Screening of Probiotic Candidates in Human Oral Bacteria for the Prevention of Dental Disease

PubMed Central

Terai, Tomohiko; Okumura, Takekazu; Imai, Susumu; Nakao, Masumi; Yamaji, Kazuaki; Ito, Masahiko; Nagata, Tsuyoshi; Kaneko, Kimiyuki; Miyazaki, Kouji; Okada, Ayako; Nomura, Yoshiaki; Hanada, Nobuhiro

2015-01-01

The oral cavity in healthy subjects has a well-balanced microbiota that consists of more than 700 species. However, a disturbance of this balance, with an increase of harmful microbes and a decrease of beneficial microbes, causes oral disorders such as periodontal disease or dental caries. Nowadays, probiotics are expected to confer oral health benefits by modulating the oral microbiota. This study screened new probiotic candidates with potential oral health benefits and no harmful effects on the oral cavity. We screened 14 lactobacillus strains and 36 streptococcus strains out of 896 oral isolates derived from healthy subjects. These bacteria did not produce volatile sulfur compounds or water-insoluble glucan, had higher antibacterial activity against periodontal bacteria, and had higher adherence activity to oral epithelial cells or salivary-coated hydroxyapatite in vitro. We then evaluated the risk of primary cariogenicity and infective endocarditis of the selected oral isolates. As a result, Lactobacillus crispatus YIT 12319, Lactobacillus fermentum YIT 12320, Lactobacillus gasseri YIT 12321, and Streptococcus mitis YIT 12322 were selected because they showed no cariogenic potential in an artificial mouth system and a lower risk of experimental infective endocarditis in a rat model. These candidates are expected as new probiotics with potential oral health benefits and no adverse effects on general health. PMID:26053410

Screening of Probiotic Candidates in Human Oral Bacteria for the Prevention of Dental Disease.

PubMed

Terai, Tomohiko; Okumura, Takekazu; Imai, Susumu; Nakao, Masumi; Yamaji, Kazuaki; Ito, Masahiko; Nagata, Tsuyoshi; Kaneko, Kimiyuki; Miyazaki, Kouji; Okada, Ayako; Nomura, Yoshiaki; Hanada, Nobuhiro

2015-01-01

The oral cavity in healthy subjects has a well-balanced microbiota that consists of more than 700 species. However, a disturbance of this balance, with an increase of harmful microbes and a decrease of beneficial microbes, causes oral disorders such as periodontal disease or dental caries. Nowadays, probiotics are expected to confer oral health benefits by modulating the oral microbiota. This study screened new probiotic candidates with potential oral health benefits and no harmful effects on the oral cavity. We screened 14 lactobacillus strains and 36 streptococcus strains out of 896 oral isolates derived from healthy subjects. These bacteria did not produce volatile sulfur compounds or water-insoluble glucan, had higher antibacterial activity against periodontal bacteria, and had higher adherence activity to oral epithelial cells or salivary-coated hydroxyapatite in vitro. We then evaluated the risk of primary cariogenicity and infective endocarditis of the selected oral isolates. As a result, Lactobacillus crispatus YIT 12319, Lactobacillus fermentum YIT 12320, Lactobacillus gasseri YIT 12321, and Streptococcus mitis YIT 12322 were selected because they showed no cariogenic potential in an artificial mouth system and a lower risk of experimental infective endocarditis in a rat model. These candidates are expected as new probiotics with potential oral health benefits and no adverse effects on general health.

[Exploring New Drug Targets through the Identification of Target Molecules of Bioactive Natural Products].

PubMed

Arai, Masayoshi

2016-01-01

With the development of cell biology and microbiology, it has become easy to culture many types of animal cells and microbes, and they are frequently used for phenotypic screening to explore medicinal seeds. On the other hand, it is recognized that cells and pathogenic microbes present in pathologic sites and infected regions of the human body display unique properties different from those under general culture conditions. We isolated several bioactive compounds from marine medicinal resources using constructed bioassay-guided separation focusing on the unique changes in the characteristics of cells and pathogenic microbes (Mycobacterium spp.) in the human body under disease conditions. In addition, we also carried out identification studies of target molecules of the bioactive compounds by methods utilizing the gene expression profile, transformants of cells or microbes, synthetic probe molecules of the isolated compounds, etc., since bioactive compounds isolated from the phenotypic screening system often target new molecules. This review presents our phenotypic screening systems, isolation of bioactive compounds from marine medicinal resources, and target identification of bioactive compounds.

Multiplex Identification of Microbes ▿ †

PubMed Central

Hyman, Richard W.; St.Onge, Robert P.; Allen, Edward A.; Miranda, Molly; Aparicio, Ana Maria; Fukushima, Marilyn; Davis, Ronald W.

2010-01-01

We have adapted molecular inversion probe technology to identify microbes in a highly multiplexed procedure. This procedure does not require growth of the microbes. Rather, the technology employs DNA homology twice: once for the molecular probe to hybridize to its homologous DNA and again for the 20-mer oligonucleotide barcode on the molecular probe to hybridize to a commercially available molecular barcode array. As proof of concept, we have designed, tested, and employed 192 molecular probes for 40 microbes. While these particular molecular probes are aimed at our interest in the microbes in the human vagina, this molecular probe method could be employed to identify the microbes in any ecological niche. PMID:20418427

Oral cavity infection: an adverse effect after the treatment of oral cancer in aged individuals.

PubMed

Pan, Jie; Zhao, Jun; Jiang, Ning

2014-01-01

The immune compromised patients after treatment of oral cancer may have a chance of infection by drug-resistant opportunistic microbes. We investigated the occurrence of opportunistic microorganisms in aged individuals receiving follow-up examinations after treatment of oral cancer in China. These patients were used as test group and the respective age grouped healthy individuals as control group. In this study, the oral cavity microorganisms such as bacteria and yeast were taken for the analysis. After the screening of representative microorganisms, their aptitude of pervasiveness against drugs was studied. Here, we used antimicrobial agents which are common in clinical practice. We also performed studies to investigate the presence of toxin genes in methicillin-resistant S. aureus (MRSA). The results indicate that the prevalence of drug-resistant microbes was more pronounced in oral cancer patients after initial treatment above 70 years old. The oxacillin resistance of S. aureus isolate confirms that the prevalence of MRSA is increasing in accordance to age-factor and immune compromise in elderly patients. This study reveals the occurrence of drug-resistant opportunistic microorganisms in oral cavity after treatment for oral cancer in aged individuals. Special attention should be directed to MRSA during the treatment of oral cancer, and to realize the fact of immune compromise in elderly patients.

Prelude to Oral Microbes and Chronic Diseases: Past, Present and Future

PubMed Central

Atanasova, Kalina R; Yilmaz, Özlem

2015-01-01

Associations between oral and systemic health are ancient. Oral opportunistic bacteria, particularly, Porphyromonas gingivalis and Fusobacterium nucleatum, have recently been deviated from their traditional roles and arguably ascended to central players based on their participations in complex co-dependent mechanisms of diverse systemic chronic diseases risk and pathogenesis, including cancers, rheumatoid-arthritis, and diabetes. PMID:25813714

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.

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.

Use of an electronic-nose device for profiling headspace volatile metabolites to rapidly identify phytopathogenic microbes [Abstract].

Treesearch

A. Dan Wilson; D.G. Lester

1997-01-01

A new electronic-nose device (AromaScan A32S), consisting of an organic matrix-coated polymer-type 32-detector array, was tested as a novel tool for the detection, identification, and discrimination of phytopathogenic microbes. The sensor array detects the unique mixture of volatile metabolites released by microbes growing on standardized growth media by measuring...

Experimental Activities in Primary School to Learn about Microbes in an Oral Health Education Context

ERIC Educational Resources Information Center

Mafra, Paulo; Lima, Nelson; Carvalho, Graça S.

2015-01-01

Experimental science activities in primary school enable important cross-curricular learning. In this study, experimental activities on microbiology were carried out by 16 pupils in a Portuguese grade-4 classroom (9-10?years old) and were focused on two problem-questions related to microbiology and health: (1) do your teeth carry microbes? (2) why…

Epidemiology of Oral and Maxillofacial Infections.

PubMed

Rajendra Santosh, Arvind Babu; Ogle, Orrett E; Williams, Dwight; Woodbine, Edward F

2017-04-01

Dental caries and periodontal disease are the most common dental infections and are constantly increasing worldwide. Distribution, occurrence of dental caries, gingivitis, periodontitis, odontogenic infections, antibiotic resistance, oral mucosal infections, and microbe-related oral cancer are important to understand the public impact and methods of controlling such disease. Distribution of human papilloma virus and human immunodeficiency virus -related oral cancers in the US population is presented. Copyright © 2016 Elsevier Inc. All rights reserved.

Noninvasive photoacoustic identification and imaging of gut microbes.

PubMed

Huang, Xiaoxiao; Shi, Ying; Liu, Yajing; Xu, Hongzhi; Liu, Yu; Xiao, Chuanxing; Ren, Jianlin; Nie, Liming

2017-08-01

Homeostasis of the gut microbiota is indispensable for various physiological functions. Its composition and activity co-develop with the host, and especially associate with human colorectal cancer. However, current composition identification methods are complicated and not timely without spatial distribution information. In this Letter, we explored the photoacoustic imaging (PAI) technique to characterize the composition and quantify the proportions of the gut microbes after optical probe labeling. Our experimental results demonstrated that PAI has the potential to identify different gut bacterial species on the spot.

Oral delivery of dsRNA by microbes: Beyond pest control.

PubMed

Abrieux, Antoine; Chiu, Joanna C

2016-01-01

RNA interference (RNAi) by oral delivery of dsRNA in insects has great potential as a tool for integrated pest management (IPM), especially with respect to addressing the need to reduce off-target effect and slow down resistance development to chemical insecticides. Employing the natural association existing between insect and yeast, we developed a novel method to enable the knock down of vital genes in the pest insect Drosophila suzukii through oral delivery of species-specific dsRNA using genetically modified Saccharomyces cerevisae. D. suzukii that were fed with our "yeast biopesticide" showed a significant decrease in fitness. In this perspective article, we postulate that this approach could be adapted to a large number of species, given the great diversity of symbiotic interactions involving microorganisms and host species. Furthermore, we speculate that beyond its application as biopesticide, dsRNA delivery by genetically modified microbes can also serve to facilitate reverse genetic applications, specifically in non-model organisms.

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

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.

PubMed

Cross, Karissa L; Chirania, Payal; Xiong, Weili; Beall, Clifford J; Elkins, James G; Giannone, Richard J; Griffen, Ann L; Guss, Adam M; Hettich, Robert L; Joshi, Snehal S; Mokrzan, Elaine M; Martin, Roman K; Zhulin, Igor B; Leys, Eugene J; Podar, Mircea

2018-03-13

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives, D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury were also lost by D. oralis , a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. IMPORTANCE Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing. Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome "dark matter," cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.

Porphyromonas gingivalis sinks teeth into the oral microbiota and periodontal disease.

PubMed

Honda, Kenya

2011-11-17

Periodontitis is linked to polymicrobial interactions and the presence of Porphyromonas gingivalis. In this issue of Cell Host & Microbe, Hajishengallis et al. (2011) demonstrate that P. gingivalis colonization in the oral cavity changes the composition of the oral commensal microbiota and accelerates microbiota-mediated bone-destructive periodontitis, indicating that this single, low-abundance species is a keystone in periodontal disease. Copyright © 2011 Elsevier Inc. All rights reserved.

Co-occurrence of anaerobic bacteria in colorectal carcinomas.

