, Navpreet; Gupta, Rahul

2014-01-01

Healthy teeth and oral tissues and the need for oral health care are important for any section of society. Dental caries is an infectious microbial disease of multifactorial origin in which diet, host, and microbial flora interacts over a period of time in such a way so as to encourage demineralization of the tooth enamel with resultant caries formation. Dental caries, the product of man's progress towards civilization, has a very high morbidity potential and thus, is coming into focus of the mankind. To assess the prevalence of dental caries among 12-15 year old government and private school children of Bharatpur city. This was a cross-sectional study carried out on total 1400 school children, of which 700 school children were from government schools and 700 were from private schools. Simple random sampling methodology was used to select the sample. The subjects were examined for dental caries according to WHO 1997 assessment form. Significant Caries Index was also used to assess the prevalence of dental caries. The prevalence of dental caries was found higher among government school children, that is, 53%, when compared to private school children, that is, 47% and this difference was found to be statistically significant. The mean decayed, missing, and filled teeth were found to be higher in government school children (7.61 ± 2.86) as compared to private school children (4.76 ± 2.42). Dental caries was found to be the major public health problems among both the government and private school children of Bharatpur city, which need immediate attention. Regular dental checkups and practice of routine oral hygiene procedures will enable them to lead a healthier life.

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

PubMed Central

Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

2014-01-01

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material. PMID:24705618

Oral Microbiome of Deep and Shallow Dental Pockets In Chronic Periodontitis

PubMed Central

Ge, Xiuchun; Rodriguez, Rafael; Trinh, My; Gunsolley, John; Xu, Ping

2013-01-01

We examined the subgingival bacterial biodiversity in untreated chronic periodontitis patients by sequencing 16S rRNA genes. The primary purpose of the study was to compare the oral microbiome in deep (diseased) and shallow (healthy) sites. A secondary purpose was to evaluate the influences of smoking, race and dental caries on this relationship. A total of 88 subjects from two clinics were recruited. Paired subgingival plaque samples were taken from each subject, one from a probing site depth >5 mm (deep site) and the other from a probing site depth ≤3mm (shallow site). A universal primer set was designed to amplify the V4–V6 region for oral microbial 16S rRNA sequences. Differences in genera and species attributable to deep and shallow sites were determined by statistical analysis using a two-part model and false discovery rate. Fifty-one of 170 genera and 200 of 746 species were found significantly different in abundances between shallow and deep sites. Besides previously identified periodontal disease-associated bacterial species, additional species were found markedly changed in diseased sites. Cluster analysis revealed that the microbiome difference between deep and shallow sites was influenced by patient-level effects such as clinic location, race and smoking. The differences between clinic locations may be influenced by racial distribution, in that all of the African Americans subjects were seen at the same clinic. Our results suggested that there were influences from the microbiome for caries and periodontal disease and these influences are independent. PMID:23762384

Modelling microbial exchanges between forms of soil nitrogen in contrasting ecosystems

NASA Astrophysics Data System (ADS)

Pansu, M.; Machado, D.; Bottner, P.; Sarmiento, L.

2014-02-01

Although nitrogen (N) is often combined with carbon (C) in organic molecules, C passes from the air to the soil through plant photosynthesis, whereas N passes from the soil to plants through a chain of microbial conversions. However, dynamic models do not fully consider the microorganisms at the centre of exchange processes between organic and mineral forms of N. This study monitored the transfer of 14C and 15N between plant materials, microorganisms, humified compartments, and inorganic forms in six very different ecosystems along an altitudinal transect. The microbial conversions of the 15N forms appear to be strongly linked to the previously modelled C cycle, and the same equations and parameters can be used to model both C and N cycles. The only difference is in the modelling of the flows between microbial and inorganic forms. The processes of mineralization and immobilization of N appear to be regulated by a two-way microbial exchange depending on the C : N ratios of microorganisms and available substrates. The MOMOS (Modelling of Organic Matter of Soils) model has already been validated for the C cycle and also appears to be valid for the prediction of microbial transformations of N forms. This study shows that the hypothesis of microbial homeostasis can give robust predictions at global scale. However, the microbial populations did not appear to always be independent of the external constraints. At some altitudes their C : N ratio could be better modelled as decreasing during incubation and increasing with increasing C storage in cold conditions. The ratio of potentially mineralizable-15N/inorganic-15N and the 15N stock in the plant debris and the microorganisms was modelled as increasing with altitude, whereas the 15N storage in stable humus was modelled as decreasing with altitude. This predicts that there is a risk that mineralization of organic reserves in cold areas may increase global warming.

Microbial biofilms are able to destroy hydroxyapatite in the absence of host immunity in vitro.

PubMed

Junka, Adam Feliks; Szymczyk, Patrycja; Smutnicka, Danuta; Kos, Marcin; Smolina, Iryna; Bartoszewicz, Marzenna; Chlebus, Edward; Turniak, Michal; Sedghizadeh, Parish P

2015-03-01

It is widely thought that inflammation and osteoclastogenesis result in hydroxyapatite (HA) resorption and sequestrum formation during osseous infections, and microbial biofilm pathogens induce the inflammatory destruction of HA. We hypothesized that biofilms associated with infectious bone disease can directly resorb HA in the absence of host inflammation or osteoclastogenesis. Therefore we developed an in vitro model to test this hypothesis. Customized HA discs were manufactured as a substrate for growing clinically relevant biofilm pathogens. Single-species biofilms of Streptococcus mutans, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans and mixed-species biofilms of C albicans plus S mutans were incubated on HA discs for 72 hours to grow mature biofilms. Three different non-biofilm control groups also were established for testing. HA discs were then evaluated by means of scanning electron microscopy, micro-computed tomography metrotomography, x-ray spectroscopy, and confocal microscopy with planimetric analysis. In addition, quantitative cultures and pH assessment were performed. Analysis of variance was used to test for significance between treatment and control groups. All investigated biofilms were able to cause significant (P < .05) and morphologically characteristic alterations in HA structure as compared with controls. The highest number of alterations observed was caused by mixed biofilms of C albicans plus S mutans. S mutans biofilm incubated in medium with additional sucrose content was the most detrimental to HA surfaces among single-species biofilms. Our findings suggest that direct microbial resorption of bone is possible in addition to immune-mediated destruction, which has important translational implications for the pathogenesis of chronic bone infections and for targeted antimicrobial therapeutics. Copyright © 2015 American Association of Oral and Maxillofacial Surgeons. All rights reserved.

Photodynamic therapy for localized infections – state of the art

PubMed Central

Dai, Tianhong; Huang, Ying-Ying; Hamblin, Michael R

2009-01-01

Photodynamic therapy (PDT) was discovered over one hundred years ago by observing the killing of microorganisms when harmless dyes and visible light were combined in vitro. Since then it has primarily been developed as a treatment for cancer, ophthalmologic disorders and in dermatology. However in recent years interest in the antimicrobial effects of PDT has revived and it has been proposed as a therapy for a large variety of localized infections. This revival of interest has largely been driven by the inexorable increase in drug resistance amongst many classes of pathogen. Advantages of PDT include equal killing effectiveness regardless of antibiotic resistance, and a lack of induction of PDT resistance. Disadvantages include the cessation of the antimicrobial effect when the light is turned off, and less than perfect selectivity for microbial cells over host tissue. This review will cover the use of PDT to kill or inactivate pathogens in ex vivo tissues and in biological materials such as blood. PDT has been successfully used to kill pathogens and even to save life in several animal models of localized infections such as surface wounds, burns, oral sites, abscesses and the middle ear. A large number of clinical studies of PDT for viral papillomatosis lesions and for acne refer to its anti-microbial effect, but it is unclear how important this microbial killing is to the overall therapeutic outcome. PDT for periodontitis is a rapidly growing clinical application and other dental applications are under investigation. PDT is being clinically studied for other dermatological infections such as leishmaniasis and mycobacteria. Antimicrobial PDT will become more important in the future as antibiotic resistance is only expected to continue to increase. PMID:19932449

Quantitative Microbial Risk Assessment Tutorial Installation of Software for Watershed Modeling in Support of QMRA - Updated 2017

EPA Science Inventory

This tutorial provides instructions for accessing, retrieving, and downloading the following software to install on a host computer in support of Quantitative Microbial Risk Assessment (QMRA) modeling: • QMRA Installation • SDMProjectBuilder (which includes the Microbial ...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wieder, William R.; Allison, Steven D.; Davidson, Eric A.

Microbes influence soil organic matter (SOM) decomposition and the long-term stabilization of carbon (C) in soils. We contend that by revising the representation of microbial processes and their interactions with the physicochemical soil environment, Earth system models (ESMs) may make more realistic global C cycle projections. Explicit representation of microbial processes presents considerable challenges due to the scale at which these processes occur. Thus, applying microbial theory in ESMs requires a framework to link micro-scale process-level understanding and measurements to macro-scale models used to make decadal- to century-long projections. Here, we review the diversity, advantages, and pitfalls of simulating soilmore » biogeochemical cycles using microbial-explicit modeling approaches. We present a roadmap for how to begin building, applying, and evaluating reliable microbial-explicit model formulations that can be applied in ESMs. Drawing from experience with traditional decomposition models we suggest: (1) guidelines for common model parameters and output that can facilitate future model intercomparisons; (2) development of benchmarking and model-data integration frameworks that can be used to effectively guide, inform, and evaluate model parameterizations with data from well-curated repositories; and (3) the application of scaling methods to integrate microbial-explicit soil biogeochemistry modules within ESMs. With contributions across scientific disciplines, we feel this roadmap can advance our fundamental understanding of soil biogeochemical dynamics and more realistically project likely soil C response to environmental change at global scales.« less

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

NASA Astrophysics Data System (ADS)

Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

2015-10-01

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

HIV Infection and Compromised Mucosal Immunity: Oral Manifestations and Systemic Inflammation

PubMed Central

Heron, Samantha E.; Elahi, Shokrollah

2017-01-01

Mucosal surfaces account for the vast majority of HIV transmission. In adults, HIV transmission occurs mainly by vaginal and rectal routes but rarely via oral route. By contrast, pediatric HIV infections could be as the result of oral route by breastfeeding. As such mucosal surfaces play a crucial role in HIV acquisition, and spread of the virus depends on its ability to cross a mucosal barrier. HIV selectively infects, depletes, and/or dysregulates multiple arms of the human immune system particularly at the mucosal sites and causes substantial irreversible damage to the mucosal barriers. This leads to microbial products translocation and subsequently hyper-immune activation. Although introduction of antiretroviral therapy (ART) has led to significant reduction in morbidity and mortality of HIV-infected patients, viral replication persists. As a result, antigen presence and immune activation are linked to “inflammaging” that attributes to a pro-inflammatory environment and the accelerated aging process in HIV patients. HIV infection is also associated with the prevalence of oral mucosal infections and dysregulation of oral microbiota, both of which may compromise the oral mucosal immunity of HIV-infected individuals. In addition, impaired oral immunity in HIV infection may predispose the patients to periodontal diseases that are associated with systemic inflammation and increased risk of cardiovascular diseases. The purpose of this review is to examine existing evidence regarding the role of innate and cellular components of the oral cavity in HIV infection and how HIV infection may drive systemic hyper-immune activation in these patients. We will also discuss current knowledge on HIV oral transmission, HIV immunosenescence in relation to the oral mucosal alterations during the course of HIV infection and periodontal disease. Finally, we discuss oral manifestations associated with HIV infection and how HIV infection and ART influence the oral microbiome. Therefore, unraveling how HIV compromises the integrity of the oral mucosal tissues and innate immune components of the oral cavity and its association with induction of chronic inflammation are critical for the development of effective preventive interventions and therapeutic strategies. PMID:28326084

HIV Infection and Compromised Mucosal Immunity: Oral Manifestations and Systemic Inflammation.

PubMed

Heron, Samantha E; Elahi, Shokrollah

2017-01-01

Mucosal surfaces account for the vast majority of HIV transmission. In adults, HIV transmission occurs mainly by vaginal and rectal routes but rarely via oral route. By contrast, pediatric HIV infections could be as the result of oral route by breastfeeding. As such mucosal surfaces play a crucial role in HIV acquisition, and spread of the virus depends on its ability to cross a mucosal barrier. HIV selectively infects, depletes, and/or dysregulates multiple arms of the human immune system particularly at the mucosal sites and causes substantial irreversible damage to the mucosal barriers. This leads to microbial products translocation and subsequently hyper-immune activation. Although introduction of antiretroviral therapy (ART) has led to significant reduction in morbidity and mortality of HIV-infected patients, viral replication persists. As a result, antigen presence and immune activation are linked to "inflammaging" that attributes to a pro-inflammatory environment and the accelerated aging process in HIV patients. HIV infection is also associated with the prevalence of oral mucosal infections and dysregulation of oral microbiota, both of which may compromise the oral mucosal immunity of HIV-infected individuals. In addition, impaired oral immunity in HIV infection may predispose the patients to periodontal diseases that are associated with systemic inflammation and increased risk of cardiovascular diseases. The purpose of this review is to examine existing evidence regarding the role of innate and cellular components of the oral cavity in HIV infection and how HIV infection may drive systemic hyper-immune activation in these patients. We will also discuss current knowledge on HIV oral transmission, HIV immunosenescence in relation to the oral mucosal alterations during the course of HIV infection and periodontal disease. Finally, we discuss oral manifestations associated with HIV infection and how HIV infection and ART influence the oral microbiome. Therefore, unraveling how HIV compromises the integrity of the oral mucosal tissues and innate immune components of the oral cavity and its association with induction of chronic inflammation are critical for the development of effective preventive interventions and therapeutic strategies.

[Study on Microbial Diversity of Peri-implantitis Subgingival by High-throughput Sequencing].

PubMed

Li, Zhi-jie; Wang, Shao-guo; Li, Yue-hong; Tu, Dong-xiang; Liu, Shi-yun; Nie, Hong-bing; Li, Zhi-qiang; Zhang, Ju-mei

2015-07-01

To study microbial diversity of peri-implantitis subgingival with high-throughput sequencing, and investigate microbiological etiology of peri-implantitis. Subgingival plaques were sampled from the patients with peri-implantitis (D group) and non-peri-implantitis subjects (N group). The microbiological diversity of the subgingival plaques was detected by sequencing V4 region of 16S rRNA with Illumina Miseq platform. The diversity of the community structure was analyzed using Mothur software. A total of 156 507 gene sequences were detected in nine samples and 4 402 operational taxonomic units (OTUs) were found. Selenomonas, Pseudomonas, and Fusobacterium were dominant bacteria in D group, while Fusobacterium, Veillonella and Streptococcus were dominant bacteria in N group. Differences between peri-implantitis and non-peri-implantitis bacterial communities were observed at all phylogenetic levels by LEfSe, which was also found in PcoA test. The occurrence of peri-implantitis is not only related to periodontitis pathogenic microbe, but also related with the changes of oral microbial community structure. Treponema, Herbaspirillum, Butyricimonas and Phaeobacte may be closely related to the occurrence and development of peri-implantitis.

Multispecies Biofilms and Host Responses: “Discriminating the Trees from the Forest”

PubMed Central

Peyyala, R.; Ebersole, J.L.

2014-01-01

Periodontal diseases reflect a tissue destructive process of the hard and soft tissues of the periodontium that are initiated by the accumulation of multispecies bacterial biofilms in the subgingival sulcus. This accumulation, in both quantity and quality of bacteria, results in a chronic immunoinflammatory response of the host to control this noxious challenge, leading to collateral damage of the tissues. As knowledge of the characteristics of the host-bacterial interactions in the oral cavity has expanded, new knowledge has become available on the complexity of the microbial challenge and the repertoire of host responses to this challenge. Recent results from the Human Microbiome Project continue to extend the array of taxa, genera, and species of bacteria that inhabit the multiple niches in the oral cavity; however, there is rather sparse information regarding variations in how host cells discriminate commensal from pathogenic species, as well as how the host response is affected by the 3-dimensional architecture and interbacterial interactions that occur in the oral biofilms. This review provides some insights into thes- processes by including existing literature on the biology of nonoral bacterial biofilms, and the more recent literature just beginning to document how the oral cavity responds to multispecies biofilms. PMID:23141757

The Murine Lung Microbiome Changes During Lung Inflammation and Intranasal Vancomycin Treatment

PubMed Central

Barfod, Kenneth Klingenberg; Vrankx, Katleen; Mirsepasi-Lauridsen, Hengameh Chloé; Hansen, Jitka Stilund; Hougaard, Karin Sørig; Larsen, Søren Thor; Ouwenhand, Arthur C.; Krogfelt, Karen Angeliki

2015-01-01

Most microbiome research related to airway diseases has focused on the gut microbiome. This is despite advances in culture independent microbial identification techniques revealing that even healthy lungs possess a unique dynamic microbiome. This conceptual change raises the question; if lung diseases could be causally linked to local dysbiosis of the local lung microbiota. Here, we manipulate the murine lung and gut microbiome, in order to show that the lung microbiota can be changed experimentally. We have used four different approaches: lung inflammation by exposure to carbon nano-tube particles, oral probiotics and oral or intranasal exposure to the antibiotic vancomycin. Bacterial DNA was extracted from broncho-alveolar and nasal lavage fluids, caecum samples and compared by DGGE. Our results show that: the lung microbiota is sex dependent and not just a reflection of the gut microbiota, and that induced inflammation can change lung microbiota. This change is not transferred to offspring. Oral probiotics in adult mice do not change lung microbiome detectible by DGGE. Nasal vancomycin can change the lung microbiome preferentially, while oral exposure does not. These observations should be considered in future studies of the causal relationship between lung microbiota and lung diseases. PMID:26668669

Influence of the Toothpaste with Brazilian Ethanol Extract Propolis on the Oral Cavity Health

PubMed Central

Skaba, Dariusz; Morawiec, Tadeusz; Tanasiewicz, Marta; Bobela, Elżbieta; Skucha-Nowak, Małgorzata; Dawiec, Monika; Yamamoto, Rindai; Makita, Yuki; Redzynia, Małgorzata; Janoszka, Beata; Niedzielska, Iwona; Król, Wojciech

2013-01-01

Propolis-based therapeutic agents represent this potential for the development of new drugs in dental care. The aim of a clinical-cohort study was to determine the influence of application of toothpaste enriched with Brazilian extract of propolis (EEP) on health status of oral cavity. Laboratory analysis was conducted in order to assess the chemical composition of EEP including total phenolic compounds, the DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity, ABTS radical cation scavenging activity, and FRAP assay. Clinical research involved two groups of subjects comprising 32 adult patients, with assessment based on the preliminary evaluation of the state of their marginal periodontium. The investigation of oral health indices API, OHI, and SBI and microbiological examination of oral microflora were also carried out. Results obtained indicated time-dependent microbial action of EEP at 50 mg/L concentration, with antimicrobial activity against Gram-positive bacteria. The total decrease of API, OHI, and SBI mean values was observed. Hygienic preparations with 3% content of Brazilian ethanol extract of green propolis (EEP) efficiently support removal of dental plaque and improve the state of marginal periodontium. PMID:23861699

Teaching the Microbial Growth Curve Concept Using Microalgal Cultures and Flow Cytometry

ERIC Educational Resources Information Center

Forget, Nathalie; Belzile, Claude; Rioux, Pierre; Nozais, Christian

2010-01-01

The microbial growth curve is widely studied within microbiology classes and bacteria are usually the microbial model used. Here, we describe a novel laboratory protocol involving flow cytometry to assess the growth dynamics of the unicellular microalgae "Isochrysis galbana." The algal model represents an appropriate alternative to…

Capturing microbial sources distributed in a mixed-use watershed within an integrated environmental modeling workflow

EPA Science Inventory

Many watershed models simulate overland and instream microbial fate and transport, but few provide loading rates on land surfaces and point sources to the waterbody network. This paper describes the underlying equations for microbial loading rates associated with 1) land-applied ...

Capturing microbial sources distributed in a mixed-use watershed within an integrated environmental modeling workflow

USDA-ARS?s Scientific Manuscript database

Many watershed models simulate overland and instream microbial fate and transport, but few provide loading rates on land surfaces and point sources to the waterbody network. This paper describes the underlying equations for microbial loading rates associated with 1) land-applied manure on undevelope...

Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities

PubMed Central

Mahadevan, Radhakrishnan; Henson, Michael A.

2012-01-01

Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research. PMID:24688668

Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities.

PubMed

Mahadevan, Radhakrishnan; Henson, Michael A

2012-01-01

Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

Representing life in the Earth system with soil microbial functional traits in the MIMICS model

NASA Astrophysics Data System (ADS)

Wieder, W. R.; Grandy, A. S.; Kallenbach, C. M.; Taylor, P. G.; Bonan, G. B.

2015-02-01

Projecting biogeochemical responses to global environmental change requires multi-scaled perspectives that consider organismal diversity, ecosystem processes and global fluxes. However, microbes, the drivers of soil organic matter decomposition and stabilization, remain notably absent from models used to project carbon cycle-climate feedbacks. We used a microbial trait-based soil carbon (C) model, with two physiologically distinct microbial communities to improve current estimates of soil C storage and their likely response to perturbations. Drawing from the application of functional traits used to model other ecosystems, we incorporate copiotrophic and oligotrophic microbial functional groups in the MIcrobial-MIneral Carbon Stabilization (MIMICS) model, which incorporates oligotrophic and copiotrophic functional groups, akin to "gleaner" vs. "opportunist" plankton in the ocean, or r vs. K strategists in plant and animals communities. Here we compare MIMICS to a conventional soil C model, DAYCENT, in cross-site comparisons of nitrogen (N) enrichment effects on soil C dynamics. MIMICS more accurately simulates C responses to N enrichment; moreover, it raises important hypotheses involving the roles of substrate availability, community-level enzyme induction, and microbial physiological responses in explaining various soil biogeochemical responses to N enrichment. In global-scale analyses, we show that current projections from Earth system models likely overestimate the strength of the land C sink in response to increasing C inputs with elevated carbon dioxide (CO2). Our findings illustrate that tradeoffs between theory and utility can be overcome to develop soil biogeochemistry models that evaluate and advance our theoretical understanding of microbial dynamics and soil biogeochemical responses to environmental change.

Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease.

PubMed

Dagli, Namrata; Dagli, Rushabh; Darwish, Shrouq; Baroudi, Kusai

2016-01-01

Recently, oral microbiome has gained popularity among scientists. Microorganisms are no longer considered as disease-producing pathogens, rather they are now considered as partners of human in maintaining health. Since ancient times, changes in our lifestyle have affected our microbiome and the balance with their human host has been perturbed. The present review includes the description about factors affecting oral microbiome and establishing symbiosis with the human host so that they contribute in maintaining health rather than eliciting diseases. A comprehensive literature search was performed on databases such as Google Scholar, PubMed and Medline until April 2015. First, articles were selected on the basis of their titles and then abstracts were screened and unwanted articles were excluded. Articles obtained from all the databases were checked and duplicate articles were removed. Articles obtained from various databases: PubMed = 35, Google Scholar=8. Out of these 43 articles, total 29 articles were finally selected for this review. The published literature suggests that the modern oral microbiome is less biodiverse, and possess more pathogenic bacterial species and lesser beneficial bacteria. The possible factors mainly responsible for this shift in microbiome were found to be change in diet, industrial revolution and indiscriminate use of antibiotics. Various changes in lifestyles have affected oral microbiome adversely and perturb the symbiosis between the microbiome and their hosts. The present oral microbiome is found to be less diverse and more pathogenic. The present review may be helpful in understanding the relationship between the microbiome and their human hosts so that microbiome contributes in maintaining healthy state of the body.

Mechanistic modelling of the inhibitory effect of pH on microbial growth.

PubMed

Akkermans, Simen; Van Impe, Jan F

2018-06-01

Modelling and simulation of microbial dynamics as a function of processing, transportation and storage conditions is a useful tool to improve microbial food safety and quality. The goal of this research is to improve an existing methodology for building mechanistic predictive models based on the environmental conditions. The effect of environmental conditions on microbial dynamics is often described by combining the separate effects in a multiplicative way (gamma concept). This idea was extended further in this work by including the effects of the lag and stationary growth phases on microbial growth rate as independent gamma factors. A mechanistic description of the stationary phase as a function of pH was included, based on a novel class of models that consider product inhibition. Experimental results on Escherichia coli growth dynamics indicated that also the parameters of the product inhibition equations can be modelled with the gamma approach. This work has extended a modelling methodology, resulting in predictive models that are (i) mechanistically inspired, (ii) easily identifiable with a limited work load and (iii) easily extended to additional environmental conditions. Copyright © 2017. Published by Elsevier Ltd.

Oral microbiota reveals signs of acculturation in Mexican American women

PubMed Central

Hutchinson, Diane S.; Fowler, Jerry; Smith, Daniel P.; Ajami, Nadim J.; Zhao, Hua; Scheet, Paul; Chow, Wong-Ho; Petrosino, Joseph F.; Daniel, Carrie R.

2018-01-01

The oral microbiome has been linked to a number of chronic inflammatory conditions, including obesity, diabetes, periodontitis, and cancers of the stomach and liver. These conditions disproportionately affect Mexican American women, yet few studies have examined the oral microbiota in this at-risk group. We characterized the 16S rDNA oral microbiome in 369 non-smoking women enrolled in the MD Anderson Mano a Mano Mexican American Cohort Study. Lower bacterial diversity, a potential indicator of oral health, was associated with increased age and length of US residency among recent immigrants. Grouping women by overarching bacterial community type (e.g., “Streptococcus,” “Fusobacterium,” and “Prevotella” clusters), we observed differences across a number of acculturation-related variables, including nativity, age at immigration, time in the US, country of longest residence, and a multi-dimensional acculturation scale. Participants in the cluster typified by higher abundance of Streptococcus spp. exhibited the lowest bacterial diversity and appeared the most acculturated as compared to women in the “Prevotella” group. Computationally-predicted functional analysis suggested the Streptococcus-dominated bacterial community had greater potential for carbohydrate metabolism while biosynthesis of essential amino acids and nitrogen metabolism prevailed among the Prevotella-high group. Findings suggest immigration and adaption to life in the US, a well-established mediator of disease risk, is associated with differences in oral microbial profiles in Mexican American women. These results warrant further investigation into the joint and modifying effects of acculturation and oral bacteria on the health of Mexican American women and other immigrant populations. The oral microbiome presents an easily accessible biomarker of disease risk, spanning biological, behavioral, and environmental factors. PMID:29694348

Effects of lactoferrin and lactoperoxidase-containing food on the oral microbiota of older individuals.

PubMed

Nakano, Manabu; Wakabayashi, Hiroyuki; Sugahara, Hirosuke; Odamaki, Toshitaka; Yamauchi, Koji; Abe, Fumiaki; Xiao, Jin-Zhong; Murakami, Kohji; Ishikawa, Kentaro; Hironaka, Shouji

2017-10-01

The oral microbiota influences health and disease states. Some gram-negative anaerobic bacteria play important roles in tissue destruction associated with periodontal disease. Lactoferrin (LF) and lactoperoxidase (LPO) are antimicrobial proteins found in saliva; however, their influence on the whole oral microbiota currently remains unknown. In this randomized, double-blinded, placebo-controlled study, the effects of long-term ingestion of LF and LPO-containing tablets on the microbiota of supragingival plaque and tongue coating were assessed. Forty-six older individuals ingested placebo or test tablets after every meal for 8 weeks. The relative abundance of bacterial species was assessed by 16S rRNA gene high-throughput sequencing. Most of the bacterial species in supragingival plaque and tongue coating that exhibited significant decreases in the test group were gram-negative bacteria, including periodontal pathogens. Decreases in the total relative abundance of gram-negative organisms in supragingival plaque and tongue coating correlated with improvements in assessed variables related to oral health, such as oral malodor and plaque accumulation. Furthermore, there was significantly less microbiota diversity in supragingival plaque at 8 weeks in the test group than in the placebo group and low microbiota diversity correlated with improvements in assessed variables related to oral health. These results suggest that LF and LPO-containing tablets promote a shift from a highly diverse and gram-negative-dominated to a gram-positive-dominated community in the microbiota of supragingival plaque and tongue coating. This microbial shift may contribute to improvements in oral health, including oral malodor and state of the gingiva. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

Candida albicans Inhibits Pseudomonas aeruginosa Virulence through Suppression of Pyochelin and Pyoverdine Biosynthesis

PubMed Central

Lopez-Medina, Eduardo; Fan, Di; Coughlin, Laura A.; Ho, Evi X.; Lamont, Iain L.; Reimmann, Cornelia; Hooper, Lora V.; Koh, Andrew Y.

2015-01-01

Bacterial-fungal interactions have important physiologic and medical ramifications, but the mechanisms of these interactions are poorly understood. The gut is host to trillions of microorganisms, and bacterial-fungal interactions are likely to be important. Using a neutropenic mouse model of microbial gastrointestinal colonization and dissemination, we show that the fungus Candida albicans inhibits the virulence of the bacterium Pseudomonas aeruginosa by inhibiting P. aeruginosa pyochelin and pyoverdine gene expression, which plays a critical role in iron acquisition and virulence. Accordingly, deletion of both P. aeruginosa pyochelin and pyoverdine genes attenuates P. aeruginosa virulence. Heat-killed C. albicans has no effect on P. aeruginosa, whereas C. albicans secreted proteins directly suppress P. aeruginosa pyoverdine and pyochelin expression and inhibit P. aeruginosa virulence in mice. Interestingly, suppression or deletion of pyochelin and pyoverdine genes has no effect on P. aeruginosa’s ability to colonize the GI tract but does decrease P. aeruginosa’s cytotoxic effect on cultured colonocytes. Finally, oral iron supplementation restores P. aeruginosa virulence in P. aeruginosa and C. albicans colonized mice. Together, our findings provide insight into how a bacterial-fungal interaction can modulate bacterial virulence in the intestine. Previously described bacterial-fungal antagonistic interactions have focused on growth inhibition or colonization inhibition/modulation, yet here we describe a novel observation of fungal-inhibition of bacterial effectors critical for virulence but not important for colonization. These findings validate the use of a mammalian model system to explore the complexities of polymicrobial, polykingdom infections in order to identify new therapeutic targets for preventing microbial disease. PMID:26313907

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

NASA Astrophysics Data System (ADS)

Tartakovsky, G. D.; Tartakovsky, A. M.; Scheibe, T. D.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

2013-09-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Tartakovsky, G.; Tartakovsky, A. M.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

2012-12-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Guzel D.; Tartakovsky, Alexandre M.; Scheibe, Timothy D.

2013-09-07

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated withmore » microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparisonto prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).« less

Modeling of Sustainable Base Production by Microbial Electrolysis Cell.

PubMed

Blatter, Maxime; Sugnaux, Marc; Comninellis, Christos; Nealson, Kenneth; Fischer, Fabian

2016-07-07

A predictive model for the microbial/electrochemical base formation from wastewater was established and compared to experimental conditions within a microbial electrolysis cell. A Na2 SO4 /K2 SO4 anolyte showed that model prediction matched experimental results. Using Shewanella oneidensis MR-1, a strong base (pH≈13) was generated using applied voltages between 0.3 and 1.1 V. Due to the use of bicarbonate, the pH value in the anolyte remained unchanged, which is required to maintain microbial activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Age-Dependent Enterocyte Invasion and Microcolony Formation by Salmonella

PubMed Central

Zhang, Kaiyi; Dupont, Aline; Torow, Natalia; Gohde, Fredrik; Leschner, Sara; Lienenklaus, Stefan; Weiss, Siegfried; Brinkmann, Melanie M.; Kühnel, Mark; Hensel, Michael; Fulde, Marcus; Hornef, Mathias W.

2014-01-01

The coordinated action of a variety of virulence factors allows Salmonella enterica to invade epithelial cells and penetrate the mucosal barrier. The influence of the age-dependent maturation of the mucosal barrier for microbial pathogenesis has not been investigated. Here, we analyzed Salmonella infection of neonate mice after oral administration. In contrast to the situation in adult animals, we observed spontaneous colonization, massive invasion of enteroabsorptive cells, intraepithelial proliferation and the formation of large intraepithelial microcolonies. Mucosal translocation was dependent on enterocyte invasion in neonates in the absence of microfold (M) cells. It further resulted in potent innate immune stimulation in the absence of pronounced neutrophil-dominated pathology. Our results identify factors of age-dependent host susceptibility and provide important insight in the early steps of Salmonella infection in vivo. We also present a new small animal model amenable to genetic manipulation of the host for the analysis of the Salmonella enterocyte interaction in vivo. PMID:25210785

A whole blood bactericidal assay for tuberculosis.

PubMed

Wallis, R S; Palaci, M; Vinhas, S; Hise, A G; Ribeiro, F C; Landen, K; Cheon, S H; Song, H Y; Phillips, M; Dietze, R; Ellner, J J

2001-04-15

The bactericidal activity of orally administered antituberculosis (anti-TB) drugs was determined in a whole blood culture model of intracellular infection in which microbial killing reflects the combined effects of drug and immune mechanisms. Rifampin (Rif) was the most active compound studied and reduced the number of viable bacilli by >4 logs. Isoniazid (INH), 2 quinolones, and pyrazinamide (PZA) showed intermediate levels of activity. Ethambutol exerted only a bacteristatic effect; amoxicillin/clavulanate was inactive. The combination of INH-Rif-PZA showed strong activity against 11 drug-sensitive isolates (mean, -3.8 log) but no activity against 12 multidrug-resistant (MDR) strains. The combination of levofloxacin-PZA-ethambutol had intermediate bactericidal activity against MDR isolates (mean, -1.2 log) but failed to equal that of INH-Rif-PZA against sensitive isolates (P<.001). The whole blood BACTEC method (Becton Dickinson) may be useful for the early clinical evaluation of new anti-TB drugs and in the management of individual patients.

Microgravity as a novel environmental signal affecting Salmonella enterica serovar Typhimurium virulence

NASA Technical Reports Server (NTRS)

Nickerson, C. A.; Ott, C. M.; Mister, S. J.; Morrow, B. J.; Burns-Keliher, L.; Pierson, D. L.

2000-01-01

The effects of spaceflight on the infectious disease process have only been studied at the level of the host immune response and indicate a blunting of the immune mechanism in humans and animals. Accordingly, it is necessary to assess potential changes in microbial virulence associated with spaceflight which may impact the probability of in-flight infectious disease. In this study, we investigated the effect of altered gravitational vectors on Salmonella virulence in mice. Salmonella enterica serovar Typhimurium grown under modeled microgravity (MMG) were more virulent and were recovered in higher numbers from the murine spleen and liver following oral infection compared to organisms grown under normal gravity. Furthermore, MMG-grown salmonellae were more resistant to acid stress and macrophage killing and exhibited significant differences in protein synthesis than did normal-gravity-grown cells. Our results indicate that the environment created by simulated microgravity represents a novel environmental regulatory factor of Salmonella virulence.

Companion animals symposium: role of microbes in canine and feline health.