PubMed

Warren, René L; Freeman, Douglas J; Pleasance, Stephen; Watson, Peter; Moore, Richard A; Cochrane, Kyla; Allen-Vercoe, Emma; Holt, Robert A

2013-05-15

Numerous cancers have been linked to microorganisms. Given that colorectal cancer is a leading cause of cancer deaths and the colon is continuously exposed to a high diversity of microbes, the relationship between gut mucosal microbiome and colorectal cancer needs to be explored. Metagenomic studies have shown an association between Fusobacterium species and colorectal carcinoma. Here, we have extended these studies with deeper sequencing of a much larger number (n = 130) of colorectal carcinoma and matched normal control tissues. We analyzed these data using co-occurrence networks in order to identify microbe-microbe and host-microbe associations specific to tumors. We confirmed tumor over-representation of Fusobacterium species and observed significant co-occurrence within individual tumors of Fusobacterium, Leptotrichia and Campylobacter species. This polymicrobial signature was associated with over-expression of numerous host genes, including the gene encoding the pro-inflammatory chemokine Interleukin-8. The tumor-associated bacteria we have identified are all Gram-negative anaerobes, recognized previously as constituents of the oral microbiome, which are capable of causing infection. We isolated a novel strain of Campylobacter showae from a colorectal tumor specimen. This strain is substantially diverged from a previously sequenced oral Campylobacter showae isolate, carries potential virulence genes, and aggregates with a previously isolated tumor strain of Fusobacterium nucleatum. A polymicrobial signature of Gram-negative anaerobic bacteria is associated with colorectal carcinoma tissue.

The antibacterial and antifungal activity of essential oils extracted from Guatemalan medicinal plants.

PubMed

Miller, Andrew B; Cates, Rex G; Lawrence, Michael; Soria, J Alfonso Fuentes; Espinoza, Luis V; Martinez, Jose Vicente; Arbizú, Dany A

2015-04-01

Essential oils are prevalent in many medicinal plants used for oral hygiene and treatment of diseases. Medicinal plant species were extracted to determine the essential oil content. Those producing sufficient oil were screened for activity against Staphylococcus aureus, Escherichia coli, Streptococcus mutans, Lactobacillus acidophilus, and Candida albicans. Plant samples were collected, frozen, and essential oils were extracted by steam distillation. Minimum inhibitory concentrations (MIC) were determined using a tube dilution assay for those species yielding sufficient oil. Fifty-nine of the 141 plant species produced sufficient oil for collection and 12 species not previously reported to produce essential oils were identified. Essential oil extracts from 32 species exhibited activity against one or more microbes. Oils from eight species were highly inhibitory to S. mutans, four species were highly inhibitory to C. albicans, and 19 species yielded MIC values less than the reference drugs. RESULTS suggest that 11 species were highly inhibitory to the microbes tested and merit further investigation. Oils from Cinnamomum zeylanicum Blume (Lauraceae), Citrus aurantiifolia (Christm.) Swingle (Rutaceae), Lippia graveolens Kunth (Verbenaceae), and Origanum vulgare L. (Lamiaceae) yielded highly significant or moderate activity against all microbes and have potential as antimicrobial agents. Teas prepared by decoction or infusion are known methods for extracting essential oils. Oils from 11 species were highly active against the microbes tested and merit investigation as to their potential for addressing health-related issues and in oral hygiene.

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

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

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

DOE PAGES

Cross, Karissa L.; Chirania, Payal; Xiong, Weili; ...

2018-03-13

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously unculturedDesulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives,D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury weremore » also lost byD. oralis, a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing.Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome “dark matter,” cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.« less

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

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

Cross, Karissa L.; Chirania, Payal; Xiong, Weili

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously unculturedDesulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives,D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury weremore » also lost byD. oralis, a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing.Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome “dark matter,” cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.« less

Food Commensals as a Potential Major Avenue in Transmitting Antibiotic Resistance Genes

DTIC Science & Technology

2005-08-01

bacteria in the G1 system (Levy 1998). Particularly, oral cavity could bl an important ,rcea where man1y initial interactions bctwccn fibid microbes anti...the oral cavity . In fact, the zeiS/M and ennB genes were lbund to be abundant in bacteria isolated from foods, which is in agreement with the...Wilson M, Mullany P. 2005. TIhe maintenance in the oral cavity of children of tctracyclinc-rcsistant bacteria and the genes encoding such rcsistanee. J

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

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.

Spectrometric microbiological analyzer

NASA Astrophysics Data System (ADS)

Schlager, Kenneth J.; Meissner, Ken E.

1996-04-01

Currently, there are four general approaches to microbiological analysis, i.e., the detection, identification and quantification of micro-organisms: (1) Traditional culturing and staining procedures, metabolic fermentations and visual morphological characteristics; (2) Immunological approaches employing microbe-specific antibodies; (3) Biotechnical techniques employing DNA probes and related genetic engineering methods; and (4) Physical measurement techniques based on the biophysical properties of micro-organisms. This paper describes an instrumentation development in the fourth of the above categories, physical measurement, that uses a combination of fluorometric and light scatter spectra to detect and identify micro-organisms at the species level. A major advantage of this approach is the rapid turnaround possible in medical diagnostic or water testing applications. Fluorometric spectra serve to define the biochemical characteristics of the microbe, and light scatter spectra the size and shape morphology. Together, the two spectra define a 'fingerprint' for each species of microbe for detection, identification and quantification purposes. A prototype instrument has been developed and tested under NASA sponsorship based on fluorometric spectra alone. This instrument demonstrated identification and quantification capabilities at the species level. The paper reports on test results using this instrument, and the benefits of employing a combination of fluorometric and light scatter spectra.

Maturation of Oral Microbiota in Children with or without Dental Caries.

PubMed

Lif Holgerson, Pernilla; Öhman, Carina; Rönnlund, Agneta; Johansson, Ingegerd

2015-01-01

The aim of this longitudinal study was to evaluate the oral microbiota in children from age 3 months to 3 years, and to determine the association of the presence of caries at 3 years of age. Oral biofilms and saliva were sampled from children at 3 months (n = 207) and 3 years (n = 155) of age, and dental caries was scored at 3 years of age. Oral microbiota was assessed by culturing of total lactobacilli and mutans streptococci, PCR detection of Streptococcus mutans and Streptococcus sobrinus, 454 pyrosequencing and HOMIM (Human Oral Microbe Identification Microarray) microarray detection of more then 300 species/ phylotypes. Species richness and taxa diversity significantly increased from 3 months to 3 years. Three bacterial genera, present in all the 3-month-old infants, persisted at 3 years of age, whereas three other genera had disappeared by this age. A large number of new taxa were also observed in the 3-year-olds. The microbiota at 3 months of age, except for lactobacilli, was unrelated to caries development at a later age. In contrast, several taxa in the oral biofilms of the 3-year-olds were linked with the presence or absence of caries. The main species/phylotypes associated with caries in 3-year-olds belonged to the Actinobaculum, Atopobium, Aggregatibacter, and Streptococcus genera, whereas those influencing the absence of caries belonged to the Actinomyces, Bergeyella, Campylobacter, Granulicatella, Kingella, Leptotrichia, and Streptococcus genera. Thus, during the first years of life, species richness and taxa diversity in the mouth increase significantly. Besides the more prevalent colonization of lactobacilli, the composition of the overall microbiota at 3 months of age was unrelated to caries development at a later age. Several taxa within the oral biofilms of the 3-year-olds could be linked to the presence or absence of caries.

Maturation of Oral Microbiota in Children with or without Dental Caries

PubMed Central

Lif Holgerson, Pernilla; Öhman, Carina; Rönnlund, Agneta; Johansson, Ingegerd

2015-01-01

Background The aim of this longitudinal study was to evaluate the oral microbiota in children from age 3 months to 3 years, and to determine the association of the presence of caries at 3 years of age. Methods and findings Oral biofilms and saliva were sampled from children at 3 months (n = 207) and 3 years (n = 155) of age, and dental caries was scored at 3 years of age. Oral microbiota was assessed by culturing of total lactobacilli and mutans streptococci, PCR detection of Streptococcus mutans and Streptococcus sobrinus, 454 pyrosequencing and HOMIM (Human Oral Microbe Identification Microarray) microarray detection of more then 300 species/ phylotypes. Species richness and taxa diversity significantly increased from 3 months to 3 years. Three bacterial genera, present in all the 3-month-old infants, persisted at 3 years of age, whereas three other genera had disappeared by this age. A large number of new taxa were also observed in the 3-year-olds. The microbiota at 3 months of age, except for lactobacilli, was unrelated to caries development at a later age. In contrast, several taxa in the oral biofilms of the 3-year-olds were linked with the presence or absence of caries. The main species/phylotypes associated with caries in 3-year-olds belonged to the Actinobaculum, Atopobium, Aggregatibacter, and Streptococcus genera, whereas those influencing the absence of caries belonged to the Actinomyces, Bergeyella, Campylobacter, Granulicatella, Kingella, Leptotrichia, and Streptococcus genera. Conclusions Thus, during the first years of life, species richness and taxa diversity in the mouth increase significantly. Besides the more prevalent colonization of lactobacilli, the composition of the overall microbiota at 3 months of age was unrelated to caries development at a later age. Several taxa within the oral biofilms of the 3-year-olds could be linked to the presence or absence of caries. PMID:26020247

Lactobacillus salivarius and L. gasseri down-regulate Aggregatibacter actinomycetemcomitans exotoxins expression.

PubMed

Nissen, Lorenzo; Sgorbati, Barbara; Biavati, Bruno; Belibasakis, Georgios N

2014-01-01

Beneficial microbes, such as lactobacilli establish a symbiosis with the host and confer health-associated effects, by limiting the growth of indigenous pathogens and challenging microbes introduced by altered foods. Nevertheless, there is scarce information on the effects of beneficial microbes on the virulence properties of bacterial species associated with oral diseases, such as periodontitis. Aggregatibacter actinomycetemcomitans is a Gram-negative species highly implicated in the etiology of localized aggressive periodontitis. The objective of this study was to investigate the effect of lactobacilli on the expression of the two major virulence factors of A. actinomycetemcomitans . Lactobacillus salivarius and L. gasseri were selected as beneficial species. The gene expressions of leukotoxin ( LtxA ) and cytolethal distending toxin ( CdtB ) by A. actinomycetemcomitans were analyzed in response to challenge by lactobacilli cell-free supernatants. Neither lactobacilli affected the growth, but strongly attenuated the expressions of both CdtB and LtxA in the two A. actinomycetemcomitans strains tested. This reduction of the expression of these two exotoxins was time-dependent. These fundamental findings may indicate that lactobacilli can reduce the virulence of putative opportunistic oral pathogens, and may provide insights to future therapeutic approaches for the respective diseases.

New Record of Rhinopoma microphyllum with the Invested Parasites and Microbes in the Developed Ecotourism Area of South Lombok Island NTB

NASA Astrophysics Data System (ADS)

Fajri, S. R.; NPrimawati, S.; Hadi, I.; Tresnani, G.

2018-01-01

Rhinopoma microphyllum is a bat species that lives in a habitat covered by grove of trees and shrubs in the primary forest vegetation. These species is included in the IUCN Red List list with Least Concern (LC) status or at the least information. This study was to describe of R. microphyllum as a new record in the southern of Lombok, and to examine the parasites and microbes that infest it. The study was carried out in the developed ecotourism area of southern Lombok Island of NTB during February-April 2017. A modified net and quadrant for cave ceiling was used to collect bat sample. Ectoparasite collection was done by combing the bat’s hair and the falling specimens were collected. The endoparasite examination was done by the flotation methods of intestinal contents, while microbial examination was done by collecting the microbes from oral cavity and feces. The results showed the discovery of R. microphyllum in two ecotourism development sites, The Buwun Cave and The Gale Gale Bangkang Cave Prabu Village, Central Lombok. The endoparasit examination found 4 species of endoparasit, 1 species of Coccidia sp, 2 species of Trematodes from Lecithodendridae Family (Prosthodendrium sp and Acanthatrium sp) and 1 unidentified Nematode specimen. The ectoparasite examination found only 1 species, Ischnopsyllus hexactenus (The long Eared Bat Flea), and the microbes found from oral cavity analysis are the Gram positive Coccus (Stphylococcus aureus) and faecal analysis are the Coccobacil Gram negative (Providensia penneri).