PubMed

Kil, D Y; Swanson, K S

2011-05-01

Whether in an ocean reef, a landfill, or a gastrointestinal tract (GIT), invisible communities of highly active and adaptable microbes prosper. Over time, mammals have developed a symbiosis with microbes that are important inhabitants not only in the GIT, but also in the mouth, skin, and urogenital tract. In the GIT, the number of commensal microbes exceeds the total number of host cells by at least 10 times. The GIT microbes play a critical role in nutritional, developmental, defensive, and physiologic processes in the host. Recent evidence also suggests a role of GIT microbes in metabolic phenotype and disease risk (e.g., obesity, metabolic syndrome) of the host. Proper balance is a key to maintaining GIT health. Balanced microbial colonization is also important for other body regions such as the oral cavity, the region with the greatest prevalence of disease in dogs and cats. A significant obstruction to studying microbial populations has been the lack of tools to identify and quantify microbial communities accurately and efficiently. Most of the current knowledge of microbial populations has been established by traditional cultivation methods that are not only laborious, time-consuming, and often inaccurate, but also greatly limited in scope. However, recent advances in molecular-based techniques have resulted in a dramatic improvement in studying microbial communities. These DNA-based high-throughput technologies have enabled us to more clearly characterize the identity and metabolic activity of microbes living in the host and their association with health and diseases. Despite this recent progress, however, published data pertaining to microbial communities of dogs and cats are still lacking in comparison with data in humans and other animals. More research is required to provide a more detailed description of the canine and feline microbiome and its role in health and disease.

Effect of probiotics (Saccharomyces boulardii) on microbial translocation and inflammation in HIV-treated patients: a double-blind, randomized, placebo-controlled trial.

PubMed

Villar-García, Judit; Hernández, Juan J; Güerri-Fernández, Robert; González, Alicia; Lerma, Elisabet; Guelar, Ana; Saenz, David; Sorlí, Lluisa; Montero, Milagro; Horcajada, Juan P; Knobel Freud, Hernando

2015-03-01

Microbial translocation has been associated with an increase in immune activation and inflammation in HIV infection despite effective highly active antiretroviral therapy. It has been shown that some probiotics have a beneficial effect by reducing intestinal permeability and, consequently, microbial translocation. To assess changes in microbial translocation and inflammation after treatment with probiotics (Saccharomyces boulardii) in HIV-1-infected patients with virologic suppression. A double-blind, randomized, placebo-controlled trial was conducted in 44 nonconsecutive HIV-1-infected patients with viral load of <20 copies per milliliter for at least 2 years. Patients were randomized to oral supplementation with probiotics or placebo during 12 weeks. Markers of microbial translocation (lipopolysaccharide-binding protein [LBP] and soluble CD14), inflammation (interleukin 6 [IL-6], tumor necrosis factor alpha, interferon gamma, high-sensitivity C-reactive protein), and immunological and clinical data were determined before and after the intervention and 3 months after treatment discontinuation. Quantitative variables were compared using the Mann-Whitney U test, and categorical variables were compared using the Fisher exact test. After 12 weeks of treatment, differences between the probiotic arm and the placebo arm were observed in LBP values (-0.30 vs +0.70 pg/mL) and IL-6 (-0.60 vs +0.78 pg/mL). These differences were also noted at 3 months after treatment withdrawal. Qualitative analysis was performed, defining a variable as "decreased" or "increased" from baseline LBP. A significant decrease of LBP at 12 weeks of treatment was observed (57.9% patients in the probiotic group vs 6.2% in the placebo group, P = 0.002). Treatment with S. boulardii decreases microbial translocation (LBP) and inflammation parameters (IL-6) in HIV-1-infected patients with long-term virologic suppression.

Exploration of Human Salivary Microbiomes—Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects

PubMed Central

Wang, Shaoguo; Hu, Xiaopan; Jiao, Kangli; He, Xiangyi; Li, Zhiqiang; Wang, Jizeng

2016-01-01

Recently, high-throughput sequencing has improved the understanding of the microbiological etiology of caries, but the characteristics of the microbial community structure in the human oral cavity with and without caries are not completely clear. To better understand these characteristics, Illumina MiSeq high-throughput sequencing was utilized to analyze 20 salivary samples (10 caries-free and 10 caries) from subjects from the same town in Dongxiang, Gansu, China. A total of 5,113 OTUs (Operational Taxonomic Units, 97% cutoff) were characterized in all of the salivary samples obtained from the 20 subjects. A comparison of the two groups revealed that (i) the predominant phyla were constant between the two groups; (ii) the relative abundance of the genera Veillonella, Bifidobacterium, Selenomonas, Olsenella, Parascardovia, Scardovia, Chryseobacterium, Terrimonas, Burkholderia and Sporobacter was significantly higher in the group with caries (P < 0.05); and (iii) four genera with low relative abundance (< 0.01% on average), including two characteristic genera in caries (Chryseobacterium and Scardovia), significantly influenced the microbial community structure at the genus and OTU levels. Moreover, via co-occurrence and principal component analyses, the co-prevalence of the pathogenic genera was detected in the caries samples, but in the caries-free samples, the function of clustered genera was more random. This result suggests that a synergistic effect may be influencing the assembly of the caries microbial community, whereas competition may play a more dominant role in governing the microbial community in the caries-free group. Our findings regarding the characteristics of the microbial communities of the groups with and without caries might improve the understanding of the microbiological etiology of caries and might improve the prevention and cure of caries in the future. PMID:26784334

Health behavior models and oral health: a review.

PubMed

Hollister, M Catherine; Anema, Marion G

2004-01-01

Dental hygienists help their clients develop health promoting behaviors, by providing essential information about general health, and oral health in particular. Individual health practices such as oral self-care are based on personal choices. The guiding principles found in health behavior models provide useful methods to the oral health care providers in promoting effective individual client behaviors. Theories provide explanations about observable facts in a systematic manner. Research regarding health behavior has explored the effectiveness and applicability of various health models in oral health behavior modification. The Health Belief Model, Transtheoretical Model and Stages of Change, Theory of Reasoned Action, Self-Efficacy, Locus of Control, and Sense of Coherence are examples of models that focus on individuals assuming responsibility for their own health. Understanding the strengths of each and their applicability to health behaviors is critical for oral health care providers who work with patients to adopt methods and modify behaviors that contribute to good oral health. This paper describes health behavior models that have been applied to oral health education, presents a critical analysis of the effectiveness of each model in oral health education, and provides examples of application to oral health education.

Representing life in the Earth system with soil microbial functional traits in the MIMICS model

NASA Astrophysics Data System (ADS)

Wieder, W. R.; Grandy, A. S.; Kallenbach, C. M.; Taylor, P. G.; Bonan, G. B.

2015-06-01

Projecting biogeochemical responses to global environmental change requires multi-scaled perspectives that consider organismal diversity, ecosystem processes, and global fluxes. However, microbes, the drivers of soil organic matter decomposition and stabilization, remain notably absent from models used to project carbon (C) cycle-climate feedbacks. We used a microbial trait-based soil C model with two physiologically distinct microbial communities, and evaluate how this model represents soil C storage and response to perturbations. Drawing from the application of functional traits used to model other ecosystems, we incorporate copiotrophic and oligotrophic microbial functional groups in the MIcrobial-MIneral Carbon Stabilization (MIMICS) model; these functional groups are akin to "gleaner" vs. "opportunist" plankton in the ocean, or r- vs. K-strategists in plant and animal communities. Here we compare MIMICS to a conventional soil C model, DAYCENT (the daily time-step version of the CENTURY model), in cross-site comparisons of nitrogen (N) enrichment effects on soil C dynamics. MIMICS more accurately simulates C responses to N enrichment; moreover, it raises important hypotheses involving the roles of substrate availability, community-level enzyme induction, and microbial physiological responses in explaining various soil biogeochemical responses to N enrichment. In global-scale analyses, we show that MIMICS projects much slower rates of soil C accumulation than a conventional soil biogeochemistry in response to increasing C inputs with elevated carbon dioxide (CO2) - a finding that would reduce the size of the land C sink estimated by the Earth system. Our findings illustrate that tradeoffs between theory and utility can be overcome to develop soil biogeochemistry models that evaluate and advance our theoretical understanding of microbial dynamics and soil biogeochemical responses to environmental change.

Microbial mutualism at a distance: The role of geometry in diffusive exchanges

NASA Astrophysics Data System (ADS)

Peaudecerf, François J.; Bunbury, Freddy; Bhardwaj, Vaibhav; Bees, Martin A.; Smith, Alison G.; Goldstein, Raymond E.; Croze, Ottavio A.

2018-02-01

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.

The presence of cariogenic and periodontal pathogens in the oral cavity of one-year-old infants delivered pre-term with very low birthweights: a case control study

PubMed Central

2014-01-01

Background Recently, the dental literature has focused mainly on the microbial colonization of healthy full-term infants and their mothers or caretakers. However, oral microbial acquisition by premature infants has not been adequately investigated, and the correlation between pre-term birth and the presence of cariogenic and periodontal pathogens has not been determined. The aim of this study was to identify the presence and quantities of representative cariogenic and periodontal pathogens in the oral cavities of 12-month-old infants and compare the occurrence of these microbes between a cohort of pre-term infants with very low birthweights and a control cohort comprising full-term infants. Methods The research cohort was composed of 69 one-year-old infants, of whom 24 were born prematurely with very low birthweights and 45 of whom were carried to full term. Information regarding the infants’ gestational age, mode of delivery, general health status, birthweight and antibiotic use were obtained from hospital records and through oral interviews. At 12 months of age, both groups of infants were examined, and unstimulated saliva samples from the dorsum of the tongue and dental plaque samples were collected. The microorganisms (Streptococcus mutans, Lactobacillus spp., Actinomyces spp., Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Peptostreptococcus micros, Prevotella intermedia, Fusobacterium nucleatum) were identified and their quantities were evaluated using a PCR-based method. The chi-squared and Fisher’s factorial tests were used for the statistical evaluations. Results The infants had a high prevalence of cariogenic microbes and of Fusosbacterium nucleatum and Aggregatibacter actinomycetemcomitans. Cariogenic microbes were detected in 91.7% of the very low birthweight infants and in all full-term infants. Periodontal pathogens were present in 83% of the pre-term infants and in 96% of the full-term infants. A significant difference was found between the cohorts in terms of the presence of S. mutans. Most of the very low birthweight infants had negative values of this microbe, while the full-term infants had positive values. Conclusions This study confirms the early transmission of representative cariogenic and periodontal pathogens to the oral cavity of one-year-old infants and a higher prevalence of S. mutans in full-term infants than in premature infants. PMID:25178742

Accounting for microbial habitats in modeling soil organic matter dynamics

NASA Astrophysics Data System (ADS)

Chenu, Claire; Garnier, Patricia; Nunan, Naoise; Pot, Valérie; Raynaud, Xavier; Vieublé, Laure; Otten, Wilfred; Falconer, Ruth; Monga, Olivier

2017-04-01

The extreme heterogeneity of soils constituents, architecture and inhabitants at the microscopic scale is increasingly recognized. Microbial communities exist and are active in a complex 3-D physical framework of mineral and organic particles defining pores of various sizes, more or less inter-connected. This results in a frequent spatial disconnection between soil carbon, energy sources and the decomposer organisms and a variety of microhabitats that are more or less suitable for microbial growth and activity. However, current biogeochemical models account for C dynamics at the macroscale (cm, m) and consider time- and spatially averaged relationships between microbial activity and soil characteristics. Different modelling approaches have intended to account for this microscale heterogeneity, based either on considering aggregates as surrogates for microbial habitats, or pores. Innovative modelling approaches are based on an explicit representation of soil structure at the fine scale, i.e. at µm to mm scales: pore architecture and their saturation with water, localization of organic resources and of microorganisms. Three recent models are presented here, that describe the heterotrophic activity of either bacteria or fungi and are based upon different strategies to represent the complex soil pore system (Mosaic, LBios and µFun). These models allow to hierarchize factors of microbial activity in soil's heterogeneous architecture. Present limits of these approaches and challenges are presented, regarding the extensive information required on soils at the microscale and to up-scale microbial functioning from the pore to the core scale.

Development and evaluation of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

USDA-ARS?s Scientific Manuscript database

Microbial contamination of waters in agricultural watershed is the critical public health issue. The watershed-scale model has been proven to be one of the candidate tools for predicting microbial water quality and evaluating management practices. The Agricultural Policy/Environmental eXtender (APEX...

[Carbon Source Utilization Characteristics of Soil Microbial Community for Apple Orchard with Interplanting Herbage].

PubMed

Du, Yi-fei; Fang, Kai-kai; Wang, Zhi-kang; Li, Hui-ke; Mao, Peng-juan; Zhang, Xiang-xu; Wang, Jing

2015-11-01

As soil fertility in apple orchard with clean tillage is declined continuously, interplanting herbage in orchard, which is a new orchard management model, plays an important role in improving orchard soil conditions. By using biolog micro-plate technique, this paper studied the functional diversity of soil microbial community under four species of management model in apple orchards, including clear tillage model, interplanting white clover model, interplanting small crown flower model and interplanting cocksfoot model, and the carbon source utilization characteristics of microbial community were explored, which could provide a reference for revealing driving mechanism of ecological process of orchard soil. The results showed that the functional diversity of microbial community had a significant difference among different treatments and in the order of white clover > small crown flower > cocksfoot > clear tillage. The correlation analysis showed that the average well color development (AWCD), Shannon index, Richness index and McIntosh index were all highly significantly positively correlated with soil organic carbon, total nitrogen, microbial biomass carbon, and Shannon index was significantly positively correlated with soil pH. The principal component analysis and the fingerprints of the physiological carbon metabolism of the microbial community demonstrated that grass treatments improved carbon source metabolic ability of soil microbial community, and the soil microbes with perennial legumes (White Clover and small crown flower) had a significantly higher utilization rate in carbohydrates (N-Acetyl-D-Glucosamine, D-Mannitol, β-Methyl-D-Glucoside), amino acids (Glycyl-L-Glutamic acid, L-Serine, L-Threonine) and polymers (Tween 40, Glycogen) than the soil microbes with clear tillage. It was considered that different treatments had the unique microbial community structure and peculiar carbon source utilization characteristics.

Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model.

PubMed

Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

2015-03-01

A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.

Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model

PubMed Central

Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

2015-01-01

A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs. PMID:26074626

Antimicrobial activity of Arctium lappa constituents against microorganisms commonly found in endodontic infections.

PubMed

Pereira, Juliana Vianna; Bergamo, Débora Cristina Baldoqui; Pereira, José Odair; França, Suzelei de Castro; Pietro, Rosemeire Cristina Linhares Rodrigues; Silva-Sousa, Yara T Corrêa

2005-01-01

This study evaluated in vitro the antimicrobial activity of rough extracts from leaves of Arctium lappa and their phases. The following microorganisms, commonly found in the oral cavity, specifically in endodontic infections, were used: Enterococcus faecalis, Staphylococcus aureus, Pseudomonas aeruginosa, Bacillus subtilis and Candida albicans. The agar-diffusion method allowed detection of the hexanic phase as an inhibitor of microbial growth. Bioautographic assays identified antimicrobial substances in the extract. The results showed the existence, in the rough hexanic phase and in its fractions, of constituents that have retention factors (Rf) in three distinct zones, thereby suggesting the presence of active constituents with chemical structures of different polarities that exhibited specificity against the target microorganisms. It may be concluded that the Arctium lappa constituents exhibited a great microbial inhibition potential against the tested endodontic pathogens.

A Faropenem, Linezolid, and Moxifloxacin Regimen for Both Drug-Susceptible and Multidrug-Resistant Tuberculosis in Children: FLAME Path on the Milky Way

PubMed Central

Deshpande, Devyani; Srivastava, Shashikant; Nuermberger, Eric; Pasipanodya, Jotam G.; Swaminathan, Soumya; Gumbo, Tawanda

2016-01-01

Background. The regimen of linezolid and moxifloxacin was found to be efficacious in the hollow fiber system model of pediatric intracellular tuberculosis. However, its kill rate was slower than the standard 3-drug regimen of isoniazid, rifampin, and pyrazinamide. We wanted to examine the effect of adding a third oral agent, faropenem, to this dual combination. Methods. We performed a series of studies in the hollow fiber system model of intracellular Mycobacterium tuberculosis, by mimicking pediatric pharmacokinetics of each antibiotic. First, we varied the percentage of time that faropenem persisted above minimum inhibitory concentration (TMIC) on the moxifloxacin-linezolid regimen. After choosing the best faropenem exposure, we performed experiments in which we varied the moxifloxacin and linezolid doses in the triple regimen. Finally, we performed longer-duration therapy validation experiments. Bacterial burden was quantified using both colony-forming units per milliliter (CFU/mL) and time to positivity (TTP). Kill slopes were modeled using exponential regression. Results. TTP was a more sensitive measure of bacterial burden than CFU/mL. A faropenem TMIC > 62% was associated with steepest microbial kill slope. Regimens of standard linezolid and moxifloxacin plus faropenem TMIC > 60%, as well as higher-dose moxifloxacin, achieved slopes equivalent to those of the standard regimen based by both TTP and CFU/mL over 28 days of treatment. Conclusions. We have developed an oral faropenem-linezolid-moxifloxacin (FLAME) regimen that is free of first-line drugs. The regimen could be effective against both multidrug-resistant and drug-susceptible tuberculosis in children. PMID:27742640

A health-promoting community dental service in Melbourne, Victoria, Australia: protocol for the North Richmond model of oral health care.