Antimicrobial Decapeptide KSL-W Attenuates Candida albicans Virulence by Modulating Its Effects on Toll-Like Receptor, Human Beta-Defensin, and Cytokine Expression by Engineered human Oral Mucosa

DTIC Science & Technology

2011-02-02

against phytopathogenic fungi that cause postharvest decay in fruits . Mol Plant Microbe Interact 2000;13:837–46. [28] Montesinos E, Antimicrobial peptides...inactivated KSL-W did not affect epithelial cell proliferation (Fig. 2). 3.3. KSL-W pre-treatment reduced Candida growth in the infected oral mucosa tissue...against fungi , such as C. albi- cans, remains to be determined. Oral candidiasis is associatedwith gingival tissuewhere epithe- lial cells are the primary

Variations of oral microbiota are associated with pancreatic diseases including pancreatic cancer

PubMed Central

Farrell, James J; Zhang, Lei; Zhou, Hui; Chia, David; Elashoff, David; Akin, David; Paster, Bruce J; Joshipura, Kaumudi; Wong, David T W

2012-01-01

Objective The associations between oral diseases and increased risk of pancreatic cancer have been reported in several prospective cohort studies. In this study, we measured variations of salivary microbiota and evaluated their potential associations with pancreatic cancer and chronic pancreatitis. Methods This study was divided into three phases: (1) microbial profiling using the Human Oral Microbe Identification Microarray to investigate salivary microbiota variation between 10 resectable patients with pancreatic cancer and 10 matched healthy controls, (2) identification and verification of bacterial candidates by real-time quantitative PCR (qPCR) and (3) validation of bacterial candidates by qPCR on an independent cohort of 28 resectable pancreatic cancer, 28 matched healthy control and 27 chronic pancreatitis samples. Results Comprehensive comparison of the salivary microbiota between patients with pancreatic cancer and healthy control subjects revealed a significant variation of salivary microflora. Thirty-one bacterial species/clusters were increased in the saliva of patients with pancreatic cancer (n=10) in comparison to those of the healthy controls (n=10), whereas 25 bacterial species/clusters were decreased. Two out of six bacterial candidates (Neisseria elongata and Streptococcus mitis) were validated using the independent samples, showing significant variation (p<0.05, qPCR) between patients with pancreatic cancer and controls (n=56). Additionally, two bacteria (Granulicatella adiacens and S mitis) showed significant variation (p<0.05, qPCR) between chronic pancreatitis samples and controls (n=55). The combination of two bacterial biomarkers (N elongata and S mitis) yielded a receiver operating characteristic plot area under the curve value of 0.90 (95% CI 0.78 to 0.96, p<0.0001) with a 96.4% sensitivity and 82.1% specificity in distinguishing patients with pancreatic cancer from healthy subjects. Conclusions The authors observed associations between variations of patients’ salivary microbiota with pancreatic cancer and chronic pancreatitis. This report also provides proof of salivary microbiota as an informative source for discovering non-invasive biomarkers of systemic diseases. PMID:21994333

Expanding Single Particle Mass Spectrometer Analyses for the Identification of Microbe Signatures in Sea Spray Aerosol.

PubMed

Sultana, Camille M; Al-Mashat, Hashim; Prather, Kimberly A

2017-10-03

Ocean-derived microbes in sea spray aersosol (SSA) have the potential to influence climate and weather by acting as ice nucleating particles in clouds. Single particle mass spectrometers (SPMSs), which generate in situ single particle composition data, are excellent tools for characterizing aerosols under changing environmental conditions as they can provide high temporal resolution and require no sample preparation. While SPMSs have proven capable of detecting microbes, these instruments have never been utilized to definitively identify aerosolized microbes in ambient sea spray aersosol. In this study, an aerosol time-of-flight mass spectrometer was used to analyze laboratory generated SSA produced from natural seawater in a marine aerosol reference tank. We present the first description of a population of biological SSA mass spectra (BioSS), which closely match the ion signatures observed in previous terrestrial microbe studies. The fraction of BioSS dramatically increased in the largest supermicron particles, consistent with field and laboratory measurements of microbes ejected by bubble bursting, further supporting the assignment of BioSS mass spectra as microbes. Finally, as supported by analysis of inorganic ion signals, we propose that dry BioSS particles have heterogeneous structures, with microbes adhered to sodium chloride nodules surrounded by magnesium-enriched coatings. Consistent with this structure, chlorine-containing ion markers were ubiquitous in BioSS spectra and identified as possible tracers for distinguishing recently aerosolized marine from terrestrial microbes.

In Situ Bioreactor

ScienceCinema

Blackwelder, Brad

2018-05-11

At Idaho National Laboratory, researchers have developed bioreactor technology that permits identification, bioremediation testing and treatment at the source using naturally occurring microbes to disarm contaminants.

Fluctuation-Enhanced Sensing for Biological Agent Detection and Identification

DTIC Science & Technology

2009-01-01

method for bacterium detection published earlier; sensing and evaluating the odors of microbes ; and spectral and amplitude distribution analysis of noise...REPORT TYPE 3. DATES COVERED 00-00-2009 to 00-00-2009 4. TITLE AND SUBTITLE Fluctuation-Enhanced Sensing for Biological Agent Detection and...evaluating the odors of microbes ; and spectral and amplitude distribution analysis of noise in light scattering to identify spores based on their

Microbe Detector

NASA Technical Reports Server (NTRS)

1985-01-01

Under NASA contracts, McDonnell Douglas developed a microbial load monitor to detect bacterial contamination. Vitek Systems, Inc., a subsidiary, was created to commercialize the product for analyzing body fluids. With the AutoMicrobic System, infections may be treated more quickly. The process involves injecting the fluid into identification cards and screening the reaction. Antibiotic treatments are also suggested. Time in hospital and human error is reduced. There are also possible industrial and environmental applications.

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

PubMed Central

Ghodsi, Mohammad; Sommer, Daniel D.; Gibbons, Theodore R.; Treangen, Todd J.; Chang, Yi-Chien; Li, Shan; Stine, O. Colin; Hasturk, Hatice; Kasif, Simon; Segrè, Daniel; Pop, Mihai; Amar, Salomon

2012-01-01

The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (∼2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ∼90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes. PMID:22675498

The $100 Genome: Implications for the DoD

DTIC Science & Technology

2010-12-15

Phenotypes Influenced by the Microbiome In a recent study (Vijay-Kumar et al. 2010), gut microbes from obese mice were transferred to thin mice whose gut ...extraordinary genetic diversity of the gut microbiome , it is expected that these organisms (which usually have the first chance to interact with orally...Human Microbiome . In some cases it may be useful to sequence metagenomic samples of the microbiomes that colonize the human gut . oral cavity or other

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.

Oral and Craniofacial Clinical Signs Associated to Genetic Conditions in Human Identification Part I: A Review

PubMed Central

Ayoub, Fouad; Aoun, Nicole; el Husseini, Hassan; Jassar, Houssam; Sayah, Fida; Salameh, Ziad

2015-01-01

Background: Forensic dentistry is one of the most reliable methods used in human identification when other technique as fingerprint, DNA, visual identification cannot be used. Genetic disorders have several manifestations that can target the intra-oral cavity, the cranio-facial area or any location in the human body. Materials and Methods: A literature search of the scientific database (Medline and Science Direct) for the years 1990 to 2014 was carried out to find out all the available papers that indicate oral, cranio-facial signs, genetic and human identification. Results: A table with 10 genetic conditions was described with oral and cranio-facial signs that can help forensic specialist in human identification. Conclusion: This review showed a correlation between genetics, facial and intra-oral signs that would help forensic ondontologist in the identification procedures. PMID:26028912

Drone Transport of Microbes in Blood and Sputum Laboratory Specimens

PubMed Central

Street, Jeff; Carroll, Karen; Miller, Heather; Zhang, Sean X.

2016-01-01

Unmanned aerial vehicles (UAVs) could potentially be used to transport microbiological specimens. To examine the impact of UAVs on microbiological specimens, blood and sputum culture specimens were seeded with usual pathogens and flown in a UAV for 30 ± 2 min. Times to recovery, colony counts, morphologies, and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based identifications of the flown and stationary specimens were similar for all microbes studied. PMID:27535683

Ecological approaches to oral biofilms: control without killing.

PubMed

Marsh, Phil D; Head, David A; Devine, Deirdre A

2015-01-01

Humans have co-evolved with micro-organisms and have a symbiotic or mutualistic relationship with their resident microbiome. As at other body surfaces, the mouth has a diverse microbiota that grows on oral surfaces as structurally and functionally organised biofilms. The oral microbiota is natural and provides important benefits to the host, including immunological priming, down-regulation of excessive pro-inflammatory responses, regulation of gastrointestinal and cardiovascular systems, and colonisation by exogenous microbes. On occasions, this symbiotic relationship breaks down, and previously minor components of the microbiota outcompete beneficial bacteria, thereby increasing the risk of disease. Antimicrobial agents have been formulated into many oral care products to augment mechanical plaque control. A delicate balance is needed, however, to control the oral microbiota at levels compatible with health, without killing beneficial bacteria and losing the key benefits delivered by these resident microbes. These antimicrobial agents may achieve this by virtue of their recommended twice daily topical use, which results in pharmacokinetic profiles indicating that they are retained in the mouth for relatively long periods at sublethal levels. At these concentrations they are still able to inhibit bacterial traits implicated in disease (e.g. sugar transport/acid production; protease activity) and retard growth without eliminating beneficial species. In silico modelling studies have been performed which support the concept that either reducing the frequency of acid challenge and/or the terminal pH, or by merely slowing bacterial growth, results in maintaining a community of beneficial bacteria under conditions that might otherwise lead to disease (control without killing). 2015 S. Karger AG, Basel

TLR4, NOD1 and NOD2 mediate immune recognition of putative newly identified periodontal pathogens.

PubMed

Marchesan, Julie; Jiao, Yizu; Schaff, Riley A; Hao, Jie; Morelli, Thiago; Kinney, Janet S; Gerow, Elizabeth; Sheridan, Rachel; Rodrigues, Vinicius; Paster, Bruce J; Inohara, Naohiro; Giannobile, William V

2016-06-01

Periodontitis is a polymicrobial inflammatory disease that results from the interaction between the oral microbiota and the host immunity. Although the innate immune response is important for disease initiation and progression, the innate immune receptors that recognize both classical and putative periodontal pathogens that elicit an immune response have not been elucidated. By using the Human Oral Microbe Identification Microarray (HOMIM), we identified multiple predominant oral bacterial species in human plaque biofilm that strongly associate with severe periodontitis. Ten of the identified species were evaluated in greater depth, six being classical pathogens and four putative novel pathogens. Using human peripheral blood monocytes (HPBM) and murine bone-marrow-derived macrophages (BMDM) from wild-type (WT) and Toll-like receptor (TLR)-specific and MyD88 knockouts (KOs), we demonstrated that heat-killed Campylobacter concisus, Campylobacter rectus, Selenomonas infelix, Porphyromonas endodontalis, Porphyromonas gingivalis, and Tannerella forsythia mediate high immunostimulatory activity. Campylobacter concisus, C. rectus, and S. infelix exhibited robust TLR4 stimulatory activity. Studies using mesothelial cells from WT and NOD1-specific KOs and NOD2-expressing human embryonic kidney cells demonstrated that Eubacterium saphenum, Eubacterium nodatum and Filifactor alocis exhibit robust NOD1 stimulatory activity, and that Porphyromonas endodontalis and Parvimonas micra have the highest NOD2 stimulatory activity. These studies allowed us to provide important evidence on newly identified putative pathogens in periodontal disease pathogenesis showing that these bacteria exhibit different immunostimulatory activity via TLR4, NOD1, and NOD2 (Clinicaltrials.gov NCT01154855). © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

TLR4, NOD1 and NOD2 Mediate Immune Recognition of Putative Newly-Identified Periodontal Pathogens

PubMed Central

Schaff, Riley A.; Hao, Jie; Morelli, Thiago; Kinney, Janet S.; Gerow, Elizabeth; Sheridan, Rachel; Rodrigues, Vinicius; Paster, Bruce J.; Inohara, Naohiro; Giannobile, William V.

2015-01-01

SUMMARY Periodontitis is a polymicrobial inflammatory disease that results from the interaction between the oral microbiota and the host immunity. While the innate immune response is important for disease initiation and progression, the innate immune receptors that recognize both classical and putative periodontal pathogens that elicit an immune response have not been elucidated. By using the Human Oral Microbe Identification Microarray (HOMIM), we identified multiple predominant oral bacterial species in human plaque biofilm that strongly associate with severe periodontitis. Ten of the identified species were evaluated in greater depth, 6 being classical pathogens and 4 putative novel pathogens. Using human peripheral blood monocytes (HPBM) and murine bone marrow–derived macrophages (BMDM) from wild-type (WT) and toll-like receptor (TLR)-specific and MyD88 knockouts (KOs), we demonstrated that heat-killed Campylobacter concisus, Campylobacter rectus, Selenomonas infelix, Porphyromonas endodontalis, Porphyromonas gingivalis, and Tannerella forsythia mediate high immunostimulatory activity. C. concisus, C. rectus, and S. infelix exhibited robust TLR4 stimulatory activity. Studies using mesothelial cells from WT and NOD1-specific KOs and NOD2-expressing human embryonic kidney (HEK) cells demonstrated that Eubacterium saphenum, Eubacterium nodatum and Filifactor alocis exhibit robust NOD1 stimulatory activity, and that Porphyromonas endodontalis and Parvimonas micra have the highest NOD2-stimulatory activity. These studies allowed us to provide important evidence on newly-identified putative pathogens in periodontal disease pathogenesis showing that these bacteria exhibit different immunostimulatory activity via TLR4, NOD1, and NOD2 (Clinicaltrials.gov NCT01154855). PMID:26177212

Development of Conductive Polymer Analysis for the Rapid Detection and Identification of Phytopathogenic Microbes

Treesearch

A. Dan Wilson; D.G. Lester; C.S. Oberle

2004-01-01

Conductive polymer analysis, a type of electronic aroma detection technology, was evaluated for its efficacy in the detection, identification, and discrimination of plant-pathogenic microorganisms on standardized media and in diseased plant tissues. The method is based on the acquisition of a diagnostic electronic fingerprint derived from multisensor responses to...

Breast, milk and microbes: a complex relationship that does not end with lactation.

PubMed

Urbaniak, Camilla; Burton, Jeremy P; Reid, Gregor

2012-07-01

Until relatively recently, the extent of microbiota presence in the human breast was under-appreciated. A high-throughput sequencing study and culture-based studies have demonstrated the extensive presence of microbes in human milk, with their origin believed to be from the skin, oral cavity and via gut translocation. Since formula milk substitutes do not contain these bacteria, what benefits are denied to these infants? The addition of probiotic bacteria to some infant formula is meant to provide some benefits, but these only contain one species and the dose is relatively high compared with breast milk. Many questions of importance to women's health arise from these findings. When, how and what types of microbes colonize the breast at different stages of a woman's life, including postlactation, and what effect do they have on the host in the short and long term? This article discusses some aspects of these questions.

Exploring the potential of laser capture microdissection technology in integrated oral biosciences.

PubMed

Thennavan, A; Sharma, M; Chandrashekar, C; Hunter, K; Radhakrishnan, R

2017-09-01

Laser capture microdissection (LCM) is a high-end research and diagnostic technology that helps in obtaining pure cell populations for the purpose of cell- or lesion-specific genomic and proteomic analysis. Literature search on the application of LCM in oral tissues was made through PubMed. There is ample evidence to substantiate the utility of LCM in understanding the underlying molecular mechanism involving an array of oral physiological and pathological processes, including odontogenesis, taste perception, eruptive tooth movement, oral microbes, and cancers of the mouth and jaw tumors. This review is aimed at exploring the potential application of LCM in oral tissues as a high-throughput tool for integrated oral sciences. The indispensable application of LCM in the construction of lesion-specific genomic libraries with emphasis on some of the novel molecular markers thus discovered is also highlighted. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Drone Transport of Microbes in Blood and Sputum Laboratory Specimens.

PubMed

Amukele, Timothy K; Street, Jeff; Carroll, Karen; Miller, Heather; Zhang, Sean X

2016-10-01

Unmanned aerial vehicles (UAVs) could potentially be used to transport microbiological specimens. To examine the impact of UAVs on microbiological specimens, blood and sputum culture specimens were seeded with usual pathogens and flown in a UAV for 30 ± 2 min. Times to recovery, colony counts, morphologies, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identifications of the flown and stationary specimens were similar for all microbes studied. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health.

PubMed

Gomez, Andres; Nelson, Karen E

2017-02-01

In the era of applied meta-omics and personalized medicine, the oral microbiome is a valuable asset. From biomarker discovery to being a powerful source of therapeutic targets and to presenting an opportunity for developing non-invasive approaches to health care, it has become clear that oral microbes may hold the answer for understanding disease, even beyond the oral cavity. Although our understanding of oral microbiome diversity has come a long way in the past 50 years, there are still many areas that need to be fine-tuned for better risk assessment and diagnosis, especially in early developmental stages of human life. Here, we discuss the factors that impact development of the oral microbiome and explore oral markers of disease, with a focus on the early oral cavity. Our ultimate goal is to put different experimental and methodological views into perspective for better assessment of early oral and systemic disease at an early age and discuss how oral microbiomes-at the community level-could provide improved assessment in individuals and populations at risk.

The Oral Microbiome of Children: Development, Disease and Implications Beyond Oral Health

PubMed Central

Gomez, Andres; Nelson, Karen E.

2016-01-01

In the era of applied meta-omics and personalized medicine, the oral microbiome is a valuable asset. From biomarker discovery to being a powerful source of therapeutic targets, and to presenting an opportunity for developing non-invasive approaches to health care, it has become clear that oral microbes may hold the answer for understanding disease, even beyond the oral cavity. Although our understanding of oral microbiome diversity has come a long way in the past 50 years, there are still many areas that need to be fine-tuned for better risk assessment and diagnosis, especially in early developmental stages of human life. Here, we discuss the factors that impact development of the oral microbiome, and explore oral markers of disease, with a focus on the early oral cavity. Our ultimate goal is to put different experimental and methodological views into perspective for better assessment of early oral and systemic disease at an early age, and discuss how oral microbiomes- at the community level, could provide improved assessment in individuals, and populations at risk. PMID:27628595

Invited review: The preterm pig as a model in pediatric gastroenterology

USDA-ARS?s Scientific Manuscript database

At birth, the newborn mammal undergoes a transition from a sterile uterine environment with a constant nutrient supply, to a microbe-rich environment with intermittent oral intake of complex milk nutrients via the gastrointestinal tract (GIT). These functional challenges partly explain the relativel...

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.

Role of oral microbiome on oral cancers, a review.

PubMed

Gholizadeh, Pourya; Eslami, Hosein; Yousefi, Mehdi; Asgharzadeh, Mohammad; Aghazadeh, Mohammad; Kafil, Hossein Samadi

2016-12-01

The oral cavity is inhibited by many of the bacterial species. Some of them have a key role in the development of oral disease. Interrelationships between oral microbiome and systemic conditions such as head-and-neck cancer have become increasingly appreciated in recent years. Emerging evidence also suggests a link between periodontal disease and oral cancer, and the explanation being that chronic inflammation could be a major factor in both diseases. Squamous cell carcinoma is that the most frequently occurring malignancy of the oral cavity and adjacent sites, representing over 90% of all cancers. The incidence of oral cancer is increasing, significantly among young people and women. Worldwide there are 350,000-400,000 new cases diagnosed every year. Bacteria, viruses, and fungi are strongly implicated as etiological factors in certain cancers. In this review we will discuss the association between the development of oral cancer in potentially malignant oral lesions with chronic periodontitis, chronic Porphyromonas gingivalis, Fusobacterium nucleatum, candida, other microbes and described mechanisms which may be involved in these carcinoma. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Expression of a wolf spider toxin in tobacco inhibits the growth of microbes and insects

USDA-ARS?s Scientific Manuscript database

Abstract Lycotoxin I, from the wolf spider (Lycosa carolinensis), is an amphipathic pore-forming peptide that has antimicrobial and anti-insect activity. Constitutive expression of a lycotoxin I odified for oral toxicity to insects in tobacco (Nicotiana abacum) conferred significantly enhanced resis...

Taxonomy, Epidemiology, and Clinical Relevance of the Genus Arcobacter

PubMed Central

Collado, Luis; Figueras, Maria José

2011-01-01

Summary: The genus Arcobacter, defined almost 20 years ago from members of the genus Campylobacter, has become increasingly important because its members are being considered emergent enteropathogens and/or potential zoonotic agents. Over recent years information that is relevant for microbiologists, especially those working in the medical and veterinary fields and in the food safety sector, has accumulated. Recently, the genus has been enlarged with several new species. The complete genomes of Arcobacter butzleri and Arcobacter nitrofigilis are available, with the former revealing diverse pathways characteristic of free-living microbes and virulence genes homologous to those of Campylobacter. The first multilocus sequence typing analysis showed a great diversity of sequence types, with no association with specific hosts or geographical regions. Advances in detection and identification techniques, mostly based on molecular methods, have been made. These microbes have been associated with water outbreaks and with indicators of fecal pollution, with food products and water as the suspected routes of transmission. This review updates this knowledge and provides the most recent data on the taxonomy, species diversity, methods of detection, and identification of these microbes as well as on their virulence potential and implication in human and animal diseases. PMID:21233511

Phylogenetic characterization of culturable bacteria and fungi associated with tarballs from Betul beach, Goa, India.

PubMed

Shinde, Varsha Laxman; Meena, Ram Murti; Shenoy, Belle Damodara

2018-03-01

Tarballs are semisolid blobs of crude oil, normally formed due to weathering of crude-oil in the sea after any kind of oil spills. Microorganisms are believed to thrive on hydrocarbon-rich tarballs and possibly assist in biodegradation. The taxonomy of ecologically and economically important tarball-associated microbes, however, needs improvement as DNA-based identification and phylogenetic characterization have been scarcely incorporated into it. In this study, bacteria and fungi associated with tarballs from touristic Betul beach in Goa, India were isolated, followed by phylogenetic analyses of 16S rRNA gene and the ITS sequence-data to decipher their clustering patterns with closely-related taxa. The gene-sequence analyses identified phylogenetically diverse 20 bacterial genera belonging to the phyla Proteobacteria (14), Actinobacteria (3), Firmicutes (2) and Bacteroidetes (1), and 8 fungal genera belonging to the classes Eurotiomycetes (6), Sordariomycetes (1) and Leotiomycetes (1) associated with the Betul tarball samples. Future studies employing a polyphasic approach, including multigene sequence-data, are needed for species-level identification of culturable tarball-associated microbes. This paper also discusses potentials of tarball-associated microbes to degrade hydrocarbons. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microfabricated Microbial Fuel Cell Arrays Reveal Electrochemically Active Microbes

PubMed Central

Cho, Younghak; de Figueiredo, Paul; Han, Arum

2009-01-01

Microbial fuel cells (MFCs) are remarkable “green energy” devices that exploit microbes to generate electricity from organic compounds. MFC devices currently being used and studied do not generate sufficient power to support widespread and cost-effective applications. Hence, research has focused on strategies to enhance the power output of the MFC devices, including exploring more electrochemically active microbes to expand the few already known electricigen families. However, most of the MFC devices are not compatible with high throughput screening for finding microbes with higher electricity generation capabilities. Here, we describe the development of a microfabricated MFC array, a compact and user-friendly platform for the identification and characterization of electrochemically active microbes. The MFC array consists of 24 integrated anode and cathode chambers, which function as 24 independent miniature MFCs and support direct and parallel comparisons of microbial electrochemical activities. The electricity generation profiles of spatially distinct MFC chambers on the array loaded with Shewanella oneidensis MR-1 differed by less than 8%. A screen of environmental microbes using the array identified an isolate that was related to Shewanella putrefaciens IR-1 and Shewanella sp. MR-7, and displayed 2.3-fold higher power output than the S. oneidensis MR-1 reference strain. Therefore, the utility of the MFC array was demonstrated. PMID:19668333

Rapid identification of single microbes by various Raman spectroscopic techniques

NASA Astrophysics Data System (ADS)

Rösch, Petra; Harz, Michaela; Schmitt, Michael; Peschke, Klaus-Dieter; Ronneberger, Olaf; Burkhardt, Hans; Motzkus, Hans-Walter; Lankers, Markus; Hofer, Stefan; Thiele, Hans; Popp, Jürgen

2006-02-01

A fast and unambiguous identification of microorganisms is necessary not only for medical purposes but also in technical processes such as the production of pharmaceuticals. Conventional microbiological identification methods are based on the morphology and the ability of microbes to grow under different conditions on various cultivation media depending on their biochemical properties. These methods require pure cultures which need cultivation of at least 6 h but normally much longer. Recently also additional methods to identify bacteria are established e.g. mass spectroscopy, polymerase chain reaction (PCR), flow cytometry or fluorescence spectroscopy. Alternative approaches for the identification of microorganisms are vibrational spectroscopic techniques. With Raman spectroscopy a spectroscopic fingerprint of the microorganisms can be achieved. Using UV-resonance Raman spectroscopy (UVRR) macromolecules like DNA/RNA and proteins are resonantly enhanced. With an excitation wavelength of e.g. 244 nm it is possible to determine the ratio of guanine/cytosine to all DNA bases which allows a genotypic identification of microorganisms. The application of UVRR requires a large amount of microorganisms (> 10 6 cells) e.g. at least a micro colony. For the analysis of single cells micro-Raman spectroscopy with an excitation wavelength of 532 nm can be used. Here, the obtained information is from all type of molecules inside the cells which lead to a chemotaxonomic identification. In this contribution we show how wavelength dependent Raman spectroscopy yields significant molecular information applicable for the identification of microorganisms on a single cell level.