PubMed

Hall, Martin; Christian, Bradley

2017-10-01

Despite the best efforts and commitment of oral health programs, there is no evidence that the current surgical output-based model of oral health care is delivering better oral health outcomes to the community. In fact, Australian evidence indicates the oral health of the community could be getting worse. It is now well-understood that this traditional surgical model of oral health care will never successfully manage the disease itself. It is proposed that a health-promoting, minimally invasive oral disease management model of care may lead to a sustainable benefit to the oral health status of the individual and community groups. The aim of this paper is to describe such a model of oral health care (MoC) currently being implemented by the North Richmond Community Health Oral Health (NRCH-OH) program in Melbourne, Victoria, Australia; this model may serve as a template for other services to re-orient their healthcare delivery towards health promotion and prevention. The paper describes the guiding principles and theories for the model and also its operational components, which are: pre-engagement while on the waitlist; client engagement at the reception area; the assessment phase; oral health education (high-risk clients only); disease management; and reviews and recall.

Comparison of model microbial allocation parameters in soils of varying texture

NASA Astrophysics Data System (ADS)

Hagerty, S. B.; Slessarev, E.; Schimel, J.

2017-12-01

The soil microbial community decomposes the majority of carbon (C) inputs to the soil. However, not all of this C is respired—rather, a substantial portion of the carbon processed by microbes may remain stored in the soil. The balance between C storage and respiration is controlled by microbial turnover rates and C allocation strategies. These microbial community properties may depend on soil texture, which has the potential to influence both the nature and the fate of microbial necromass and extracellular products. To evaluate the role of texture on microbial turnover and C allocation, we sampled four soils from the University of California's Hastings Reserve that varied in texture (one silt loam, two sandy loam, and on clay soil), but support similar grassland plant communities. We added 14C- glucose to the soil and measured the concentration of the label in the carbon dioxide (CO2), microbial biomass, and extractable C pools over 7 weeks. The labeled biomass turned over the slowest in the clay soil; the concentration of labeled biomass was more than 1.5 times the concentration of the other soils after 8 weeks. The clay soil also had the lowest mineralization rate of the label, and mineralization slowed after two weeks. In contrast, in the sandier soils mineralization rates were higher and did not plateau until 5 weeks into the incubation period. We fit the 14C data to a microbial allocation model and estimated microbial parameters; assimilation efficiency, exudation, and biomass specific respiration and turnover for each soil. We compare these parameters across the soil texture gradient to assess the extent to which models may need to account for variability in microbial C allocation across soils of different texture. Our results suggest that microbial C turns over more slowly in high-clay soils than in sandy soils, and that C lost from microbial biomass is retained at higher rates in high-clay soils. Accounting for these differences in microbial allocation and carbon stabilization could improve model representations of C cycling across a range of soil types.

The Novel Candida albicans Transporter Dur31 Is a Multi-Stage Pathogenicity Factor

PubMed Central

Mayer, François L.; Wilson, Duncan; Jacobsen, Ilse D.; Miramón, Pedro; Große, Katharina; Hube, Bernhard

2012-01-01

Candida albicans is the most frequent cause of oral fungal infections. However, the exact pathogenicity mechanisms that this fungus employs are largely unknown and many of the genes expressed during oral infection are uncharacterized. In this study we sought to functionally characterize 12 previously unknown function genes associated with oral candidiasis. We generated homozygous knockout mutants for all 12 genes and analyzed their interaction with human oral epithelium in vitro. Eleven mutants caused significantly less epithelial damage and, of these, deletion of orf19.6656 (DUR31) elicited the strongest reduction in pathogenicity. Interestingly, DUR31 was not only involved in oral epithelial damage, but in multiple stages of candidiasis, including surviving attack by human neutrophils, endothelial damage and virulence in vivo. In silico analysis indicated that DUR31 encodes a sodium/substrate symporter with 13 transmembrane domains and no human homologue. We provide evidence that Dur31 transports histatin 5. This is one of the very first examples of microbial driven import of this highly cytotoxic antimicrobial peptide. Also, in contrast to wild type C. albicans, dur31Δ/Δ was unable to actively increase local environmental pH, suggesting that Dur31 lies in the extracellular alkalinization hyphal auto-induction pathway; and, indeed, DUR31 was required for morphogenesis. In agreement with this observation, dur31Δ/Δ was unable to assimilate the polyamine spermidine. PMID:22438810

Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota.

PubMed

Campbell, Alisha G; Schwientek, Patrick; Vishnivetskaya, Tatiana; Woyke, Tanja; Levy, Shawn; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, Mircea

2014-09-01

Many microbial phyla that are widely distributed in open environments have few or no representatives within animal-associated microbiota. Among them, the Chloroflexi comprises taxonomically and physiologically diverse lineages adapted to a wide range of aquatic and terrestrial habitats. A distinct group of uncultured chloroflexi related to free-living anaerobic Anaerolineae inhabits the mammalian gastrointestinal tract and includes low-abundance human oral bacteria that appear to proliferate in periodontitis. Using a single-cell genomics approach, we obtained the first draft genomic reconstruction for these organisms and compared their inferred metabolic potential with free-living chloroflexi. Genomic data suggest that oral chloroflexi are anaerobic heterotrophs, encoding abundant carbohydrate transport and metabolism functionalities, similar to those seen in environmental Anaerolineae isolates. The presence of genes for a unique phosphotransferase system and N-acetylglucosamine metabolism suggests an important ecological niche for oral chloroflexi in scavenging material from lysed bacterial cells and the human tissue. The inferred ability to produce sialic acid for cell membrane decoration may enable them to evade the host defence system and colonize the subgingival space. As with other low abundance but persistent members of the microbiota, discerning community and host factors that influence the proliferation of oral chloroflexi may help understand the emergence of oral pathogens and the microbiota dynamics in health and disease states. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial Source Module (MSM): Documenting the Science ...

EPA Pesticide Factsheets

The Microbial Source Module (MSM) estimates microbial loading rates to land surfaces from non-point sources, and to streams from point sources for each subwatershed within a watershed. A subwatershed, the smallest modeling unit, represents the common basis for information consumed and produced by the MSM which is based on the HSPF (Bicknell et al., 1997) Bacterial Indicator Tool (EPA, 2013b, 2013c). Non-point sources include numbers, locations, and shedding rates of domestic agricultural animals (dairy and beef cows, swine, poultry, etc.) and wildlife (deer, duck, raccoon, etc.). Monthly maximum microbial storage and accumulation rates on the land surface, adjusted for die-off, are computed over an entire season for four land-use types (cropland, pasture, forest, and urbanized/mixed-use) for each subwatershed. Monthly point source microbial loadings to instream locations (i.e., stream segments that drain individual sub-watersheds) are combined and determined for septic systems, direct instream shedding by cattle, and POTWs/WWTPs (Publicly Owned Treatment Works/Wastewater Treatment Plants). The MSM functions within a larger modeling system that characterizes human-health risk resulting from ingestion of water contaminated with pathogens. The loading estimates produced by the MSM are input to the HSPF model that simulates flow and microbial fate/transport within a watershed. Microbial counts within recreational waters are then input to the MRA-IT model (Soller et

Divergence in plant and microbial allocation strategies explains continental patterns in microbial allocation and biogeochemical fluxes.

PubMed

Averill, Colin

2014-10-01

Allocation trade-offs shape ecological and biogeochemical phenomena at local to global scale. Plant allocation strategies drive major changes in ecosystem carbon cycling. Microbial allocation to enzymes that decompose carbon vs. organic nutrients may similarly affect ecosystem carbon cycling. Current solutions to this allocation problem prioritise stoichiometric tradeoffs implemented in plant ecology. These solutions may not maximise microbial growth and fitness under all conditions, because organic nutrients are also a significant carbon resource for microbes. I created multiple allocation frameworks and simulated microbial growth using a microbial explicit biogeochemical model. I demonstrate that prioritising stoichiometric trade-offs does not optimise microbial allocation, while exploiting organic nutrients as carbon resources does. Analysis of continental-scale enzyme data supports the allocation patterns predicted by this framework, and modelling suggests large deviations in soil C loss based on which strategy is implemented. Therefore, understanding microbial allocation strategies will likely improve our understanding of carbon cycling and climate. © 2014 John Wiley & Sons Ltd/CNRS.

Microbial community pattern detection in human body habitats via ensemble clustering framework.

PubMed

Yang, Peng; Su, Xiaoquan; Ou-Yang, Le; Chua, Hon-Nian; Li, Xiao-Li; Ning, Kang

2014-01-01

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is varied systematically across body habitats and host genders. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome.

Microbial community pattern detection in human body habitats via ensemble clustering framework

PubMed Central

2014-01-01

Background The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. Results To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. Conclusions In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is varied systematically across body habitats and host genders. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome. PMID:25521415

The microbiome in PTEN hamartoma tumor syndrome.

PubMed

Byrd, Victoria; Getz, Ted; Padmanabhan, Roshan; Arora, Hans; Eng, Charis

2018-03-01

Germline PTEN mutations defining PTEN hamartoma tumor syndrome (PHTS) confer heritable predisposition to breast, endometrial, thyroid and other cancers with known age-related risks, but it remains impossible to predict if any individual will develop cancer. In the general population, gut microbial dysbiosis has been linked to cancer, yet is unclear whether these are associated in PHTS patients. In this pilot study, we aimed to characterize microbial composition of stool, urine, and oral wash from 32 PTEN mutation-positive individuals using 16S rRNA gene sequencing. PCoA revealed clustering of the fecal microbiome by cancer history ( P  = 0.03, R 2  = 0.04). Fecal samples from PHTS cancer patients had relatively more abundant operational taxonomic units (OTUs) from family Rikenellaceae and unclassified members of Clostridia compared to those from non-cancer patients, whereas families Peptostreptococcaceae, Enterobacteriaceae, and Bifidobacteriaceae represented relatively more abundant OTUs among fecal samples from PHTS non-cancer patients. Functional metagenomic prediction revealed enrichment of the folate biosynthesis, genetic information processing and cell growth and death pathways among fecal samples from PHTS cancer patients compared to non-cancer patients. We found no major shifts in overall diversity and no clustering by cancer history among oral wash or urine samples. Our observations suggest the utility of an expanded study to interrogate gut dysbiosis as a potential cancer risk modifier in PHTS patients. © 2018 The authors.

Levorotatory carbohydrates and xylitol subdue Streptococcus mutans and Candida albicans adhesion and biofilm formation.

PubMed

Brambilla, Eugenio; Ionescu, Andrei C; Cazzaniga, Gloria; Ottobelli, Marco; Samaranayake, Lakshman P

2016-05-01

Dietary carbohydrates and polyols affect the microbial colonization of oral surfaces by modulating adhesion and biofilm formation. The aim of this study was to evaluate the influence of a select group of l-carbohydrates and polyols on either Streptococcus mutans or Candida albicans adhesion and biofilm formation in vitro. S. mutans or C. albicans suspensions were inoculated on polystyrene substrata in the presence of Tryptic soy broth containing 5% of the following compounds: d-glucose, d-mannose, l-glucose, l-mannose, d- and l-glucose (raceme), d- and l-mannose (raceme), l-glucose and l-mannose, sorbitol, mannitol, and xylitol. Microbial adhesion (2 h) and biofilm formation (24 h) were evaluated using MTT-test and Scanning Electron Microscopy (SEM). Xylitol and l-carbohydrates induced the lowest adhesion and biofilm formation in both the tested species, while sorbitol and mannitol did not promote C. albicans biofilm formation. Higher adhesion and biofilm formation was noted in both organisms in the presence of d-carbohydrates relative to their l-carbohydrate counterparts. These results elucidate, hitherto undescribed, interactions of the individually tested strains with l- and d-carbohydrates, and how they impact fungal and bacterial colonization. In translational terms, our data raise the possibility of using l-form of carbohydrates and xylitol for dietary control of oral plaque biofilms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Salivary Microbiome Diversity in Caries-Free and Caries-Affected Children.

PubMed

Jiang, Shan; Gao, Xiaoli; Jin, Lijian; Lo, Edward C M

2016-11-25

Dental caries (tooth decay) is an infectious disease. Its etiology is not fully understood from the microbiological perspective. This study characterizes the diversity of microbial flora in the saliva of children with and without dental caries. Children (3-4 years old) with caries ( n = 20) and without caries ( n = 20) were recruited. Unstimulated saliva (2 mL) was collected from each child and the total microbial genomic DNA was extracted. DNA amplicons of the V3-V4 hypervariable region of the bacterial 16S rRNA gene were generated and subjected to Illumina Miseq sequencing. A total of 17 phyla, 26 classes, 40 orders, 80 families, 151 genera, and 310 bacterial species were represented in the saliva samples. There was no significant difference in the microbiome diversity between caries-affected and caries-free children ( p > 0.05). The relative abundance of several species ( Rothia dentocariosa , Actinomyces graevenitzii , Veillonella sp. oral taxon 780 , Prevotella salivae , and Streptococcus mutans ) was higher in the caries-affected group than in the caries-free group ( p < 0.05). Fusobacterium periodonticum and Leptotrichia sp. oral clone FP036 were more abundant in caries-free children than in caries-affected children ( p < 0.05). The salivary microbiome profiles of caries-free and caries-affected children were similar. Salivary counts of certain bacteria such as R. dentocariosa and F. periodonticum may be useful for screening/assessing children's risk of developing caries.

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

NASA Astrophysics Data System (ADS)

Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

2015-08-01

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework which is developed as part of an interdisciplinary, iterative, model-data based approach fully integrating fieldwork and laboratory experiments with model development, testing, and application. SHIMMER is designed to simulate the establishment of microbial biomass and associated biogeochemical cycling during the initial stages of ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The model mechanistically describes and predicts transformations in carbon, nitrogen and phosphorus through aggregated components of the microbial community as a set of coupled ordinary differential equations. The rationale for development of the model arises from decades of empirical observation on the initial stages of soil development in glacier forefields. SHIMMER enables a quantitative and process focussed approach to synthesising the existing empirical data and advancing understanding of microbial and biogeochemical dynamics. Here, we provide a detailed description of SHIMMER. The performance of SHIMMER is then tested in two case studies using published data from the Damma Glacier forefield in Switzerland and the Athabasca Glacier in Canada. In addition, a sensitivity analysis helps identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass, and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Simulation results indicate that primary production is responsible for the initial build-up of substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter are identified as important in sustaining this productivity. Microbial production in young soils is supported by labile organic matter, whereas carbon stocks in older soils are more refractory. Nitrogen fixing bacteria are responsible for the initial accumulation of available nitrates in the soil. Biogeochemical rates are highly seasonal, as observed in experimental data. The development and application of SHIMMER not only provides important new insights into forefield dynamics, but also highlights aspects of these systems that require further field and laboratory research. The most pressing advances need to come in quantifying nutrient budgets and biogeochemical rates, in exploring seasonality, the fate of allochthonous deposition in relation to autochthonous production, and empirical studies of microbial growth and cell death, to increase understanding of how glacier forefield development contributes to the global biogeochemical cycling and climate in the future.

Microbial dormancy improves development and experimental validation of ecosystem model

DOE PAGES

Wang, Gangsheng; Jagadamma, Sindhu; Mayes, Melanie; ...

2014-07-11

Climate feedbacks from soils can result from environmental change followed by response of plant and microbial communities, and/or associated changes in nutrient cycling. Explicit consideration of microbial life history traits and functions may be necessary to predict climate feedbacks due to changes in the physiology and community composition of microbes and their associated effect on carbon cycling. Here, we enhanced the Microbial-Enzyme-mediated Decomposition (MEND) model by incorporating microbial dormancy and the ability to track multiple isotopes of carbon. We tested two versions of MEND, i.e., MEND with dormancy and MEND without dormancy, against long-term (270 d) lab incubations of fourmore » soils with isotopically-labeled substrates. MEND without dormancy adequately fitted multiple observations (total and 14C respiration, and dissolved organic carbon), but at the cost of significantly underestimating the total microbial biomass. The MEND with dormancy improved estimates of microbial biomass by 20 71% over the MEND without dormancy. We observed large differences for two fitted model parameters, the specific maintenance and growth rates for active microbes, depending on whether dormancy was considered. Together our model extrapolations of the incubation study show that long-term soil incubations with observations in multiple carbon pools are necessary to estimate both decomposition and microbial parameters. These efforts should provide essential support to future field- and global-scale simulations and enable more confident predictions of feedbacks between environmental change and carbon cycling.« less

Simulated Carbon Cycling in a Model Microbial Mat.

NASA Astrophysics Data System (ADS)

Decker, K. L.; Potter, C. S.

2006-12-01

We present here the novel addition of detailed organic carbon cycling to our model of a hypersaline microbial mat ecosystem. This ecosystem model, MBGC (Microbial BioGeoChemistry), simulates carbon fixation through oxygenic and anoxygenic photosynthesis, and the release of C and electrons for microbial heterotrophs via cyanobacterial exudates and also via a pool of dead cells. Previously in MBGC, the organic portion of the carbon cycle was simplified into a black-box rate of accumulation of simple and complex organic compounds based on photosynthesis and mortality rates. We will discuss the novel inclusion of fermentation as a source of carbon and electrons for use in methanogenesis and sulfate reduction, and the influence of photorespiration on labile carbon exudation rates in cyanobacteria. We will also discuss the modeling of decomposition of dead cells and the ultimate release of inorganic carbon. The detailed modeling of organic carbon cycling is important to the accurate representation of inorganic carbon flux through the mat, as well as to accurate representation of growth models of the heterotrophs under different environmental conditions. Because the model ecosystem is an analog of ancient microbial mats that had huge impacts on the atmosphere of early earth, this MBGC can be useful as a biological component to either early earth models or models of other planets that potentially harbor life.

Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stegen, James C.; Konopka, Allan; McKinely, Jim

Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, diversity, and community composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial diversity—the number ofmore » microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.« less

Variable-Internal-Stores models of microbial growth and metabolism with dynamic allocation of cellular resources.

PubMed

Nev, Olga A; van den Berg, Hugo A

2017-01-01

Variable-Internal-Stores models of microbial metabolism and growth have proven to be invaluable in accounting for changes in cellular composition as microbial cells adapt to varying conditions of nutrient availability. Here, such a model is extended with explicit allocation of molecular building blocks among various types of catalytic machinery. Such an extension allows a reconstruction of the regulatory rules employed by the cell as it adapts its physiology to changing environmental conditions. Moreover, the extension proposed here creates a link between classic models of microbial growth and analyses based on detailed transcriptomics and proteomics data sets. We ascertain the compatibility between the extended Variable-Internal-Stores model and the classic models, demonstrate its behaviour by means of simulations, and provide a detailed treatment of the uniqueness and the stability of its equilibrium point as a function of the availabilities of the various nutrients.

Changes in the Size of the Active Microbial Pool Explain Short-Term Soil Respiratory Responses to Temperature and Moisture

PubMed Central

Salazar-Villegas, Alejandro; Blagodatskaya, Evgenia; Dukes, Jeffrey S.

2016-01-01

Heterotrophic respiration contributes a substantial fraction of the carbon flux from soil to atmosphere, and responds strongly to environmental conditions. However, the mechanisms through which short-term changes in environmental conditions affect microbial respiration still remain unclear. Microorganisms cope with adverse environmental conditions by transitioning into and out of dormancy, a state in which they minimize rates of metabolism and respiration. These transitions are poorly characterized in soil and are generally omitted from decomposition models. Most current approaches to model microbial control over soil CO2 production relate responses to total microbial biomass (TMB) and do not differentiate between microorganisms in active and dormant physiological states. Indeed, few data for active microbial biomass (AMB) exist with which to compare model output. Here, we tested the hypothesis that differences in soil microbial respiration rates across various environmental conditions are more closely related to differences in AMB (e.g., due to activation of dormant microorganisms) than in TMB. We measured basal respiration (SBR) of soil incubated for a week at two temperatures (24 and 33°C) and two moisture levels (10 and 20% soil dry weight [SDW]), and then determined TMB, AMB, microbial specific growth rate, and the lag time before microbial growth (tlag) using the Substrate-Induced Growth Response (SIGR) method. As expected, SBR was more strongly correlated with AMB than with TMB. This relationship indicated that each g active biomass C contributed ~0.04 g CO2-C h−1 of SBR. TMB responded very little to short-term changes in temperature and soil moisture and did not explain differences in SBR among the treatments. Maximum specific growth rate did not respond to environmental conditions, suggesting that the dominant microbial populations remained similar. However, warmer temperatures and increased soil moisture both reduced tlag, indicating that favorable abiotic conditions activated soil microorganisms. We conclude that soil respiratory responses to short-term changes in environmental conditions are better explained by changes in AMB than in TMB. These results suggest that decomposition models that explicitly represent microbial carbon pools should take into account the active microbial pool, and researchers should be cautious in comparing modeled microbial pool sizes with measurements of TMB. PMID:27148213

Measurements and modeling of surface-atmosphere exchange of microorganisms in Mediterranean grassland

NASA Astrophysics Data System (ADS)

Carotenuto, Federico; Georgiadis, Teodoro; Gioli, Beniamino; Leyronas, Christel; Morris, Cindy E.; Nardino, Marianna; Wohlfahrt, Georg; Miglietta, Franco

2017-12-01

Microbial aerosols (mainly composed of bacterial and fungal cells) may constitute up to 74 % of the total aerosol volume. These biological aerosols are not only relevant to the dispersion of pathogens, but they also have geochemical implications. Some bacteria and fungi may, in fact, serve as cloud condensation or ice nuclei, potentially affecting cloud formation and precipitation and are active at higher temperatures compared to their inorganic counterparts. Simulations of the impact of microbial aerosols on climate are still hindered by the lack of information regarding their emissions from ground sources. This present work tackles this knowledge gap by (i) applying a rigorous micrometeorological approach to the estimation of microbial net fluxes above a Mediterranean grassland and (ii) developing a deterministic model (the PLAnET model) to estimate these emissions on the basis of a few meteorological parameters that are easy to obtain. The grassland is characterized by an abundance of positive net microbial fluxes and the model proves to be a promising tool capable of capturing the day-to-day variability in microbial fluxes with a relatively small bias and sufficient accuracy. PLAnET is still in its infancy and will benefit from future campaigns extending the available training dataset as well as the inclusion of ever more complex and critical phenomena triggering the emission of microbial aerosol (such as rainfall). The model itself is also adaptable as an emission module for dispersion and chemical transport models, allowing further exploration of the impact of land-cover-driven microbial aerosols on the atmosphere and climate.

Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-05-01

The sensitivity of polar regions to raising global temperatures is reflected in rapidly changing hydrological processes associated with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and stimulation of other soil-borne greenhouse gas emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and other environmental factors. Soil structural elements such as aggregates and layering affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hot spots). We developed a mechanistic individual-based model to quantify microbial activity dynamics in soil pore networks considering transport processes and enzymatic activity associated with methane production in soil. The model was upscaled from single aggregates to the soil profile where freezing/thawing provides macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged profile) for resolving methane production and oxidation rates. Methane transport pathways by diffusion and ebullition of bubbles vary with hydration dynamics. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability and enzyme activity) on long-term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

The social structure of microbial community involved in colonization resistance.

PubMed

He, Xuesong; McLean, Jeffrey S; Guo, Lihong; Lux, Renate; Shi, Wenyuan

2014-03-01

It is well established that host-associated microbial communities can interfere with the colonization and establishment of microbes of foreign origins, a phenomenon often referred to as bacterial interference or colonization resistance. However, due to the complexity of the indigenous microbiota, it has been extremely difficult to elucidate the community colonization resistance mechanisms and identify the bacterial species involved. In a recent study, we have established an in vitro mice oral microbial community (O-mix) and demonstrated its colonization resistance against an Escherichia coli strain of mice gut origin. In this study, we further analyzed the community structure of the O-mix by using a dilution/regrowth approach and identified the bacterial species involved in colonization resistance against E. coli. Our results revealed that, within the O-mix there were three different types of bacterial species forming unique social structure. They act as 'Sensor', 'Mediator' and 'Killer', respectively, and have coordinated roles in initiating the antagonistic action and preventing the integration of E. coli. The functional role of each identified bacterial species was further confirmed by E. coli-specific responsiveness of the synthetic communities composed of different combination of the identified players. The study reveals for the first time the sophisticated structural and functional organization of a colonization resistance pathway within a microbial community. Furthermore, our results emphasize the importance of 'Facilitation' or positive interactions in the development of community-level functions, such as colonization resistance.

A Stoichioproteomic Analysis of Samples from the Human Microbiome Project

PubMed Central

Vecchio-Pagan, Briana; Bewick, Sharon; Mainali, Kumar; Karig, David K.; Fagan, William F.

2017-01-01

Ecological stoichiometry (ES) uses organism-specific elemental content to explain differences in species life histories, species interactions, community organization, environmental constraints and even ecosystem function. Although ES has been successfully applied to a range of different organisms, most emphasis on microbial ecological stoichiometry focuses on lake, ocean, and soil communities. With the recent advances in human microbiome research, however, large amounts of data are being generated that describe differences in community composition across body sites and individuals. We suggest that ES may provide a framework for beginning to understand the structure, organization, and function of human microbial communities, including why certain organisms exist at certain locations, and how they interact with both the other microbes in their environment and their human host. As a first step, we undertake a stoichioproteomic analysis of microbial communities from different body sites. Specifically, we compare and contrast the elemental composition of microbial protein samples using annotated sequencing data from 690 gut, vaginal, oral, nares, and skin samples currently available through the Human Microbiome Project. Our results suggest significant differences in both the median and variance of the carbon, oxygen, nitrogen, and sulfur contents of microbial protein samples from different locations. For example, whereas proteins from vaginal sites are high in carbon, proteins from skin and nasal sites are high in nitrogen and oxygen. Meanwhile, proteins from stool (the gut) are particularly high in sulfur content. We interpret these differences in terms of the local environments at different human body sites, including atmospheric exposure and food intake rates. PMID:28769875

Histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses

NASA Astrophysics Data System (ADS)

Borgwardt, Derek S.; Martin, Aaron D.; van Hemert, Jonathan R.; Yang, Jianyi; Fischer, Carol L.; Recker, Erica N.; Nair, Prashant R.; Vidva, Robinson; Chandrashekaraiah, Shwetha; Progulske-Fox, Ann; Drake, David; Cavanaugh, Joseph E.; Vali, Shireen; Zhang, Yang; Brogden, Kim A.

2014-01-01

Histatins are human salivary gland peptides with anti-microbial and anti-inflammatory activities. In this study, we hypothesized that histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and attenuates HagB-induced chemokine responses in human myeloid dendritic cells. Histatin 5 bound to immobilized HagB in a surface plasmon resonance (SPR) spectroscopy-based biosensor system. SPR spectroscopy kinetic and equilibrium analyses, protein microarray studies, and I-TASSER structural modeling studies all demonstrated two histatin 5 binding sites on HagB. One site had a stronger affinity with a KD1 of 1.9 μM and one site had a weaker affinity with a KD2 of 60.0 μM. Binding has biological implications and predictive modeling studies and exposure of dendritic cells both demonstrated that 20.0 μM histatin 5 attenuated (p < 0.05) 0.02 μM HagB-induced CCL3/MIP-1α, CCL4/MIP-1β, and TNFα responses. Thus histatin 5 is capable of attenuating chemokine responses, which may help control oral inflammation.

Ecological and soil hydraulic implications of microbial responses to stress - A modeling analysis

NASA Astrophysics Data System (ADS)

Brangarí, Albert C.; Fernàndez-Garcia, Daniel; Sanchez-Vila, Xavier; Manzoni, Stefano

2018-06-01

A better understanding of microbial dynamics in porous media may lead to improvements in the design and management of a number of technological applications, ranging from the degradation of contaminants to the optimization of agricultural systems. To this aim, there is a recognized need for predicting the proliferation of soil microbial biomass (often organized in biofilms) under different environments and stresses. We present a general multi-compartment model to account for physiological responses that have been extensively reported in the literature. The model is used as an explorative tool to elucidate the ecological and soil hydraulic consequences of microbial responses, including the production of extracellular polymeric substances (EPS), the induction of cells into dormancy, and the allocation and reuse of resources between biofilm compartments. The mechanistic model is equipped with indicators allowing the microorganisms to monitor environmental and biological factors and react according to the current stress pressures. The feedbacks of biofilm accumulation on the soil water retention are also described. Model runs simulating different degrees of substrate and water shortage show that adaptive responses to the intensity and type of stress provide a clear benefit to microbial colonies. Results also demonstrate that the model may effectively predict qualitative patterns in microbial dynamics supported by empirical evidence, thereby improving our understanding of the effects of pore-scale physiological mechanisms on the soil macroscale phenomena.

Current therapies for xerostomia and salivary gland hypofunction associated with cancer therapies.

PubMed

Nieuw Amerongen, A V; Veerman, E C I

2003-04-01

In cancer patients, as in the general population, medication is the most common cause of xerostomia. In general, saliva flow in these patients can be stimulated by mechanical or pharmacological stimulation of the salivary glands. Painful damaged oral mucosa can be treated by softening, lubricating mouthwashes or gels. A specific group of patients are those receiving radiotherapy for malignant tumours in the head and neck region. This treatment is inevitably associated with damages to the oral tissues, including the salivary glands, resulting in salivary gland hypofunction. When residual secretory capacity is present, it is advisable to stimulate the salivary glands by mechanical or gustatory stimuli regularly in these patients as supportive oral care. Alternatively, salivary flow can be stimulated by the use of cholinergic pharmaceutical preparations, such as pilocarpine or cevimeline. After the radiation therapy is ended, a dental check-up should be done every 3 months to allow control of any incipient oral inflammation and dental decay. For daily use, a special dentifrice (e.g. children's toothpaste) is recommended, since the taste of a regular dentifrice may be too strong for these patients. Nocturnal oral dryness can be alleviated by spraying the oral surfaces with water, or by applying a small amount of dentifrice on the dental smooth surfaces. When stimulation of salivary secretion fails, patients can be given palliative oral care in the form of application of mouthwashes and saliva substitutes. The daily use of a mouthwash, e.g. Biotène, Oral Balance or Zendium, or one of the saliva substitutes is indicated. Different types of saliva substitutes are now commercially available, containing different polymers as thickening agents, e.g. carboxymethylcellulose (Oralube and Glandosane), polyacrylic acid, and xanthan gum (Xialine). Recent developments, which are, however, still in the experimental stage, are bio-active saliva substitutes and mouthwashes containing antimicrobial peptides to protect the oral tissues against microbial colonization and to suppress and to cure mucosal and gingival inflammation.

Models of microbiome evolution incorporating host and microbial selection.

PubMed

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong parental contribution, when host-mediated selection acts on microbes concomitantly. We present a computational framework that integrates different selective processes acting on the evolution of microbiomes. Our framework demonstrates that selection acting on microbes can have a strong effect on microbial diversities and fitnesses, whereas selection on hosts can have weaker outcomes.

Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes

PubMed Central

Abeles, Shira R.; Ly, Melissa; Santiago-Rodriguez, Tasha M.; Pride, David T.

2015-01-01

Viruses are integral members of the human microbiome. Many of the viruses comprising the human virome have been identified as bacteriophage, and little is known about how they respond to perturbations within the human ecosystem. The intimate association of phage with their cellular hosts suggests their communities may change in response to shifts in bacterial community membership. Alterations to human bacterial biota can result in human disease including a reduction in the host's resilience to pathogens. Here we report the ecology of oral and fecal viral communities and their responses to long-term antibiotic therapy in a cohort of human subjects. We found significant differences between the viral communities of each body site with a more heterogeneous fecal virus community compared with viruses in saliva. We measured the relative diversity of viruses, and found that the oral viromes were significantly more diverse than fecal viromes. There were characteristic changes in the membership of oral and fecal bacterial communities in response to antibiotics, but changes in fecal viral communities were less distinguishing. In the oral cavity, an abundance of papillomaviruses found in subjects on antibiotics suggests an association between antibiotics and papillomavirus production. Despite the abundance of papillomaviruses identified, in neither the oral nor the fecal viromes did antibiotic therapy have any significant impact upon overall viral diversity. There was, however, an apparent expansion of the reservoir of genes putatively involved in resistance to numerous classes of antibiotics in fecal viromes that was not paralleled in oral viromes. The emergence of antibiotic resistance in fecal viromes in response to long-term antibiotic therapy in humans suggests that viruses play an important role in the resilience of human microbial communities to antibiotic disturbances. PMID:26309137

Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes.

PubMed

Abeles, Shira R; Ly, Melissa; Santiago-Rodriguez, Tasha M; Pride, David T

2015-01-01

Viruses are integral members of the human microbiome. Many of the viruses comprising the human virome have been identified as bacteriophage, and little is known about how they respond to perturbations within the human ecosystem. The intimate association of phage with their cellular hosts suggests their communities may change in response to shifts in bacterial community membership. Alterations to human bacterial biota can result in human disease including a reduction in the host's resilience to pathogens. Here we report the ecology of oral and fecal viral communities and their responses to long-term antibiotic therapy in a cohort of human subjects. We found significant differences between the viral communities of each body site with a more heterogeneous fecal virus community compared with viruses in saliva. We measured the relative diversity of viruses, and found that the oral viromes were significantly more diverse than fecal viromes. There were characteristic changes in the membership of oral and fecal bacterial communities in response to antibiotics, but changes in fecal viral communities were less distinguishing. In the oral cavity, an abundance of papillomaviruses found in subjects on antibiotics suggests an association between antibiotics and papillomavirus production. Despite the abundance of papillomaviruses identified, in neither the oral nor the fecal viromes did antibiotic therapy have any significant impact upon overall viral diversity. There was, however, an apparent expansion of the reservoir of genes putatively involved in resistance to numerous classes of antibiotics in fecal viromes that was not paralleled in oral viromes. The emergence of antibiotic resistance in fecal viromes in response to long-term antibiotic therapy in humans suggests that viruses play an important role in the resilience of human microbial communities to antibiotic disturbances.

Frequency of periodontal pathogens and Helicobacter pylori in the mouths and stomachs of obese individuals submitted to bariatric surgery: a cross-sectional study

PubMed Central

PATARO, André Luiz; CORTELLI, Sheila Cavalca; ABREU, Mauro Henrique Nogueira Guimarães; CORTELLI, José Roberto; FRANCO, Gilson Cesar Nobre; AQUINO, Davi Romeiro; COTA, Luis Otavio Miranda; COSTA, Fernando Oliveira

2016-01-01

ABSTRACT Objectives This cross-sectional study compared the frequency of oral periodontopathogens and H. pylori in the mouths and stomachs of obese individuals with or without periodontitis submitted to bariatric surgery. Material and Methods One hundred and fifty-four men and women aged 18-65 were conveniently distributed into four groups. Two groups were composed of individuals who underwent bariatric surgery with (BP) (n=40) and without (BNP) (n=39) periodontitis and two obese control groups with (CP) (n=35) and without (CNP) (n=40) periodontitis. The oral pathogens Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Parvimonas micra, Treponema denticola, Tannerella forsythia, Campylobacter rectus, and Helicobacter pylori were detected by a polymerase chain reaction technique using saliva, tongue and stomach biopsy samples. Results Statistical analysis demonstrated that periodontopathogens were highly frequent in the mouth (up to 91.4%). In the bariatric surgically treated group, orally, P. gingivalis, T. denticola and T. forsythia were more frequent in periodontitis, while C. rectus was more frequent in non-periodontitis subjects. Stomach biopsies also revealed the high frequency of five oral species in both candidates for bariatric surgery (91.6%) and the bariatric (83.3%) groups. H. pylori was frequently detected in the mouth (50.0%) and stomach (83.3%). In the stomach, oral species and H. pylori appeared in lower frequency in the bariatric group. Conclusions Obese individuals showed high frequencies of periodontopathogens and H. pylori in their mouths and stomachs. Bariatric surgery showed an inverse microbial effect on oral and stomach environments by revealing higher oral and lower stomach bacterial frequencies. PMID:27383704

Measuring and modeling C flux rates through the central metabolic pathways in microbial communities using position-specific 13C-labeled tracers

NASA Astrophysics Data System (ADS)

Dijkstra, P.; van Groenigen, K.; Hagerty, S.; Salpas, E.; Fairbanks, D. E.; Hungate, B. A.; KOCH, G. W.; Schwartz, E.