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.

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City

PubMed Central

Maritz, Julia M.; Sullivan, Steven A.; Prill, Robert J.; Aksoy, Emre; Scheid, Paul; Carlton, Jane M.

2017-01-01

Background Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with—and potential exchange of—microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Results Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency. Conclusions We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes. PMID:28384336

Preparation of an orthodontic bracket coated with an nitrogen-doped TiO(2-x)N(y) thin film and examination of its antimicrobial performance.

PubMed

Cao, Baocheng; Wang, Yuhua; Li, Na; Liu, Bin; Zhang, Yingjie

2013-01-01

A bracket coated with a nitrogen-doped (N-doped) TiO(2-x)N(y) thin film was prepared using the RF magnetron sputtering method. The physicochemical properties of the thin film were measured using X-ray diffraction and energy-dispersive X-ray spectrometry, while the antimicrobial activity of the bracket against common oral pathogenic microbes was assessed on the basis of colony counts. The rate of antimicrobial activity of the bracket coated with nano-TiO(2-x)N(y) thin film against Streptococcus mutans, Lactobacillus acidophilus, Actinomyces viscous, and Candida albicans was 95.19%, 91.00%, 69.44%, and 98.86%, respectively. Scanning electron microscopy showed that fewer microbes adhered to the surface of this newly designed bracket than to the surface of the normal edgewise bracket. The brackets coated with the N-doped TiO(2-x)N(y) thin film showed high antimicrobial and bacterial adhesive properties against normal oral pathogenic bacterial through visible light, which is effective in prevention of enamel demineralization and gingivitis in orthodontic patients.

Acetaldehyde production and microbial colonization in oral squamous cell carcinoma and oral lichenoid disease.

PubMed

Marttila, Emilia; Uittamo, Johanna; Rusanen, Peter; Lindqvist, Christian; Salaspuro, Mikko; Rautemaa, Riina

2013-07-01

The main aim of this prospective study was to explore the ability of the oral microbiome to produce acetaldehyde in ethanol incubation. A total of 90 patients [30 oral squamous cell carcinoma (OSCC); 30 oral lichenoid disease (OLD); 30 healthy controls (CO)] were enrolled in the study. Microbial samples were taken from the mucosa using a filter paper method. The density of microbial colonization was calculated and the spectrum analyzed. Microbial acetaldehyde production was measured by gas chromatography. The majority (68%) of cultures produced carcinogenic levels of acetaldehyde (>100 μM) when incubated with ethanol (22 mM). The mean acetaldehyde production by microbes cultured from smoker samples was significantly higher (213 μM) than from non-smoker samples (141 μM) (P=.0326). The oral microbiota from OSCC, OLD patients and healthy individuals are able to produce carcinogenic levels of acetaldehyde. The present provisional study suggests smoking may increase the production of acetaldehyde. Copyright © 2013 Elsevier Inc. All rights reserved.

Molecular Ecology of Drinking Water

EPA Science Inventory

The presentation consists of examples of molecular research: –Detection and control (removal and/or inactivation) of microbes in drinking source waters –Changing microbial quality of water during distribution and storage –Detection and identification of microbial agents, incl...

[Microbiology--laboratory examinations for bacterias].

PubMed

Hen, Renjun; Imafuku, Yuji; Yoshida, Hiroshi

2002-11-01

As it has been required to identify pathogenic microbes in shorter times, simple and rapid methods have been developed and used. Here, we summarized the present situation of rapid diagnostic testing in clinical microbiology in Japan, and also presented our results on PBP2' detection. The rapid test kits available in Japan for E. coli, Helicobacter pylori, Salmonella, Streptococcus and Staphylococcus aureus were described. Rapid examination methods are based mainly on immunologic reactions, which included slide agglutination using latex particle, immunochromatography and ELISA. Times required for the identification are 10 to 15 minutes. Moreover, rapid test kits employing PCR are also marketed. Further, we evaluated MRSA-LA "Seiken" which is a rapid detection kit for PBP2' produced by MRSA. The test was shown to be highly sensitive and specific. For the rapid identification of pathogenic microbes, simple and rapid test kits described here will be used more in clinical diagnosis.

The interaction of gut microbes with host ABC transporters

PubMed Central

Mercado-Lubo, Regino

2010-01-01

ATP binding cassette (ABC) transporters are increasingly recognized for their ability to modulate the absorption, distribution, metabolism, secretion and toxicity of xenobiotics. In addition to their essential function in drug resistance, there is also emerging evidence documenting the important role ABC transporters play in tissue defense. In this respect, the gastrointestinal tract represents a critical vanguard of defense against oral exposure of drugs while at the same time functions as a physical barrier between the lumenal contents (including bacteria) and the intestinal epithelium. Given emerging evidence suggesting that multidrug resistance protein (MDR) plays an important role in host-bacterial interactions in the gastrointestinal tract, this review will discuss the interplay between MDR of the intestinal epithelial cell barrier and gut microbes in health and disease. In particular, we will explore host-microbe interactions involving three apically restricted ABC transporters of the intestinal epithelium; P-glycoprotein (P-gp), multidrug resistance-associated protein 2 (MRP2) and cystic fibrosis transmembrane regulator (CFTR). PMID:21327038

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 Emerging Microbe Project: Developing Clinical Care Plans Based on Pathogen Identification and Clinical Case Studies †

PubMed Central

O’Donnell, Lauren A.; Perry, Michael W.; Doup, Dane’t R.

2015-01-01

For many students in the health sciences, including doctor of pharmacy (PharmD) students, basic and clinical sciences often appear detached from each other. In the infectious disease field, PharmD students additionally struggle with mastering the diversity of microorganisms and the corresponding therapies. The objective of this study was to design an interdisciplinary project that integrates fundamental microbiology with clinical research and decision-making skills. The Emerging Microbe Project guided students through the identification of a microorganism via genetic sequence analysis. The unknown microbe provided the basis for a patient case that asked the student to design a therapeutic treatment strategy for an infected patient. Outside of lecture, students had two weeks to identify the pathogen using nucleotide sequences, compose a microbiology report on the pathogen, and recommend an appropriate therapeutic treatment plan for the corresponding clinical case. We hypothesized that the students would develop a better understanding of the interplay between basic microbiology and infectious disease clinical practice, and that they would gain confidence and skill in independently selecting appropriate antimicrobial therapies for a new disease state. The exercise was conducted with PharmD students in their second professional year of pharmacy school in a required infectious disease course. Here, we demonstrate that the Emerging Microbe Project significantly improved student learning through two assessment strategies (assignment grades and exam questions), and increased student confidence in clinical infectious disease practice. This exercise could be modified for other health sciences students or undergraduates depending upon the level of clinical focus required of the course. PMID:26753029

Functional metagenomics to decipher food-microbe-host crosstalk.

PubMed

Larraufie, Pierre; de Wouters, Tomas; Potocki-Veronese, Gabrielle; Blottière, Hervé M; Doré, Joël

2015-02-01

The recent developments of metagenomics permit an extremely high-resolution molecular scan of the intestinal microbiota giving new insights and opening perspectives for clinical applications. Beyond the unprecedented vision of the intestinal microbiota given by large-scale quantitative metagenomics studies, such as the EU MetaHIT project, functional metagenomics tools allow the exploration of fine interactions between food constituents, microbiota and host, leading to the identification of signals and intimate mechanisms of crosstalk, especially between bacteria and human cells. Cloning of large genome fragments, either from complex intestinal communities or from selected bacteria, allows the screening of these biological resources for bioactivity towards complex plant polymers or functional food such as prebiotics. This permitted identification of novel carbohydrate-active enzyme families involved in dietary fibre and host glycan breakdown, and highlighted unsuspected bacterial players at the top of the intestinal microbial food chain. Similarly, exposure of fractions from genomic and metagenomic clones onto human cells engineered with reporter systems to track modulation of immune response, cell proliferation or cell metabolism has allowed the identification of bioactive clones modulating key cell signalling pathways or the induction of specific genes. This opens the possibility to decipher mechanisms by which commensal bacteria or candidate probiotics can modulate the activity of cells in the intestinal epithelium or even in distal organs such as the liver, adipose tissue or the brain. Hence, in spite of our inability to culture many of the dominant microbes of the human intestine, functional metagenomics open a new window for the exploration of food-microbe-host crosstalk.

Identification of butanol tolerant genes in Lactobacillus mucosae

USDA-ARS?s Scientific Manuscript database

Butanol, though in low concentrations, is produced biologically through fermentation of lignocellulosic biomass-derived substrates by Gram-positive Clostridium species. However, naturally available butanol fermenting microbes are sensitive to stress caused by increased production of butanol and the...

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.

Beyond DNA Sequencing in Space: Current and Future Omics Capabilities of the Biomolecule Sequencer Payload

NASA Technical Reports Server (NTRS)

Wallace, Sarah

2017-01-01

Why do we need a DNA sequencer to support the human exploration of space? (A) Operational environmental monitoring; (1) Identification of contaminating microbes, (2) Infectious disease diagnosis, (3) Reduce down mass (sample return for environmental monitoring, crew health, etc.). (B) Research; (1) Human, (2) Animal, (3) Microbes/Cell lines, (4) Plant. (C) Med Ops; (1) Response to countermeasures, (2) Radiation, (3) Real-time analysis can influence medical intervention. (C) Support astrobiology science investigations; (1) Technology superiorly suited to in situ nucleic acid-based life detection, (2) Functional testing for integration into robotics for extraplanetary exploration mission.

The food-gut human axis: the effects of diet on gut microbiota and metabolome.

PubMed

De Angelis, Maria; Garruti, Gabriella; Minervini, Fabio; Bonfrate, Leonilde; Portincasa, Piero; Gobbetti, Marco

2017-04-27

Gut microbiota, the largest symbiont community hosted in human organism, is emerging as a pivotal player in the relationship between dietary habits and health. Oral and, especially, intestinal microbes metabolize dietary components, affecting human health by producing harmful or beneficial metabolites, which are involved in the incidence and progression of several intestinal related and non-related diseases. Habitual diet (Western, Agrarian and Mediterranean omnivore diets, vegetarian, vegan and gluten-free diets) drives the composition of the gut microbiota and metabolome. Within the dietary components, polymers (mainly fibers, proteins, fat and polyphenols) that are not hydrolyzed by human enzymes seem to be the main leads of the metabolic pathways of gut microbiota, which in turn directly influences the human metabolome. Specific relationships between diet and microbes, microbes and metabolites, microbes and immune functions and microbes and/or their metabolites and some human diseases are being established. Dietary treatments with fibers are the most effective to benefit the metabolome profile, by improving the synthesis of short chain fatty acids and decreasing the level of molecules, such as p-cresyl sulfate, indoxyl sulfate and trimethylamine N-oxide, involved in disease state. Based on the axis diet-microbiota-health, this review aims at describing the most recent knowledge oriented towards a profitable use of diet to provide benefits to human health, both directly and indirectly, through the activity of gut microbiota. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Effects of Material Properties on Bacterial Adhesion and Biofilm Formation.

PubMed

Song, F; Koo, H; Ren, D

2015-08-01

Adhesion of microbes, such as bacteria and fungi, to surfaces and the subsequent formation of biofilms cause multidrug-tolerant infections in humans and fouling of medical devices. To address these challenges, it is important to understand how material properties affect microbe-surface interactions and engineer better nonfouling materials. Here we review the recent progresses in this field and discuss the main challenges and opportunities. In particular, we focus on bacterial biofilms and review the effects of surface energy, charge, topography, and stiffness of substratum material on bacterial adhesion. We summarize how these surface properties influence oral biofilm formation, and we discuss the important findings from nondental systems that have potential applications in dental medicine. © International & American Associations for Dental Research 2015.

The dormant blood microbiome in chronic, inflammatory diseases.

PubMed

Potgieter, Marnie; Bester, Janette; Kell, Douglas B; Pretorius, Etheresia

2015-07-01

Blood in healthy organisms is seen as a 'sterile' environment: it lacks proliferating microbes. Dormant or not-immediately-culturable forms are not absent, however, as intracellular dormancy is well established. We highlight here that a great many pathogens can survive in blood and inside erythrocytes. 'Non-culturability', reflected by discrepancies between plate counts and total counts, is commonplace in environmental microbiology. It is overcome by improved culturing methods, and we asked how common this would be in blood. A number of recent, sequence-based and ultramicroscopic studies have uncovered an authentic blood microbiome in a number of non-communicable diseases. The chief origin of these microbes is the gut microbiome (especially when it shifts composition to a pathogenic state, known as 'dysbiosis'). Another source is microbes translocated from the oral cavity. 'Dysbiosis' is also used to describe translocation of cells into blood or other tissues. To avoid ambiguity, we here use the term 'atopobiosis' for microbes that appear in places other than their normal location. Atopobiosis may contribute to the dynamics of a variety of inflammatory diseases. Overall, it seems that many more chronic, non-communicable, inflammatory diseases may have a microbial component than are presently considered, and may be treatable using bactericidal antibiotics or vaccines. © FEMS 2015.

The dormant blood microbiome in chronic, inflammatory diseases

PubMed Central

Potgieter, Marnie; Bester, Janette; Kell, Douglas B.; Pretorius, Etheresia

2015-01-01

Blood in healthy organisms is seen as a ‘sterile’ environment: it lacks proliferating microbes. Dormant or not-immediately-culturable forms are not absent, however, as intracellular dormancy is well established. We highlight here that a great many pathogens can survive in blood and inside erythrocytes. ‘Non-culturability’, reflected by discrepancies between plate counts and total counts, is commonplace in environmental microbiology. It is overcome by improved culturing methods, and we asked how common this would be in blood. A number of recent, sequence-based and ultramicroscopic studies have uncovered an authentic blood microbiome in a number of non-communicable diseases. The chief origin of these microbes is the gut microbiome (especially when it shifts composition to a pathogenic state, known as ‘dysbiosis’). Another source is microbes translocated from the oral cavity. ‘Dysbiosis’ is also used to describe translocation of cells into blood or other tissues. To avoid ambiguity, we here use the term ‘atopobiosis’ for microbes that appear in places other than their normal location. Atopobiosis may contribute to the dynamics of a variety of inflammatory diseases. Overall, it seems that many more chronic, non-communicable, inflammatory diseases may have a microbial component than are presently considered, and may be treatable using bactericidal antibiotics or vaccines. PMID:25940667

Insights into the virulence of oral biofilms: discoveries from proteomics.

PubMed

Kuboniwa, Masae; Tribble, Gena D; Hendrickson, Erik L; Amano, Atsuo; Lamont, Richard J; Hackett, Murray

2012-06-01

This review covers developments in the study of polymicrobial communities, biofilms and selected areas of host response relevant to dental plaque and related areas of oral biology. The emphasis is on recent studies in which proteomic methods, particularly those using mass spectrometry as a readout, have played a major role in the investigation. The last 5-10 years have seen a transition of such methods from the periphery of oral biology to the mainstream, as in other areas of biomedical science. For reasons of focus and space, the authors do not discuss biomarker studies relevant to improved diagnostics for oral health, as this literature is rather substantial in its own right and deserves a separate treatment. Here, global gene regulation studies of plaque-component organisms, biofilm formation, multispecies interactions and host-microbe interactions are discussed. Several aspects of proteomics methodology that are relevant to the studies of multispecies systems are commented upon.

[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.

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.

Langerhans Cells and Their Role in Oral Mucosal Diseases

PubMed Central

Upadhyay, Juhi; Upadhyay, Ram B; Agrawal, Pankaj; Jaitley, Shweta; Shekhar, Rhitu

2013-01-01

Dendritic cells are arguably the most potent antigen-presenting cells and may be the only cells capable of initiating the adaptive immune response. The epithelial residents of dendritic cells are Langerhans cells, which serve as the “sentinels” of the mucosa, altering the immune system not only to pathogen entry but also of tolerance to self antigen and commensal microbes. Oral mucosal Langerhans cells are capable of engaging and internalizing a wide variety of pathogens and have been found responsive to nickel in patients with nickel allergies, oral Candida species, oral lichen planus, lichenoid drug eruptions, graft versus host diseases, periodontal diseases median rhomboid glossitis, human immunodeficiency virus infection, hairy leukoplakia of the tongue, and oral squamous cell carcinoma. Review focuses on the role of antigen-presenting cells in particular Langerhans cells to better understand the mechanisms underlying immune responses. In this review, comprehensive detail about mucosal diseases has been compiled using the PubMed database and through textbooks. PMID:24251267

Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry.

PubMed

Stasulli, Nikolas M; Shank, Elizabeth A

2016-11-01

The ability of microbes to secrete bioactive chemical signals into their environment has been known for over a century. However, it is only in the last decade that imaging mass spectrometry has provided us with the ability to directly visualize the spatial distributions of these microbial metabolites. This technology involves collecting mass spectra from multiple discrete locations across a biological sample, yielding chemical ‘maps’ that simultaneously reveal the distributions of hundreds of metabolites in two dimensions. Advances in microbial imaging mass spectrometry summarized here have included the identification of novel strain- or coculture-specific compounds, the visualization of biotransformation events (where one metabolite is converted into another by a neighboring microbe), and the implementation of a method to reconstruct the 3D subsurface distributions of metabolites, among others. Here we review the recent literature and discuss how imaging mass spectrometry has spurred novel insights regarding the chemical consequences of microbial interactions.

Construction and Screening of Marine Metagenomic Large Insert Libraries.

PubMed

Weiland-Bräuer, Nancy; Langfeldt, Daniela; Schmitz, Ruth A

2017-01-01

The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. This chapter describes sampling in the marine environment, construction of metagenomic large insert libraries from marine habitats, and exemplarily one function based screen of metagenomic clones for identification of quorum quenching activities.

New natural products isolated from Metarhizium robertsii ARSEF 23 by chemical screening and identification of the gene cluster through engineered biosynthesis in Aspergillus nidulans A1145.

PubMed

Kato, Hiroki; Tsunematsu, Yuta; Yamamoto, Tsuyoshi; Namiki, Takuya; Kishimoto, Shinji; Noguchi, Hiroshi; Watanabe, Kenji

2016-07-01

To rapidly identify novel natural products and their associated biosynthetic genes from underutilized and genetically difficult-to-manipulate microbes, we developed a method that uses (1) chemical screening to isolate novel microbial secondary metabolites, (2) bioinformatic analyses to identify a potential biosynthetic gene cluster and (3) heterologous expression of the genes in a convenient host to confirm the identity of the gene cluster and the proposed biosynthetic mechanism. The chemical screen was achieved by searching known natural product databases with data from liquid chromatographic and high-resolution mass spectrometric analyses collected on the extract from a target microbe culture. Using this method, we were able to isolate two new meroterpenes, subglutinols C (1) and D (2), from an entomopathogenic filamentous fungus Metarhizium robertsii ARSEF 23. Bioinformatics analysis of the genome allowed us to identify a gene cluster likely to be responsible for the formation of subglutinols. Heterologous expression of three genes from the gene cluster encoding a polyketide synthase, a prenyltransferase and a geranylgeranyl pyrophosphate synthase in Aspergillus nidulans A1145 afforded an α-pyrone-fused uncyclized diterpene, the expected intermediate of the subglutinol biosynthesis, thereby confirming the gene cluster to be responsible for the subglutinol biosynthesis. These results indicate the usefulness of our methodology in isolating new natural products and identifying their associated biosynthetic gene cluster from microbes that are not amenable to genetic manipulation. Our method should facilitate the natural product discovery efforts by expediting the identification of new secondary metabolites and their associated biosynthetic genes from a wider source of microbes.

Microbe-ID: An open source toolbox for microbial genotyping and species identification

USDA-ARS?s Scientific Manuscript database

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user...

Comparison of identification methods for oral asaccharolytic Eubacterium species.

PubMed

Wade, W G; Slayne, M A; Aldred, M J

1990-12-01

Thirty one strains of oral, asaccharolytic Eubacterium spp. and the type strains of E. brachy, E. nodatum and E. timidum were subjected to three identification techniques--protein-profile analysis, determination of metabolic end-products, and the API ATB32A identification kit. Five clusters were obtained from numerical analysis of protein profiles and excellent correlations were seen with the other two methods. Protein profiles alone allowed unequivocal identification.

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.

PubMed

Yamagishi, Junya; Sato, Yukuto; Shinozaki, Natsuko; Ye, Bin; Tsuboi, Akito; Nagasaki, Masao; Yamashita, Riu

2016-01-01

The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we analyzed human oral microbes to compare the performance of three DNA extraction methods: PowerSoil (a method widely used in this field), QIAsymphony (a robotics method), and a simple boiling method. Dental plaque was initially collected from three volunteers in the pilot study and then expanded to 12 volunteers in the follow-up study. Bacterial flora was estimated by sequencing the V4 region of 16S rRNA following species-level profiling. Our results indicate that the efficiency of PowerSoil and QIAsymphony was comparable to the boiling method. Therefore, the boiling method may be a promising alternative because of its simplicity, cost effectiveness, and short handling time. Moreover, this method was reliable for estimating bacterial species and could be used in the future to examine the correlation between oral flora and health status. Despite this, differences in the efficiency of DNA extraction for various bacterial species were observed among the three methods. Based on these findings, there is no "gold standard" for DNA extraction. In future, we suggest that the DNA extraction method should be selected on a case-by-case basis considering the aims and specimens of the study.

Unexpected role of the IMD pathway in Drosophila gut defense against Staphylococcus aureus.

PubMed

Hori, Aki; Kurata, Shoichiro; Kuraishi, Takayuki

2018-01-01

In this study, fruit fly of the genus Drosophila is utilized as a suitable model animal to investigate the molecular mechanisms of innate immunity. To combat orally transmitted pathogenic Gram-negative bacteria, the Drosophila gut is armed with the peritrophic matrix, which is a physical barrier composed of chitin and glycoproteins: the Duox system that produces reactive oxygen species (ROS), which in turn sterilize infected microbes, and the IMD pathway that regulates the expression of antimicrobial peptides (AMPs), which in turn control ROS-resistant pathogens. However, little is known about the defense mechanisms against Gram-positive bacteria in the fly gut. Here, we show that the peritrophic matrix protects Drosophila against Gram-positive bacteria S. aureus. We also define the few roles of ROS in response to the infection and show that the IMD pathway is required for the clearance of ingested microbes, possibly independently from AMP expression. These findings provide a new aspect of the gut defense system of Drosophila, and helps to elucidate the processes of gut-microbe symbiosis and pathogenesis. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Effects of refrigerating preinoculated Vitek cards on microbial physiology and antibiotic susceptibility

NASA Technical Reports Server (NTRS)

Skweres, Joyce A.; Bassinger, Virginia J.; Mishra, S. K.; Pierson, Duane L.

1992-01-01

Reference cultures of 16 microorganisms obtained from the American Type Culture Collection and four clinical isolates were used in standardized solutions to inoculate 60 cards for each test strain. A set of three ID and three susceptibility cards was processed in the Vitek AutoMicrobic System (AMS) immediately after inoculation. The remaining cards were refrigerated at 4 C, and sets of six cards were removed and processed periodically for up to 17 days. The preinoculated AMS cards were evaluated for microorganism identification, percent probability of correct identification, length of time required for final result, individual substrate reactions, and antibiotic minimal inhibitory/concentration (MIC) values. Results indicate that 11 of the 20 microbes tested withstood refrigerated storage up to 17 days without detectable changes in delineating characteristics. MIC results appear variable, but certain antibiotics proved to be more stable than others. The results of these exploratory studies will be used to plan a microgravity experiment designed to study the effect of microgravity on microbial physiology and antibiotic sensitivity.