2012-12-01

The production of energy and metabolic precursors occurs in well-known processes such as glycolysis and Krebs cycle. We use position-specific 13C-labeled metabolic tracers, combined with models of microbial metabolic organization, to analyze the response of microbial community energy production, biosynthesis, and C use efficiency (CUE) in soils, decomposing litter, and aquatic communities. The method consists of adding position-specific 13C -labeled metabolic tracers to parallel soil incubations, in this case 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose. The measurement of CO2 released from the labeled tracers is used to calculate the C flux rates through the various metabolic pathways. A simplified metabolic model consisting of 23 reactions is solved using results of the metabolic tracer experiments and assumptions of microbial precursor demand. This new method enables direct estimation of fundamental aspects of microbial energy production, CUE, and soil organic matter formation in relatively undisturbed microbial communities. We will present results showing the range of metabolic patterns observed in these communities and discuss results from testing metabolic models.

Modeling microbial diversity in anaerobic digestion through an extended ADM1 model.

PubMed

Ramirez, Ivan; Volcke, Eveline I P; Rajinikanth, Rajagopal; Steyer, Jean-Philippe

2009-06-01

The anaerobic digestion process comprises a whole network of sequential and parallel reactions, of both biochemical and physicochemical nature. Mathematical models, aiming at understanding and optimization of the anaerobic digestion process, describe these reactions in a structured way, the IWA Anaerobic Digestion Model No. 1 (ADM1) being the most well established example. While these models distinguish between different microorganisms involved in different reactions, to our knowledge they all neglect species diversity between organisms with the same function, i.e. performing the same reaction. Nevertheless, available experimental evidence suggests that the structure and properties of a microbial community may be influenced by process operation and on their turn also determine the reactor functioning. In order to adequately describe these phenomena, mathematical models need to consider the underlying microbial diversity. This is demonstrated in this contribution by extending the ADM1 to describe microbial diversity between organisms of the same functional group. The resulting model has been compared with the traditional ADM1 in describing experimental data of a pilot-scale hybrid Upflow Anaerobic Sludge Filter Bed (UASFB) reactor, as well as in a more detailed simulation study. The presented model is further shown useful in assessing the relationship between reactor performance and microbial community structure in mesophilic CSTRs seeded with slaughterhouse wastewater when facing increasing levels of ammonia.

Modeling biogechemical reactive transport in a fracture zone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Molinero, Jorge; Samper, Javier; Yang, Chan Bing, and Zhang, Guoxiang

2005-01-14

A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes inmore » biochemical parameters.« less

Investigating the initial stages of soil formation in glacier forefields using the new biogeochemical model: SHIMMER

NASA Astrophysics Data System (ADS)

Bradley, James; Anesio, Alexandre; Arndt, Sandra; Sabacka, Marie; Barker, Gary; Benning, Liane; Blacker, Joshua; Singarayer, Joy; Tranter, Martyn; Yallop, Marian

2016-04-01

Glaciers and ice sheets in Polar and alpine regions are retreating in response to recent climate warming, exposing terrestrial ecosystems that have been locked under the ice for thousands of years. Exposed soils exhibit successional characteristics that can be characterised using a chronosequence approach. Decades of empirical research in glacier forefields has shown that soils are quickly colonised by microbes which drive biogeochemical cycling of elements and affect soil properties including nutrient concentrations, carbon fluxes and soil stability (Bradley et al, 2014). The characterisation of these soils is important for our understanding of the cycling of organic matter under extreme environmental and nutrient limiting conditions, and their potential contribution to global biogeochemical cycles. This is particularly important as these new areas will become more geographically expansive with continued ice retreat. SHIMMER (Soil biogeocHemIcal Model of Microbial Ecosystem Response) (Bradley et al, 2015) is a new mathematical model that simulates biogeochemical and microbial dynamics in glacier forefields. The model captures, explores and predicts the growth of different microbial groups (classified by function), and the associated cycling of carbon, nitrogen and phosphorus along a chronosequence. SHIMMER improves typical soil model formulations by including explicit representation of microbial dynamics, and those processes which are shown to be important for glacier forefields. For example, we categorise microbial groups by function to represent the diversity of soil microbial communities, and include the different metabolic needs and physiological pathways of microbial organisms commonly found in glacier forefields (e.g. microbes derived from underneath the glacier, typical soil bacteria, and microbes that can fix atmospheric nitrogen and assimilate soil nitrogen). Here, we present data from a study where we integrated modelling using SHIMMER with empirical observations from chronosequences from the forefield of Midtre Lovénbreen, Svalbard (78°N), to investigate the first 120 years of soil development. We carried out an in depth analysis of the model dynamics and determined the most sensitive parameters. We then used laboratory measurements to derive values for those parameters: bacterial growth rate, growth efficiency and temperature dependency. By applying the model to the High-Arctic forefield and integrating the measured parameter values, we could refine the model and easily predict the rapid accumulation of microbial biomass that was observed in our field data. Furthermore, we show that the bacterial production is dominated by autotrophy (rather than heterotrophy). Heterotrophic production in young soils (0-20 years) is supported by labile substrate, whereas carbon stocks in older soils (60-120 years) are more refractory. Nitrogen fixing organisms are responsible for the initial accumulation of available nitrates in the soil. However, microbial processes alone do not explain the build-up of organic matter observed in the field data record. Consequently, the model infers that allochthonous deposition of organic material may play a significant contributory role that could accelerate or facilitate further microbial growth. SHIMMER provides a quantitative evaluation on the dynamics of glacier forefield systems that have previously largely been explored through qualitative interpretation of datasets. References Bradley J.A., Singarayer J.S., Anesio A.M. (2014) Microbial community dynamics in the forefield of glaciers. Proceedings Biological sciences / The Royal Society 281(1795), 2793-2802. (doi:10.1098/rspb.2014.0882). Bradley J.A., Anesio A.M., Singarayer J.S., Heath M.R., Arndt S. (2015) SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems. Geosci Model Dev 8(10), 3441-3470. (doi:10.5194/gmd-8-3441-2015).

Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy.

PubMed

Xu, Yuan; Teng, Fei; Huang, Shi; Lin, Zhengmei; Yuan, Xiao; Zeng, Xiaowei; Yang, Fang

2014-02-01

A growing body of evidence has implicated human oral microbiota in the aetiology of oral and systemic diseases. Nasopharyngeal carcinoma (NPC), an epithelial-originated malignancy, has a complex aetiology not yet fully understood. Chemoradiation therapy of NPC can affect oral microbiota and is usually accompanied by plaque accumulation. Thus, the study aimed to understand the diversity, divergence and development of the oral microbiota in NPC patients and their associated treatment, which might provide useful insights into disease aetiology and treatment side effects. A longitudinal study was designed that included three Chinese adults with NPC. Saliva samples were collected at three time points: prior to the chemoradiation treatment (carcinoma baseline, or CB), 7 months post-treatment (carcinoma-after-therapy phase 1 or CA1) and 12 months post-treatment (carcinoma-after-therapy phase 2 or CA2). Pyrosequencing of the bacterial 16S ribosomal DNA (rDNA) V1-V3 hypervariable region was employed to characterise the microbiota. Saliva samples of three healthy subjects from our former study were employed as healthy controls. Principal coordinates analysis (PCoA), Metastats and random forest prediction models were used to reveal the key microbial members associated with NPC and its treatment programme. (1) In total, 412 bacterial species from at least 107 genera and 13 phyla were found in the saliva samples of the NPC patients. (2) PCoA revealed that not only were the microbiota from NPC patients distinct from those of healthy controls (p<0.001) but also that separation was found on the saliva microbiota between pre- and post-therapy (p<0.001) in the NPC samples. (3) At the genus level and the operational taxonomic unit (OTU) level, Streptococcus was found with lower abundance in NPC samples. (4) Chemoradiation therapy did not incur similar changes in microbiota structure among the three NPC patients; the microbiota in one of them stayed largely steady, while those in the other two showed significant alteration. This is the first study employing culture-independent techniques to interrogate the phylogenetic diversity, divergence and temporal development of oral microbiota in NPC patients. Our results indicated that certain bacterial taxa might be associated with NPC and that oral microbiota of NPC patients might respond to the chemoradiation therapy in a host-specific manner. Further investigation with larger sample size should help to validate the links between oral microbiota and NPC. Copyright © 2013 Elsevier Ltd. All rights reserved.

A bacterial extract of OM-85 Broncho-Vaxom prevents allergic rhinitis in mice.

PubMed

Han, Ling; Zheng, Chao-Pan; Sun, Yue-Qi; Xu, Geng; Wen, Weiping; Fu, Qing-Ling

2014-01-01

According to the hygiene hypothesis, bacterial infections during early life contribute to a reduced incidence of asthma in animals. However, the effects of microbial products at a safe dose and within a rational time course on the prevention of allergic rhinitis (AR) have been inconclusive. This study investigated the immunomodulatory effects of oral administration of a bacterial extract, OM-85 Broncho-Vaxom (BV), with a low dose and general time course, which is currently used for respiratory infections in humans, on AR inflammation in mice. We developed a mouse model of ovalbumin (OVA)-induced AR allergic inflammation in the nose mucosa of mice. Low doses of OM-85 BV were orally administered for 3 months (long term) before sensitization. We evaluated nasal symptoms, pathology in the nose, inflammatory cells, and the levels of T helper 1 (Th1)/Th2 cytokines in the nasal lavage fluids, and the serum levels of specific IgE and IgG1. We also observed enhanced effects of OM-85 BV with 1 month (short term) of treatment. We found that long-term pretreatment with OM-85 BV protected the mice from the majority of allergy-specific symptoms; specifically, OM-85 BV suppressed nasal symptoms, inhibited eosinophil infiltration in the nose, inhibited inflammatory infiltrates and the Th2 response by reducing cytokines (IL-4, IL-5, or IL-13) in the nasal lavage fluids, and reduced IgE and IgG1 levels. Furthermore, short-term treatment with OM-85 BV decreased the levels of Th2 cytokines and IgE. Taken together, our data suggested that OM-85 BV is a low-cost alternative candidate to prevent AR with simple oral administration.

A bacterial extract of OM-85 Broncho-Vaxom prevents allergic rhinitis in mice.

PubMed

Han, L; Zheng, C-P; Sun, Y-Q; Xu, G; Wen, W; Fu, Q-L

2013-12-06

According to the hygiene hypothesis, bacterial infections during early life contribute to a reduced incidence of asthma in animals. However, the effects of microbial products at a safe dose and within a rational time course on the prevention of allergic rhinitis (AR) have been inconclusive. This study investigated the immunomodulatory effects of oral administration of a bacterial extract, OM-85 Broncho-Vaxom (BV), with a low dose and general time course, which is currently used for respiratory infections in humans, on AR inflammation in mice. We developed a mouse model of ovalbumin (OVA)-induced AR allergic inflammation in the nose mucosa of mice. Low doses of OM-85 BV were orally administered for 3 months (long term) before sensitization. We evaluated nasal symptoms, pathology in the nose, inflammatory cells, and the levels of T helper 1 (Th1)/Th2 cytokines in the nasal lavage fluids, and the serum levels of specific IgE and IgG1. We also observed enhanced effects of OM-85BV with 1 month (short term) of treatment. We found that long-term pretreatment with OM-85 BV protected the mice from the majority of allergy-specific symptoms; specifically, OM-85 BV suppressed nasal symptoms, inhibited eosinophil infiltration in the nose, inhibited inflammatory infiltrates and the Th2 response by reducing cytokines (IL-4, IL-5, or IL-13) in the nasal lavage fluids, and reduced IgE and IgG1 levels. Furthermore, short-term treatment with OM-85 BV decreased the levels of Th2 cytokines and IgE. Taken together, our data suggested that OM-85 BV is a low-cost alternative candidate to prevent AR with simple oral administration.

Weaker soil carbon-climate feedbacks resulting from microbial and abiotic interactions

NASA Astrophysics Data System (ADS)

Tang, Jinyun; Riley, William J.

2015-01-01

The large uncertainty in soil carbon-climate feedback predictions has been attributed to the incorrect parameterization of decomposition temperature sensitivity (Q10; ref. ) and microbial carbon use efficiency. Empirical experiments have found that these parameters vary spatiotemporally, but such variability is not included in current ecosystem models. Here we use a thermodynamically based decomposition model to test the hypothesis that this observed variability arises from interactions between temperature, microbial biogeochemistry, and mineral surface sorptive reactions. We show that because mineral surfaces interact with substrates, enzymes and microbes, both Q10 and microbial carbon use efficiency are hysteretic (so that neither can be represented by a single static function) and the conventional labile and recalcitrant substrate characterization with static temperature sensitivity is flawed. In a 4-K temperature perturbation experiment, our fully dynamic model predicted more variable but weaker soil carbon-climate feedbacks than did the static Q10 and static carbon use efficiency model when forced with yearly, daily and hourly variable temperatures. These results imply that current Earth system models probably overestimate the response of soil carbon stocks to global warming. Future ecosystem models should therefore consider the dynamic interactions between sorptive mineral surfaces, substrates and microbial processes.

Data-Driven Microbial Modeling for Soil Carbon Decomposition and Stabilization

NASA Astrophysics Data System (ADS)

Luo, Yiqi; Chen, Ji; Chen, Yizhao; Feng, Wenting

2017-04-01

Microorganisms have long been known to catalyze almost all the soil organic carbon (SOC) transformation processes (e.g., decomposition, stabilization, and mineralization). Representing microbial processes in Earth system models (ESMs) has the potential to improve projections of SOC dynamics. We have recently examined (1) relationships of microbial functions with environmental factors and (2) microbial regulations of decomposition and other key soil processes. According to three lines of evidence, we have developed a data-driven enzyme (DENZY) model to simulate soil microbial decomposition and stabilization. First, our meta-analysis of 64 published field studies showed that field experimental warming significantly increased soil microbial communities abundance, which is negatively correlated with the mean annual temperature. The negative correlation indicates that warming had stronger effects in colder than warmer regions. Second, we found that the SOC decomposition, especially the transfer between labile SOC and protected SOC, is nonlinearly regulated by soil texture parameters, such as sand and silt contents. Third, we conducted a global analysis of the C-degrading enzyme activities, soil respiration, and SOC content under N addition. Our results show that N addition has contrasting effects on cellulase (hydrolytic C-degrading enzymes) and ligninase (oxidative C-degrading enzymes) activities. N-enhanced cellulase activity contributes to the minor stimulation of soil respiration whereas N-induced repression on ligninase activity drives soil C sequestration. Our analysis links the microbial extracellular C-degrading enzymes to the SOC dynamics at ecosystem scales across scores of experimental sites around the world. It offers direct evidence that N-induced changes in microbial community and physiology play fundamental roles in controlling the soil C cycle. Built upon those three lines of empirical evidence, the DENZY model includes two enzyme pools and explicitly characterizes two classes of extracellular enzyme activities: one that degrades organic molecules containing both C and N (e.g., chitin or protein) and another that degrades only C (e.g., cellulose). The DENZY model assumes that the microbes allocate resources to different enzyme pools so as to exactly satisfy microbial CN ratio stoichiometry in response to changes in climate conditions and soil attributes. The DENZY model can simulate differential effects of nitrogen fertilization on the two groups of enzymes and thus soil respiration and SOC dynamics. We will select field experimental sites to test the DENZY model. With increasing amounts of available observations and data synthesis, this DENZY model will be better parameterized and have a potential to reveal how responses of microbial enzymes to environmental changes regulate soil carbon decomposition and stabilization.

Analysis of a novel class of predictive microbial growth models and application to coculture growth.

PubMed

Poschet, F; Vereecken, K M; Geeraerd, A H; Nicolaï, B M; Van Impe, J F

2005-04-15

In this paper, a novel class of microbial growth models is analysed. In contrast with the currently used logistic type models (e.g., the model of Baranyi and Roberts [Baranyi, J., Roberts, T.A., 1994. A dynamic approach to predicting bacterial growth in food. International Journal of Food Microbiology 23, 277-294]), the novel model class, presented in Van Impe et al. (Van Impe, J.F., Poschet, F., Geeraerd, A.H., Vereecken, K.M., 2004. Towards a novel class of predictive microbial growth models. International Journal of Food Microbiology, this issue), explicitly incorporates nutrient exhaustion and/or metabolic waste product effects inducing stationary phase behaviour. As such, these novel model types can be extended in a natural way towards microbial interactions in cocultures and microbial growth in structured foods. Two illustrative case studies of the novel model types are thoroughly analysed and compared to the widely used model of Baranyi and Roberts. In a first case study, the stationary phase is assumed to be solely resulting from toxic product inhibition and is described as a function of the pH-evolution. In the second case study, substrate exhaustion is the sole cause of the stationary phase. Finally, a more complex case study of a so-called P-model is presented, dealing with a coculture inhibition of Listeria innocua mediated by lactic acid production of Lactococcus lactis.