Identification of Lactobacillus strains with probiotic features from the bottlenose dolphin (Tursiops truncatus)

PubMed Central

Diaz, MA; Bik, EM; Carlin, KP; Venn-Watson, SK; Jensen, ED; Jones, SE; Gaston, EP; Relman, DA; Versalovic, J

2013-01-01

Aims In order to develop complementary health management strategies for marine mammals, we used culture-based and culture-independent approaches to identify gastrointestinal lactobacilli of the common bottlenose dolphin, Tursiops truncatus. Methods and Results We screened 307 bacterial isolates from oral and rectal swabs, milk and gastric fluid, collected from 38 dolphins in the U.S. Navy Marine Mammal Program, for potentially beneficial features. We focused our search on lactobacilli and evaluated their ability to modulate TNF secretion by host cells and inhibit growth of pathogens. We recovered Lactobacillus salivarius strains which secreted factors that stimulated TNF production by human monocytoid cells. These Lact. salivarius isolates inhibited growth of selected marine mammal and human bacterial pathogens. In addition, we identified a novel Lactobacillus species by culture and direct sequencing with 96·3% 16S rDNA sequence similarity to Lactobacillus ceti. Conclusions Dolphin-derived Lact. salivarius isolates possess features making them candidate probiotics for clinical studies in marine mammals. Significance and Impact of the Study This is the first study to isolate lactobacilli from dolphins, including a novel Lactobacillus species and a new strain of Lact. salivarius, with potential for veterinary probiotic applications. The isolation and identification of novel Lactobacillus spp. and other indigenous microbes from bottlenose dolphins will enable the study of the biology of symbiotic members of the dolphin microbiota and facilitate the understanding of the microbiomes of these unique animals. PMID:23855505

Multipathway Quantitative Assessment of Exposure to Fecal Contamination for Young Children in Low-Income Urban Environments in Accra, Ghana: The SaniPath Analytical Approach

PubMed Central

Wang, Yuke; Moe, Christine L.; Null, Clair; Raj, Suraja J.; Baker, Kelly K.; Robb, Katharine A.; Yakubu, Habib; Ampofo, Joseph A.; Wellington, Nii; Freeman, Matthew C.; Armah, George; Reese, Heather E.; Peprah, Dorothy; Teunis, Peter F. M.

2017-01-01

Abstract. Lack of adequate sanitation results in fecal contamination of the environment and poses a risk of disease transmission via multiple exposure pathways. To better understand how eight different sources contribute to overall exposure to fecal contamination, we quantified exposure through multiple pathways for children under 5 years old in four high-density, low-income, urban neighborhoods in Accra, Ghana. We collected more than 500 hours of structured observation of behaviors of 156 children, 800 household surveys, and 1,855 environmental samples. Data were analyzed using Bayesian models, estimating the environmental and behavioral factors associated with exposure to fecal contamination. These estimates were applied in exposure models simulating sequences of behaviors and transfers of fecal indicators. This approach allows us to identify the contribution of any sources of fecal contamination in the environment to child exposure and use dynamic fecal microbe transfer networks to track fecal indicators from the environment to oral ingestion. The contributions of different sources to exposure were categorized into four types (high/low by dose and frequency), as a basis for ranking pathways by the potential to reduce exposure. Although we observed variation in estimated exposure (108–1016 CFU/day for Escherichia coli) between different age groups and neighborhoods, the greatest contribution was consistently from food (contributing > 99.9% to total exposure). Hands played a pivotal role in fecal microbe transfer, linking environmental sources to oral ingestion. The fecal microbe transfer network constructed here provides a systematic approach to study the complex interaction between contaminated environment and human behavior on exposure to fecal contamination. PMID:29031283

Microbe Detector

NASA Technical Reports Server (NTRS)

1977-01-01

The AutoMicrobic System (AMS) represents years of intensive research and development by McDonnell Douglas Corp. that originated with a NASA study aimed at development of a fully automated microbial detection and identification system for spacecraft use. A urine specimen is placed into the system, where it is subjected to different freeze-dried microbe nutrients for the nine most common pathogens. An electro-optical scanner studies each specimen once an hour through a 4-to-13 hour cycle, operating automatically. Changes in cell growths on each culture are monitored by computer. The presence of pathogens is indicated when growth reaches a predetermined level. The system also enumerates the pathogens and specifies the type. Developed initially to handle urine testing, AMS soon is expected to allow analyses of blood, spinal fluid, and other body fluids. An additional capability under development is "susceptibility testing," or the determination of which microbe-killing agents-such as penicillin or other antibiotics-would be most effective in eliminating the pathogens. The whole process of detecting, identifying, and enumerating the pathogens and determining susceptibility is accomplished in less half the time required for the manual procedure. The AMS minimizes human error, reduces technician time , and increases laboratory output.

Fungal and herbivore elicitation of a newly identified maize sesquiterpenoid, zealexin A4, is constrained by abiotic stress

USDA-ARS?s Scientific Manuscript database

The existence of microbe- or abiotic stress-inducible antimicrobials, termed phytoalexins, has only recently been discovered in maize. Identification and structural elucidation of the labdane-related diterpenoid kauralexins and sesquiterpenoid zealexins has collectively resulted in 10 novel pathogen...

The oxalic acid biosynthetic activity of Burkholderia mallei is encoded by a single locus

USDA-ARS?s Scientific Manuscript database

Although it is known that oxalic acid provides a selective advantage to the secreting microbe, our understanding of how this acid is biosynthesized remains incomplete. This study reports the identification, cloning, and partial characterization of the oxalic acid biosynthetic enzyme from the animal ...

Identification of Active Bacterial Communities in Drinking Water Using 16S rRNA-Based Sequence Analyses

EPA Science Inventory

DNA-based methods have considerably increased our understanding of the bacterial diversity of water distribution systems (WDS). However, as DNA may persist after cell death, the use of DNA-based methods cannot be used to describe metabolically-active microbes. In contrast, intra...

The subgingival microbiota of Papillon-Lefèvre syndrome.

PubMed

Albandar, Jasim M; Khattab, Razan; Monem, Fawza; Barbuto, Sara M; Paster, Bruce J

2012-07-01

There is little information about the microbiologic profiles of periodontal lesions in Papillon-Lefèvre syndrome (PLS) and the significance of bacteria in the pathogenesis of periodontitis in these patients. This comprehensive analysis of the subgingival microbiota in patients with PLS used 16S ribosomal RNA (rRNA) clonal analysis and the 16S rRNA-based Human Oral Microbe Identification Microarray (HOMIM). Thirteen patients with PLS from seven unrelated families volunteered for this microbiologic study. Subgingival plaque was collected with sterile paper points from multiple sites with ≥5 mm probing depth, and whole genomic DNA was extracted. The 16S rRNA genes were amplified, cloned, and sequenced. The samples were then probed for ≈300 predominant oral bacterial species using the HOMIM. The most commonly detected phylotypes in the clonal analysis were Gemella morbillorum, Gemella haemolysans, Granulicatella adiacens, Lachnospiraceae OT 100 (EI074), Parvimonas micra, Selenomonas noxia, and Veillonella parvula. As a group, streptococci were commonly detected in these individuals. In the HOMIM analysis, a total of 170 bacterial species/phylotypes were detected, with a range of 40 to 80 species per patient with PLS. Of these, 12 bacterial species were detected in medium to high levels in ≥50% of the individuals. The high-frequency strains were clustered into eight groups: Aggregatibacter actinomycetemcomitans, Campylobacter spp., Capnocytophaga granulosa, G. morbillorum, P. micra, Porphyromonas endodontalis, Streptococcus spp., and Tannerella forsythia. The subgingival microbiota in PLS is diverse. Periodontal pathogens commonly associated with chronic and aggressive periodontitis and opportunistic pathogens may be associated with the development of severe periodontitis in patients with PLS.

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

Automated Microbiological Detection/Identification System

PubMed Central

Aldridge, C.; Jones, P. W.; Gibson, S.; Lanham, J.; Meyer, M.; Vannest, R.; Charles, R.

1977-01-01

An automated, computerized system, the AutoMicrobic System, has been developed for the detection, enumeration, and identification of bacteria and yeasts in clinical specimens. The biological basis for the system resides in lyophilized, highly selective and specific media enclosed in wells of a disposable plastic cuvette; introduction of a suitable specimen rehydrates and inoculates the media in the wells. An automated optical system monitors, and the computer interprets, changes in the media, with enumeration and identification results automatically obtained in 13 h. Sixteen different selective media were developed and tested with a variety of seeded (simulated) and clinical specimens. The AutoMicrobic System has been extensively tested with urine specimens, using a urine test kit (Identi-Pak) that contains selective media for Escherichia coli, Proteus species, Pseudomonas aeruginosa, Klebsiella-Enterobacter species, Serratia species, Citrobacter freundii, group D enterococci, Staphylococcus aureus, and yeasts (Candida species and Torulopsis glabrata). The system has been tested with 3,370 seeded urine specimens and 1,486 clinical urines. Agreement with simultaneous conventional (manual) cultures, at levels of 70,000 colony-forming units per ml (or more), was 92% or better for seeded specimens; clinical specimens yielded results of 93% or better for all organisms except P. aeruginosa, where agreement was 86%. System expansion in progress includes antibiotic susceptibility testing and compatibility with most types of clinical specimens. Images PMID:334798

Future of diagnostic microbiology.

PubMed

Khardori, N

2014-01-01

Diagnostic Microbiology is the tool that makes it possible to identify the exact etiology of infectious diseases and the most optimal therapy at the level of individual patients as well as communities. Conventional methods require time to grow the microbes in vitro under specific conditions and not all microbes are easily cultivable. This is followed by biochemical methods for identification which also require hours and sometimes days. Transport of the specimens under less than ideal conditions, prior use of antibiotics and small number of organisms are among the factors that render culture-based methods less reliable. Newer methods depend on amplification of nucleic acids followed by use of probes for identification. This mitigates the need for higher microbial load, presence of metabolically active viable organisms and shortens the time to reporting. These methods can be used to detect antibiotic resistance genes directly from the specimen and help direct targeted therapy. Since these methods will not fulfill all the diagnostic needs, a second approach is being used to shorten the time to identification after the organism has already grown. Mass spectrometry and bioinformatics are the tools making this possible. This review gives a historical perspective on diagnostic microbiology, discusses the pitfalls of current methodology and provides an overview of newer and future methods.

Curriculum Guidelines for Predoctoral Oral Diagnosis/Oral Medicine.