Mathematical modeling of Kluyveromyces marxianus growth in solid-state fermentation using a packed-bed bioreactor.

PubMed

Mazutti, Marcio A; Zabot, Giovani; Boni, Gabriela; Skovronski, Aline; de Oliveira, Débora; Di Luccio, Marco; Rodrigues, Maria Isabel; Maugeri, Francisco; Treichel, Helen

2010-04-01

This work investigated the growth of Kluyveromyces marxianus NRRL Y-7571 in solid-state fermentation in a medium composed of sugarcane bagasse, molasses, corn steep liquor and soybean meal within a packed-bed bioreactor. Seven experimental runs were carried out to evaluate the effects of flow rate and inlet air temperature on the following microbial rates: cell mass production, total reducing sugar and oxygen consumption, carbon dioxide and ethanol production, metabolic heat and water generation. A mathematical model based on an artificial neural network was developed to predict the above-mentioned microbial rates as a function of the fermentation time, initial total reducing sugar concentration, inlet and outlet air temperatures. The results showed that the microbial rates were temperature dependent for the range 27-50 degrees C. The proposed model efficiently predicted the microbial rates, indicating that the neural network approach could be used to simulate the microbial growth in SSF.

In vitro effect of coffee on oral malodor-related parameters.

PubMed

Gov, Y; Sterer, N; Rosenberg, M

2010-06-01

In the present investigation we examined the effect of three brands of coffee on microbial volatile sulfur compound (VSC) production using a decarboxylase incubation assay. Stimulated whole saliva was added to decarboxylase medium supplemented with 0.005% hemin. Incubation was carried out anaerobically for 72 h in the presence of powdered coffee at concentrations ranging from 0.5 to 2.0% (w/v), as compared with appropriate controls. VSC levels were determined using OralChroma™ and Halimeter™ and malodor was scored by an experienced odor judge. Experimental biofilm was grown with or without coffee and examined for VSC-producing bacteria using confocal laser scanning microscopy. Results showed that VSC and malodor levels were decreased by 85% in the presence of 2% coffee. The data suggest that coffee components reduce malodor production, VSC levels and experimental biofilm VSC-producing bacteria in vitro.

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways.

PubMed

Tan, Jian; McKenzie, Craig; Vuillermin, Peter J; Goverse, Gera; Vinuesa, Carola G; Mebius, Reina E; Macia, Laurence; Mackay, Charles R

2016-06-21

The incidence of food allergies in western countries has increased dramatically in recent decades. Tolerance to food antigens relies on mucosal CD103(+) dendritic cells (DCs), which promote differentiation of regulatory T (Treg) cells. We show that high-fiber feeding in mice improved oral tolerance and protected from food allergy. High-fiber feeding reshaped gut microbial ecology and increased the release of short-chain fatty acids (SCFAs), particularly acetate and butyrate. High-fiber feeding enhanced oral tolerance and protected against food allergy by enhancing retinal dehydrogenase activity in CD103(+) DC. This protection depended on vitamin A in the diet. This feeding regimen also boosted IgA production and enhanced T follicular helper and mucosal germinal center responses. Mice lacking GPR43 or GPR109A, receptors for SCFAs, showed exacerbated food allergy and fewer CD103(+) DCs. Dietary elements, including fiber and vitamin A, therefore regulate numerous protective pathways in the gastrointestinal tract, necessary for immune non-responsiveness to food antigens. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Safety of Pochonia chlamydosporia var catenulata in acute oral and dermal toxicity/pathogenicity evaluations in rats and rabbits.

PubMed

García, Liseth; Bulnes, Carlos; Melchor, Gleiby; Vega, Ernesto; Ileana, Miranda; de Oca, Nivian Montes; Hidalgo, Leopoldo; Marrero, Eva

2004-10-01

The nematophagous fungus, Pochonia chlamydosporia var. catenulata (Kamyschlco ex Barron & Onions) Zare & W-Gams, was investigated as a potential biocontrol agent in integrated pest management strategy for Meloidogyne incognita (Kofoid and White) Chitwood in vegetable crops in Cuba. An acute oral and dermal toxicity/patogenicity study was performed to determine the safety of this fungus in non-target organisms. In the first study, a 1-dose level of 5 x 10(8) units of the microbial pest control agent/treated rat was used. Mortality or clinical signs were not evident and no adverse effects on body weight, hematology, microbiology and gross or microscopic pathology were observed. Food and water consumption was not significantly different between control and treated groups. In the acute dermal toxicity study, there was neither mortality nor clinical signs of toxicity, and no toxic effects in gross and microscopic pathology were detected. Thus, Pochonia chlamydosporia var. catenulate (Vcc-108, IMI SD 187), administered oral and dermally to rats and rabbits respectively, was safe in toxicity/pathogenicity studies.

Similarity of the oral microbiota of pre-school children with that of their caregivers in a population-based study.

PubMed

Tanner, A C R; Milgrom, P M; Kent, R; Mokeem, S A; Page, R C; Liao, S I A; Riedy, C A; Bruss, J B

2002-12-01

This study evaluated the similarity between the oral microbiota of young children and that of their adult caregivers. Oral samples from children (174 dentate and 18 pre-dentate) aged 6-36 months and their caregivers in Saipan were assayed using a DNA probe assay. Many species including Streptococcus mutans, Streptococcus sobrinus, Actinomyces species, Campylobacter rectus, Fusobacterium nucleatum, Prevotella intermedia, and Porphyromonas gingivalis were detected in dentate and pre-dentate children, whereas Bacteroides forsythus was detected only in dentate children. A higher percentage of children were positive for the detection of an individual species if the caregiver was also positive. There were significant relative risks of species detection between dentate children and their caregivers. By logistic regression, there were significant positive associations between species detection in caregiver and in child, but not between species detection and child age or maternal education level. In conclusion, dental pathogens were detected in young, including pre-dentate, children. The microbial profiles of children were strongly associated with the microbiota of their caregivers.

Oral warfarin intake affects skin inflammatory cytokine responses in rats.

PubMed

Aleksandrov, Aleksandra Popov; Mirkov, Ivana; Zolotarevski, Lidija; Ninkov, Marina; Mileusnic, Dina; Kataranovski, Dragan; Kataranovski, Milena

2017-09-01

Warfarin is an anticoagulant used in prevention/prophylaxis of thromboembolism. Besides the effects on coagulation, non-hemorrhagic reactions have also been documented. Although cutaneous reactions were reported in some patients, the impact on skin immunity was not explored. In the present paper, the effect of 30-day oral warfarin intake on skin cytokine responses in rats was analyzed. Increased release of inflammatory cytokines (TNF, IL-1β and IL-10) was noted by skin explants from rats which received warfarin, but without effect on IL-6. No impact on epidermal cell cytokine secretion was seen, except a tendency of an increase of IL-6 response to stimulation with microbial product lipopolysaccharide (LPS). Topical application of contact allergen dinitrochlorobenzene (DNCB) resulted in slight (numerical solely) increase of TNF release by skin explants of warfarin-treated animals, while epidermal cells responded by increased secretion of all four cytokines examined. The data presented provide new information on the potential of oral warfarin to modulate skin innate immune activity. Copyright © 2017 Elsevier B.V. All rights reserved.

Source-to-Outcome Microbial Exposure and Risk Modeling Framework

EPA Science Inventory

A Quantitative Microbial Risk Assessment (QMRA) is a computer-based data-delivery and modeling approach that integrates interdisciplinary fate/transport, exposure, and impact models and databases to characterize potential health impacts/risks due to pathogens. As such, a QMRA ex...

The effect of arginine on oral biofilm communities.

PubMed

Nascimento, M M; Browngardt, C; Xiaohui, X; Klepac-Ceraj, V; Paster, B J; Burne, R A

2014-02-01

Alkali production by oral bacteria via the arginine deiminase system (ADS) increases the pH of oral biofilms and reduces the risk for development of carious lesions. This study tested the hypothesis that increased availability of arginine in the oral environment through an exogenous source enhances the ADS activity levels in saliva and dental plaque. Saliva and supra-gingival plaque samples were collected from 19 caries-free (CF) individuals (DMFT = 0) and 19 caries-active (CA) individuals (DMFT ≥ 2) before and after treatment, which comprised the use of a fluoride-free toothpaste containing 1.5% arginine, or a regular fluoride-containing toothpaste twice daily for 4 weeks. ADS activity was measured by quantification of ammonia produced from arginine by oral samples at baseline, after washout period, 4 weeks of treatment, and 2 weeks post-treatment. Higher ADS activity levels were observed in plaque samples from CF compared to those of CA individuals (P = 0.048) at baseline. The use of the arginine toothpaste significantly increased ADS activity in plaque of CA individuals (P = 0.026). The plaque microbial profiles of CA treated with the arginine toothpaste showed a shift in bacterial composition to a healthier community, more similar to that of CF individuals. Thus, an anti-caries effect may be expected from arginine-containing formulations due in large part to the enhancement of ADS activity levels and potential favorable modification to the composition of the oral microbiome. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Fecal indicator organism modeling and microbial source tracking in environmental waters: Chapter 3.4.6

USGS Publications Warehouse

Nevers, Meredith; Byappanahalli, Muruleedhara; Phanikumar, Mantha S.; Whitman, Richard L.

2016-01-01

Mathematical models have been widely applied to surface waters to estimate rates of settling, resuspension, flow, dispersion, and advection in order to calculate movement of particles that influence water quality. Of particular interest are the movement, survival, and persistence of microbial pathogens or their surrogates, which may contaminate recreational water, drinking water, or shellfish. Most models devoted to microbial water quality have been focused on fecal indicator organisms (FIO), which act as a surrogate for pathogens and viruses. Process-based modeling and statistical modeling have been used to track contamination events to source and to predict future events. The use of these two types of models require different levels of expertise and input; process-based models rely on theoretical physical constructs to explain present conditions and biological distribution while data-based, statistical models use extant paired data to do the same. The selection of the appropriate model and interpretation of results is critical to proper use of these tools in microbial source tracking. Integration of the modeling approaches could provide insight for tracking and predicting contamination events in real time. A review of modeling efforts reveals that process-based modeling has great promise for microbial source tracking efforts; further, combining the understanding of physical processes influencing FIO contamination developed with process-based models and molecular characterization of the population by gene-based (i.e., biological) or chemical markers may be an effective approach for locating sources and remediating contamination in order to protect human health better.

Oral immunization of mice with live Pneumocystis murina protects against Pneumocystis pneumonia

PubMed Central

Samuelson, Derrick R.; de la Rua, Nicholas M.; Charles, Tysheena P.; Ruan, Sanbao; Taylor, Christopher M.; Blanchard, Eugene E.; Luo, Meng; Ramsay, Alistair J.; Shellito, Judd E.; Welsh, David A.

2016-01-01

Pneumocystis pneumonia is a major cause of morbidity and mortality in immunocompromised patients; particularly those infected with human immunodeficiency virus. In this study, we evaluated the potential of oral immunization with live Pneumocystis to elicit protection against respiratory infection with Pneumocystis murina. C57BL/6 mice vaccinated with live P. murina using a prime-boost vaccination strategy were protected from a subsequent lung challenge with P. murina at 2, 7, 14, and 28 days post infection even after CD4+ T cell depletion. Specifically, vaccinated immunocompetent mice had significantly faster clearance than unvaccinated immunocompetent mice and unvaccinated CD4-depleted mice remained persistently infected with P. murina. Vaccination also increased numbers of CD4+ T cells, CD8+ T cells, CD19+ B cells, and CD11b+ macrophages in the lungs following respiratory infection. In addition, levels of lung, serum, and fecal P. murina-specific IgG and IgA were increased in vaccinated animals. Further, administration of serum from vaccinated mice significantly reduced Pneumocystis lung burden in infected animals compared to control serum. We also found that the diversity of the intestinal microbial community was altered by oral immunization with P. murina. Our data demonstrate for the first time that an oral vaccination strategy prevents Pneumocystis infection. PMID:26864029

Persistent infection by Staphylococcus epidermidis in endodontic flare-up: a case report.

PubMed

Gonçalves, Simone Helena Ferreira; de Vasconcelos, Rafaela Andrade; Cavalcanti, Bruno das Neves; Camargo, Carlos Henrique Ribeiro

2016-01-01

Endodontic flare-ups are challenging situations and may result from selective growth of specific bacterial species; microbial cultures and antibiograms should be used to allow faster, successful management of refractory lesions. A 47-year-old man reported pain on percussion after uncomplicated retreatment of the maxillary left canine for prosthetic purposes. In the following days, pain dramatically increased, leading to removal of the filling and use of intracanal medication. After many unsuccessful attempts to resolve the problem, a microbial culture of the root canal detected the presence of Staphylococcus epidermidis. An antibiogram determined the best drug combination to control this infection: tetracycline (oxytetracycline hydrochloride, 500 mg orally) plus third-generation cephalosporin (ceftriaxone, 1 g intramuscularly). Once the infection was controlled, the root canal was obturated. There was a reduction in the area of radiolucency, and the patient reported no pain at a 2-year follow-up.

Evaluation of anti-plaque microbial activity of Azadirachta indica (neem oil) in vitro: A pilot study.

PubMed

Elavarasu, Sugumari; Abinaya, P; Elanchezhiyan, S; Thangakumaran; Vennila, K; Naziya, K B

2012-08-01

Probably microbial plaque is the main etiology for periodontal tissue inflammation. Various chemical agents have been evaluated over the years with respect to their antimicrobial effects in the oral cavity. However, all are associated with side effects that prohibit regular long-term use. Therefore, the effectiveness of Azadirachta indica (neem) against plaque formation is considered to be vital, with lesser side effects. The aim of the present study is to evaluate and prove the antimicrobial activity of neem using plaque samples. Culture was prepared using brain heart infusion broth reagent. Dental plaque samples were used for that. Kirby-Bauer antimicrobial susceptibility test procedure was carried away with the sample. Neem oil was kept in the agar plate with culture and the diameter of inhibition zones was calculated. Results showed inhibition zones on the agar plate around neem oil. Study shows definite antiplaque activity of neem oil.

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium

PubMed Central

Hill, David R; Huang, Sha; Nagy, Melinda S; Yadagiri, Veda K; Fields, Courtney; Mukherjee, Dishari; Bons, Brooke; Dedhia, Priya H; Chin, Alana M; Tsai, Yu-Hwai; Thodla, Shrikar; Schmidt, Thomas M; Walk, Seth

2017-01-01

The human gastrointestinal tract is immature at birth, yet must adapt to dramatic changes such as oral nutrition and microbial colonization. The confluence of these factors can lead to severe inflammatory disease in premature infants; however, investigating complex environment-host interactions is difficult due to limited access to immature human tissue. Here, we demonstrate that the epithelium of human pluripotent stem-cell-derived human intestinal organoids is globally similar to the immature human epithelium and we utilize HIOs to investigate complex host-microbe interactions in this naive epithelium. Our findings demonstrate that the immature epithelium is intrinsically capable of establishing a stable host-microbe symbiosis. Microbial colonization leads to complex contact and hypoxia driven responses resulting in increased antimicrobial peptide production, maturation of the mucus layer, and improved barrier function. These studies lay the groundwork for an improved mechanistic understanding of how colonization influences development of the immature human intestine. PMID:29110754

The microbiome of New World vultures.

PubMed

Roggenbuck, Michael; Bærholm Schnell, Ida; Blom, Nikolaj; Bælum, Jacob; Bertelsen, Mads Frost; Sicheritz-Pontén, Thomas; Pontén, Thomas Sicheritz; Sørensen, Søren Johannes; Gilbert, M Thomas P; Graves, Gary R; Hansen, Lars H

2014-11-25

Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture's gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures and their bacteria to their food source, exemplifying a specialized host-microbial alliance.

Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali N.; Or, Dani

2014-09-01

The dispersal rates of self-propelled microorganisms affect their spatial interactions and the ecological functioning of microbial communities. Microbial dispersal rates affect risk of contamination of water resources by soil-borne pathogens, the inoculation of plant roots, or the rates of spoilage of food products. In contrast with the wealth of information on microbial dispersal in water replete systems, very little is known about their dispersal rates in unsaturated porous media. The fragmented aqueous phase occupying complex soil pore spaces suppress motility and limits dispersal ranges in unsaturated soil. The primary objective of this study was to systematically evaluate key factors that shape microbial dispersal in model unsaturated porous media to quantify effects of saturation, pore space geometry, and chemotaxis on characteristics of principles that govern motile microbial dispersion in unsaturated soil. We constructed a novel 3-D angular pore network model (PNM) to mimic aqueous pathways in soil for different hydration conditions; within the PNM, we employed an individual-based model that considers physiological and biophysical properties of motile and chemotactic bacteria. The effects of hydration conditions on first passage times in different pore networks were studied showing that fragmentation of aquatic habitats under dry conditions sharply suppresses nutrient transport and microbial dispersal rates in good agreement with limited experimental data. Chemotactically biased mean travel speed of microbial cells across 9 mm saturated PNM was ˜3 mm/h decreasing exponentially to 0.45 mm/h for the PNM at matric potential of -15 kPa (for -35 kPa, dispersal practically ceases and the mean travel time to traverse the 9 mm PNM exceeds 1 year). Results indicate that chemotaxis enhances dispersal rates by orders of magnitude relative to random (diffusive) motions. Model predictions considering microbial cell sizes relative to available liquid pathways sizes were in good agreement with experimental results for unsaturated soils. The new modeling platform enables quantitative consideration of key biophysical factors (e.g., pore space heterogeneities and hydration conditions) governing microbial interactions in 3-D soil pore spaces.

[Evaluation of the protection efficiency of secretory antibodies in experimental Yersinia infection in guinea-pigs immunized with polyvalent vaccine against this infection].

PubMed

Pogorel'skiĭ, I P; Drobkov, V I

2009-01-01

The paper presents the results of experiments to elucidate the protection efficiency of secretory antibodies via parenteral and oral inoculation with pathogenic Yersinia in guinea pigs immunized with a polyvalent yersiniasis vaccine designed on the basis of the pseudotuberculosis microbial strain that synthesizes the F1 antigen of a plague microbe. Immunization of guinea pigs with the polyvalent yersiniasis vaccine protects experimental animals against pseudotuberculosis, intestinal yersiniasis, and plague infections.

Implant-abutment gap versus microbial colonization: Clinical significance based on a literature review.

PubMed

Passos, Sheila Pestana; Gressler May, Liliana; Faria, Renata; Özcan, Mutlu; Bottino, Marco Antonio

2013-10-01

Microorganisms from the oral cavity may settle at the implant-abutment interface (IAI). As a result, tissue inflammation could occur around these structures. The databases MEDLINE/PubMed and PubMed Central were used to identify articles published from 1981 through 2012 related to the microbial colonization in the implant-abutment gap and its consequence in terms of crest bone loss and osseointegration. The following considerations could be put forward, with respect to the clinical importance of IAI: (a) the space present at the IAI seems to allow bacterial leakage to occur, in spite of the size of this space; (b) bacterial leakage seems to occur at the IAI, irrespective of the type of connection. More studies are necessary to clarify the relationship between leakage at IAI and abutment connection designs; (c) losses at the peri-implant bone crests cannot be related to the IAI size, since few studies have shown no relationship. Also, the microbial leakage at the IAI cannot be related to the bone crest loss, since there are no articles reporting this relationship; remains controversial the influence of the IAI position on the bone crest losses. Copyright © 2013 Wiley Periodicals, Inc.

Temperature sensitivity of soil microbial activity modeled by the square root equation as a unifying model to differentiate between direct temperature effects and microbial community adaptation.

PubMed

Bååth, Erland

2018-07-01

Numerous models have been used to express the temperature sensitivity of microbial growth and activity in soil making it difficult to compare results from different habitats. Q10 still is one of the most common ways to express temperature relationships. However, Q10 is not constant with temperature and will differ depending on the temperature interval used for the calculation. The use of the square root (Ratkowsky) relationship between microbial activity (A) and temperature below optimum temperature, √A = a × (T-T min ), is proposed as a simple and adequate model that allow for one descriptor, T min (a theoretical minimum temperature for growth and activity), to estimate correct Q10-values over the entire in situ temperature interval. The square root model can adequately describe both microbial growth and respiration, allowing for an easy determination of T min . Q10 for any temperature interval can then be calculated by Q10 = [(T + 10 - T min )/(T-T min )] 2 , where T is the lowest temperature in the Q10 comparison. T min also describes the temperature adaptation of the microbial community. An envelope of T min covering most natural soil habitats varying between -15°C (cold habitats like Antarctica/Arctic) to 0°C (tropical habitats like rain forests and deserts) is suggested, with an 0.3°C increase in T min per 1°C increase in mean annual temperature. It is shown that the main difference between common temperature relationships used in global models is differences in the assumed temperature adaptation of the soil microbial community. The use of the square root equation will allow for one descriptor, T min , determining the temperature response of soil microorganisms, and at the same time allow for comparing temperature sensitivity of microbial activity between habitats, including future projections. © 2018 John Wiley & Sons Ltd.

Endolithic microbial model for Martian exobiology: The road to extinction

NASA Technical Reports Server (NTRS)

Oscampo-Friedmann, R.; Friedmann, E. I.

1991-01-01

Martian exobiology is based on the assumption that on early Mars, liquid water was present and that conditions were suitable for the evolution of life. The cause for life to disappear from the surface and the recognizable fingerprints of past microbial activity preserved on Mars are addressed. The Antarctic cryptoendolithic microbial ecosystem as a model for extinction in the deteriorating Martian environment is discussed.

Microbial degradation of crude oil and some model hydrocarbons

USGS Publications Warehouse

Chang, Fu-Hsian; Noben, N.N.; Brand, Danny; Hult, Marc F.

1988-01-01

Research on microbial degradation of crude oil in the shallow subsurface at a spill site near Bemidji, Minn. (fig. C-l), began in 1983 (Hull, 1984; Chang and Ehrlich, 1984). The rate and extent of crude oil and model hydrocarbon biodegradation by the indigenous microbial community was measured in the laboratory at several concentrations of inorganic nutrients, conditions of oxygen availability, incubation temperatures, and incubation time.

The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Methe, Barbara; Lipton, Mary; Mahadevan, Krishna

Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives ofmore » this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generate sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling development. The model as created is capable of predicting the response of the community structure in changing environments such as anoxic/oxic conditions or limitations by carbon or nutrients. The ability to more accurately model these responses is critical to understanding carbon and energy flows in an ecosystem is critical towards improving our ability to make predictions that can be used to design more efficient remediation and management strategies, and better understand the implications of environmental perturbations on these ecosystems.« less

Regulation of C:N:P stoichiometry of microbes and soil organic matter by optimizing enzyme allocation: an omics-informed model study

NASA Astrophysics Data System (ADS)

Song, Y.; Yao, Q.; Wang, G.; Yang, X.; Mayes, M. A.

2017-12-01

Increasing evidences is indicating that soil organic matter (SOM) decomposition and stabilization process is a continuum process and controlled by both microbial functions and their interaction with minerals (known as the microbial efficiency-matrix stabilization theory (MEMS)). Our metagenomics analysis of soil samples from both P-deficit and P-fertilization sites in Panama has demonstrated that community-level enzyme functions could adapt to maximize the acquisition of limiting nutrients and minimize energy demand for foraging (known as the optimal foraging theory). This optimization scheme can mitigate the imbalance of C/P ratio between soil substrate and microbial community and relieve the P limitation on microbial carbon use efficiency over the time. Dynamic allocation of multiple enzyme groups and their interaction with microbial/substrate stoichiometry has rarely been considered in biogeochemical models due to the difficulties in identifying microbial functional groups and quantifying the change in enzyme expression in response to soil nutrient availability. This study aims to represent the omics-informed optimal foraging theory in the Continuum Microbial ENzyme Decomposition model (CoMEND), which was developed to represent the continuum SOM decomposition process following the MEMS theory. The SOM pools in the model are classified based on soil chemical composition (i.e. Carbohydrates, lignin, N-rich SOM and P-rich SOM) and the degree of SOM depolymerization. The enzyme functional groups for decomposition of each SOM pool and N/P mineralization are identified by the relative composition of gene copy numbers. The responses of microbial activities and SOM decomposition to nutrient availability are simulated by optimizing the allocation of enzyme functional groups following the optimal foraging theory. The modeled dynamic enzyme allocation in response to P availability is evaluated by the metagenomics data measured from P addition and P-deficit soil samples in Panama sites.The implementation of dynamic enzyme allocation in response to nutrient availability in the CoMEND model enables us to capture the varying microbial C/P ratio and soil carbon dynamics in response to shifting nutrient constraints over time in tropical soils.

Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health.

PubMed

Koch, Carl D; Gladwin, Mark T; Freeman, Bruce A; Lundberg, Jon O; Weitzberg, Eddie; Morris, Alison

2017-04-01

Recent insights into the bioactivation and signaling actions of inorganic, dietary nitrate and nitrite now suggest a critical role for the microbiome in the development of cardiac and pulmonary vascular diseases. Once thought to be the inert, end-products of endothelial-derived nitric oxide (NO) heme-oxidation, nitrate and nitrite are now considered major sources of exogenous NO that exhibit enhanced vasoactive signaling activity under conditions of hypoxia and stress. The bioavailability of nitrate and nitrite depend on the enzymatic reduction of nitrate to nitrite by a unique set of bacterial nitrate reductase enzymes possessed by specific bacterial populations in the mammalian mouth and gut. The pathogenesis of pulmonary hypertension (PH), obesity, hypertension and CVD are linked to defects in NO signaling, suggesting a role for commensal oral bacteria to shape the development of PH through the formation of nitrite, NO and other bioactive nitrogen oxides. Oral supplementation with inorganic nitrate or nitrate-containing foods exert pleiotropic, beneficial vascular effects in the setting of inflammation, endothelial dysfunction, ischemia-reperfusion injury and in pre-clinical models of PH, while traditional high-nitrate dietary patterns are associated with beneficial outcomes in hypertension, obesity and CVD. These observations highlight the potential of the microbiome in the development of novel nitrate- and nitrite-based therapeutics for PH, CVD and their risk factors. Copyright © 2017 Elsevier Inc. All rights reserved.

Mechanistic modeling of thermo-hydrological processes and microbial interactions at pore to profile scales resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-04-01

The sensitivity of the Earth's polar regions to raising global temperatures is reflected in rapidly changing hydrological processes with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and the stimulation of other soil-borne GHG emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and a host of other environmental factors. Soil structural elements such as aggregates and layering and hydration status affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hotspots or hot-layers). We developed a mechanistic individual based model to quantify microbial activity dynamics within soil pore networks considering, hydration, temperature, transport processes and enzymatic activity associated with methane production in soil. The model was the upscaled from single aggregates (or hotspots) to quantifying emissions from soil profiles in which freezing/thawing processes provide macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged parts of the profile) for resolving methane production and oxidation rates. Methane transport pathways through soil by diffusion and ebullition of bubbles vary with hydration dynamics and affect emission patterns. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability, enzyme activity, PH) on long term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Genome Informed Trait-Based Models

NASA Astrophysics Data System (ADS)

Karaoz, U.; Cheng, Y.; Bouskill, N.; Tang, J.; Beller, H. R.; Brodie, E.; Riley, W. J.

2013-12-01

Trait-based approaches are powerful tools for representing microbial communities across both spatial and temporal scales within ecosystem models. Trait-based models (TBMs) represent the diversity of microbial taxa as stochastic assemblages with a distribution of traits constrained by trade-offs between these traits. Such representation with its built-in stochasticity allows the elucidation of the interactions between the microbes and their environment by reducing the complexity of microbial community diversity into a limited number of functional ';guilds' and letting them emerge across spatio-temporal scales. From the biogeochemical/ecosystem modeling perspective, the emergent properties of the microbial community could be directly translated into predictions of biogeochemical reaction rates and microbial biomass. The accuracy of TBMs depends on the identification of key traits of the microbial community members and on the parameterization of these traits. Current approaches to inform TBM parameterization are empirical (i.e., based on literature surveys). Advances in omic technologies (such as genomics, metagenomics, metatranscriptomics, and metaproteomics) pave the way to better-initialize models that can be constrained in a generic or site-specific fashion. Here we describe the coupling of metagenomic data to the development of a TBM representing the dynamics of metabolic guilds from an organic carbon stimulated groundwater microbial community. Illumina paired-end metagenomic data were collected from the community as it transitioned successively through electron-accepting conditions (nitrate-, sulfate-, and Fe(III)-reducing), and used to inform estimates of growth rates and the distribution of metabolic pathways (i.e., aerobic and anaerobic oxidation, fermentation) across a spatially resolved TBM. We use this model to evaluate the emergence of different metabolisms and predict rates of biogeochemical processes over time. We compare our results to observational outputs.

Modeling and applications in microbial food safety

USDA-ARS?s Scientific Manuscript database

Mathematical modeling is a scientific and systematic approach to study and describe the recurrent events or phenomena with successful application track for decades. When models are properly developed and validated, their applications may save costs and time. For the microbial food safety concerns, ...

Analyses of the Microbial Diversity across the Human Microbiome

PubMed Central

Li, Kelvin; Bihan, Monika; Yooseph, Shibu; Methé, Barbara A.

2012-01-01

Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, Smax, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, (“τ”), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ’s greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome. PMID:22719823

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism.

PubMed

Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C

2016-01-01

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

PubMed Central

Hsu, Tiffany; Joice, Regina; Vallarino, Jose; Abu-Ali, Galeb; Hartmann, Erica M.; Shafquat, Afrah; DuLong, Casey; Baranowski, Catherine; Gevers, Dirk; Green, Jessica L.; Spengler, John D.

2016-01-01

ABSTRACT Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics. All surfaces were dominated by human skin and oral commensals such as Propionibacterium, Corynebacterium, Staphylococcus, and Streptococcus. The detected taxa not associated with humans included generalists from alphaproteobacteria, which were especially abundant on outdoor touchscreens. Shotgun metagenomics further identified viral and eukaryotic microbes, including Propionibacterium phage and Malassezia globosa. Functional profiling showed that Propionibacterium acnes pathways such as propionate production and porphyrin synthesis were enriched on train holding surfaces (holds), while electron transport chain components for aerobic respiration were enriched on touchscreens and seats. Lastly, the transit environment was not found to be a reservoir of antimicrobial resistance and virulence genes. Our results suggest that microbial communities on transit surfaces are maintained from a metapopulation of human skin commensals and environmental generalists, with enrichments corresponding to local interactions with the human body and environmental exposures. IMPORTANCE Mass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we profiled the Boston subway system, which provides 238 million trips per year overseen by the Massachusetts Bay Transportation Authority (MBTA). This yielded the first high-precision microbial survey of a variety of surfaces, ridership environments, and microbiological functions (including tests for potential pathogenicity) in a mass transit environment. Characterizing microbial profiles for multiple transit systems will become increasingly important for biosurveillance of antibiotic resistance genes or pathogens, which can be early indicators for outbreak or sanitation events. Understanding how human contact, materials, and the environment affect microbial profiles may eventually allow us to rationally design public spaces to sustain our health in the presence of microbial reservoirs. Author Video: An author video summary of this article is available. PMID:27822528

Assessing five evolving microbial enzyme models against field measurements from a semiarid savannah—What are the mechanisms of soil respiration pulses?

NASA Astrophysics Data System (ADS)

Zhang, Xia; Niu, Guo-Yue; Elshall, Ahmed S.; Ye, Ming; Barron-Gafford, Greg A.; Pavao-Zuckerman, Mitch

2014-09-01

Soil microbial respiration pulses in response to episodic rainfall pulses (the "Birch effect") are poorly understood. We developed and assessed five evolving microbial enzyme models against field measurements from a semiarid savannah characterized by pulsed precipitation to understand the mechanisms to generate the Birch pulses. The five models evolve from an existing four-carbon (C) pool model to models with additional C pools and explicit representations of soil moisture controls on C degradation and microbial uptake rates. Assessing the models using techniques of model selection and model averaging suggests that models with additional C pools for accumulation of degraded C in the dry zone of the soil pore space result in a higher probability of reproducing the observed Birch pulses. Degraded C accumulated in dry soil pores during dry periods becomes immediately accessible to microbes in response to rainstorms, providing a major mechanism to generate respiration pulses. Explicitly representing the transition of degraded C and enzymes between dry and wet soil pores in response to soil moisture changes and soil moisture controls on C degradation and microbial uptake rates improve the models' efficiency and robustness in simulating the Birch effect. Assuming that enzymes in the dry soil pores facilitate degradation of complex C during dry periods (though at a lower rate) results in a greater accumulation of degraded C and thus further improves the models' performance. However, the actual mechanism inducing the greater accumulation of labile C needs further experimental studies.

Metabolic Network Modeling of Microbial Communities

PubMed Central

Biggs, Matthew B.; Medlock, Gregory L.; Kolling, Glynis L.

2015-01-01

Genome-scale metabolic network reconstructions and constraint-based analysis are powerful methods that have the potential to make functional predictions about microbial communities. Current use of genome-scale metabolic networks to characterize the metabolic functions of microbial communities includes species compartmentalization, separating species-level and community-level objectives, dynamic analysis, the “enzyme-soup” approach, multi-scale modeling, and others. There are many challenges inherent to the field, including a need for tools that accurately assign high-level omics signals to individual community members, new automated reconstruction methods that rival manual curation, and novel algorithms for integrating omics data and engineering communities. As technologies and modeling frameworks improve, we expect that there will be proportional advances in the fields of ecology, health science, and microbial community engineering. PMID:26109480

Lytic to temperate switching of viral communities

NASA Astrophysics Data System (ADS)

Knowles, B.; Silveira, C. B.; Bailey, B. A.; Barott, K.; Cantu, V. A.; Cobián-Güemes, A. G.; Coutinho, F. H.; Dinsdale, E. A.; Felts, B.; Furby, K. A.; George, E. E.; Green, K. T.; Gregoracci, G. B.; Haas, A. F.; Haggerty, J. M.; Hester, E. R.; Hisakawa, N.; Kelly, L. W.; Lim, Y. W.; Little, M.; Luque, A.; McDole-Somera, T.; McNair, K.; de Oliveira, L. S.; Quistad, S. D.; Robinett, N. L.; Sala, E.; Salamon, P.; Sanchez, S. E.; Sandin, S.; Silva, G. G. Z.; Smith, J.; Sullivan, C.; Thompson, C.; Vermeij, M. J. A.; Youle, M.; Young, C.; Zgliczynski, B.; Brainard, R.; Edwards, R. A.; Nulton, J.; Thompson, F.; Rohwer, F.

2016-03-01

Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in diverse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities; thus ‘more microbes, fewer viruses’.