ERIC Educational Resources Information Center

Journal of Dental Education, 1987

1987-01-01

Oral diagnosis is the area of dental practice that deals with gathering, recording, and evaluating information contributing to the identification of abnormalities of the head and neck region. A statement of general curricular goals in oral diagnosis/oral medicine is presented. (MLW)

Oral delivery of human biopharmaceuticals, autoantigens and vaccine antigens bioencapsulated in plant cells

PubMed Central

Kwon, Kwang-Chul; Verma, Dheeraj; Singh, Nameirakpam D.; Herzog, Roland; Daniell, Henry

2012-01-01

Among 12 billion injections administered annually, unsafe delivery leads to >20 million infections and >100 million reactions. In an emerging new concept, freeze-dried plant cells (lettuce) expressing vaccine antigens/biopharmaceuticals are protected in the stomach from acids/enzymes but are released to the immune or blood circulatory system when plant cell walls are digested by microbes that colonize the gut. Vaccine antigens bioencapsulated in plant cells upon oral delivery after priming, conferred both mucosal and systemic immunity and protection against bacterial, viral or protozoan pathogens or toxin challenge. Oral delivery of autoantigens was effective against complications of type 1diabetes and hemophilia, by developing tolerance. Oral delivery of proinsulin or exendin-4 expressed in plant cells regulated blood glucose levels similar to injections. Therefore, this new platform offers a low cost alternative to deliver different therapeutic proteins to combat infectious or inherited diseases by eliminating inactivated pathogens, expensive purification, cold storage/transportation and sterile injections. PMID:23099275

Insight into Oral Biofilm: Primary, Secondary and Residual Caries and Phyto-Challenged Solutions

PubMed Central

Chenicheri, Smitha; R, Usha; Ramachandran, Rajesh; Thomas, Vinoy; Wood, Andrew

2017-01-01

Introduction: Dental caries is known to be one of the most widespread, chronic infections affecting all ages and populations worldwide. The plethora of oral microbial population paves way for various endogenous infections and plays a crucial role in polymicrobial interactions contributing to biofilm-mediated diseases like caries and periodontal diseases. Methods: Extensive literature survey was conducted using the scientific databases like PubMed, Google scholar, Science Direct, etc. using the key words like dental caries, orodental infections, dental microbes, dental biofilm, secondary caries, phytotherapy, etc. The literature was analyzed thoroughly and critical review was performed. Results: The risk of development of secondary caries and residual caries further results in treatment failure. Drug resistance developed by oral microbes and further side effects pose serious hurdles in the current therapeutic strategies. The hyperactivities of various MMPs and the resulting massive ECM degradation are the challenging part in the design of effective therapeutic approaches. Anticariogenic phytotherapy is well appreciated owing to lesser side effects and versatility of their action. But appreciable outcomes regarding the phytochemical bioavailability and bioretention are still challenging. Site-specific delivery of phytoagents at the infected site may enhance the efficiency of these drugs. Accordingly emerging phytodentistry can be promising for the management of secondary and residual caries. Conclusion: This article presents major cariogens and their mechanisms in initiating and aggravating dental caries. Effectiveness of phytotherapy and different mode of action of phytochemicals against cariogens are outlined. The article also raises major concerns and possibilities of phytochemical based therapeutics to be applied in the clinical arena of caries management. PMID:28839480

[Isolation and identification of Lyssavirus strains from an area of Slovakia where oral antirabies vaccine was administered].

PubMed

Ondrejka, R; Durove, A; Svrcek, S; Benísek, Z; Süliová, J

1997-02-01

The study was aimed at isolation and subsequent identification of strains of rabies virus by means of monoclonal antibodies from foxes killed in the vaccination zone within the complex preliminary monitoring of oral antirabies vaccination. The results obtained indicate that the vaccines for oral antirabies vaccination used in Slovakia did not contain any vaccination strain pathogenic to the extremely sensitive target species-the fox (Vulpes vulpes).

Rapid identification and susceptibility testing of uropathogenic microbes via immunosorbent ATP-bioluminescence assay on a microfluidic simulator for antibiotic therapy.

PubMed

Dong, Tao; Zhao, Xinyan

2015-02-17

The incorporation of pathogen identification with antimicrobial susceptibility testing (AST) was implemented on a concept microfluidic simulator, which is well suited for personalizing antibiotic treatment of urinary tract infections (UTIs). The microfluidic device employs a fiberglass membrane sandwiched between two polypropylene components, with capture antibodies immobilized on the membrane. The chambers in the microfluidic device share the same geometric distribution as the wells in a standard 384-well microplate, resulting in compatibility with common microplate readers. Thirteen types of common uropathogenic microbes were selected as the analytes in this study. The microbes can be specifically captured by various capture antibodies and then quantified via an ATP bioluminescence assay (ATP-BLA) either directly or after a variety of follow-up tests, including urine culture, antibiotic treatment, and personalized antibiotic therapy simulation. Owing to the design of the microfluidic device, as well as the antibody specificity and the ATP-BLA sensitivity, the simulator was proven to be able to identify UTI pathogen species in artificial urine samples within 20 min and to reliably and simultaneously verify the antiseptic effects of eight antibiotic drugs within 3-6 h. The measurement range of the device spreads from 1 × 10(3) to 1 × 10(5) cells/mL in urine samples. We envision that the medical simulator might be broadly employed in UTI treatment and could serve as a model for the diagnosis and treatment of other diseases.

Human Milk Bacterial and Glycosylation Patterns Differ by Delivery Mode.

PubMed

Hoashi, Marina; Meche, Lawrence; Mahal, Lara K; Bakacs, Elizabeth; Nardella, Deanna; Naftolin, Frederick; Bar-Yam, Naomi; Dominguez-Bello, Maria G

2016-07-01

Mammals have evolved to nourish their offspring exclusively with maternal milk for around half of the lactation period, a crucial developmental window. In view of oral-breast contact during lactation and the differences in oral microbiota between cesarean section (C-section) and vaginally delivered infants, we expected differences in milk composition by delivery mode. We performed a cross-sectional study of banked human milk and found changes related to time since delivery in bacterial abundance and glycosylation patterns only in milk from women who delivered vaginally. The results warrant further research into the effects of delivery mode on milk microbes, milk glycosylation, and postpartum infant development. © The Author(s) 2015.

Understanding the microbiome: Emerging biomarkers for exploiting the microbiota for personalized medicine against cancer.

PubMed

Rajpoot, Meenakshi; Sharma, Anil K; Sharma, Anil; Gupta, Girish Kumar

2018-02-06

The human body is a home to more than 1 trillion microbes with a diverse variety of commensal microbes that play a crucial role towards the health of the individual. These microbes occupy different habitats such as gut, skin, vagina, oral etc. Not only the types and abundance of microbes are different in different organs, but also these may differ in different individuals. The genome of these microbiota and their ecosystem constitute to form a microbiome. Factors such as diet, environment, host genetics etc. may be the reason behind the wide microbial diversity. A number of studies performed on human microbiome have revealed that microbiota present in healthy and diseased individuals are distinct. Altered microbiome is many a times the reason behind the overexpression of genes which may cause complex diseases including cancer. Manipulation of the human microbiome can be done by microbial supplements such as probiotics or synbiotics, diet or prebiotics and microbial suppression strategies using antibiotics. Recent advances in genome sequencing technologies and metagenomic analysis provide us the broader understanding of these commensal microbes and highlighting the distinctive features of microbiome during healthy and disease states. Molecular pathological epidemiology (MPE) studies have been very helpful in providing insights into the pathological process behind disease evolution and progression by determining the specific etiological factors. New emerging field of research targets the microbiome for therapeutic purposes by which personalized medicines can be made for treating various types of tumors. Screening programmes might be helpful in identifying patients who are at the verge of developing cancer and in delivering appropriate approaches according to individual risk modes so that disease could be prevented. Copyright © 2018 Elsevier Ltd. All rights reserved.

Synergetic effect of pH and biochemical components on bacterial diversity during mesophilic anaerobic fermentation of biomass-origin waste.

PubMed

Lü, F; Shao, L M; Bru, V; Godon, J J; He, P J

2009-02-01

To investigate the synergetic effect of pH and biochemical components on bacterial community structure during mesophilic anaerobic degradation of solid wastes with different origins, and under acidic or neutral conditions. The bacterial community in 16 samples of solid wastes with different biochemical compositions and origins was evaluated during mesophilic anaerobic degradation at acidic and neutral pH. Denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP) were used to compare the communities. Multivariate analysis of the DGGE and SSCP results revealed that most of the dominant microbes were dependent on the content of easily degradable carbohydrates in the samples. Furthermore, the dominant microbes were divided into two types, those that preferred an acid environment and those that preferred a neutral environment. A shift in pH was found to change their preference for medium substrates. Although most of the substrates with similar origin and biochemical composition had similar microbial diversity during fermentation, some microbes were found only in substrates with specific origins. For example, two microbes were only found in substrate that contained lignocellulose and animal protein without starch. These microbes were related to micro-organisms that are found in swine manure, as well as in other intestinal or oral niches. In addition, the distribution of fermentation products was less sensitive to the changes in pH and biochemical components than the microbial community. Bacterial diversity during anaerobic degradation of organic wastes was affected by both pH and biochemical components; however, pH exerted a greater effect. The results of this study reveal that control of pH may be an effective method to produce a stable bacterial community and relatively similar product distribution during anaerobic digestion of waste, regardless of variation in the waste feedstocks.

Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice.

PubMed

Brown, Kirsty; Godovannyi, Artem; Ma, Caixia; Zhang, YiQun; Ahmadi-Vand, Zahra; Dai, Chaunbin; Gorzelak, Monika A; Chan, YeeKwan; Chan, Justin M; Lochner, Arion; Dutz, Jan P; Vallance, Bruce A; Gibson, Deanna L

2016-02-01

Accumulating evidence supports that the intestinal microbiome is involved in Type 1 diabetes (T1D) pathogenesis through the gut-pancreas nexus. Our aim was to determine whether the intestinal microbiota in the non-obese diabetic (NOD) mouse model played a role in T1D through the gut. To examine the effect of the intestinal microbiota on T1D onset, we manipulated gut microbes by: (1) the fecal transplantation between non-obese diabetic (NOD) and resistant (NOR) mice and (2) the oral antibiotic and probiotic treatment of NOD mice. We monitored diabetes onset, quantified CD4+T cells in the Peyer's patches, profiled the microbiome and measured fecal short-chain fatty acids (SCFA). The gut microbiota from NOD mice harbored more pathobionts and fewer beneficial microbes in comparison with NOR mice. Fecal transplantation of NOD microbes induced insulitis in NOR hosts suggesting that the NOD microbiome is diabetogenic. Moreover, antibiotic exposure accelerated diabetes onset in NOD mice accompanied by increased T-helper type 1 (Th1) and reduced Th17 cells in the intestinal lymphoid tissues. The diabetogenic microbiome was characterized by a metagenome altered in several metabolic gene clusters. Furthermore, diabetes susceptibility correlated with reduced fecal SCFAs. In an attempt to correct the diabetogenic microbiome, we administered VLS#3 probiotics to NOD mice but found that VSL#3 colonized the intestine poorly and did not delay diabetes. We conclude that NOD mice harbor gut microbes that induce diabetes and that their diabetogenic microbiome can be amplified early in life through antibiotic exposure. Protective microbes like VSL#3 are insufficient to overcome the effects of a diabetogenic microbiome.

Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota.

PubMed

Wu, Richard Y; Määttänen, Pekka; Napper, Scott; Scruten, Erin; Li, Bo; Koike, Yuhki; Johnson-Henry, Kathene C; Pierro, Agostino; Rossi, Laura; Botts, Steven R; Surette, Michael G; Sherman, Philip M

2017-10-10

Prebiotics are non-digestible food ingredients that enhance the growth of certain microbes within the gut microbiota. Prebiotic consumption generates immune-modulatory effects that are traditionally thought to reflect microbial interactions within the gut. However, recent evidence suggests they may also impart direct microbe-independent effects on the host, though the mechanisms of which are currently unclear. Kinome arrays were used to profile the host intestinal signaling responses to prebiotic exposures in the absence of microbes. Identified pathways were functionally validated in Caco-2Bbe1 intestinal cell line and in vivo model of murine endotoxemia. We found that prebiotics directly regulate host mucosal signaling to alter response to bacterial infection. Intestinal epithelial cells (IECs) exposed to prebiotics are hyporesponsive to pathogen-induced mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-κB) activations, and have a kinome profile distinct from non-treated cells pertaining to multiple innate immune signaling pathways. Consistent with this finding, mice orally gavaged with prebiotics showed dampened inflammatory response to lipopolysaccharide (LPS) without alterations in the gut microbiota. These findings provide molecular mechanisms of direct host-prebiotic interactions to support prebiotics as potent modulators of host inflammation.

Oral Pathology in Forensic Investigation.

PubMed

Shamim, Thorakkal

2018-01-01

Forensic odontology is the subdiscipline of dentistry which analyses dental evidence in the interest of justice. Oral pathology is the subdiscipline of dentistry that deals with the pathology affecting the oral and maxillofacial regions. This subdiscipline is utilized for identification through oral and maxillofacial pathologies with associated syndromes, enamel rod patterns, sex determination using exfoliative cytology, identification from occlusal morphology of teeth, and deoxyribonucleic acid profiling from teeth. This subdiscipline is also utilized for age estimation studies which include Gustafson's method, incremental lines of Retzius, perikymata, natal line formation in teeth, neonatal line, racemization of collagen in dentin, cemental incremental lines, thickness of the cementum, and translucency of dentin. Even though the expertise of an oral pathologist is not taken in forensic investigations, this paper aims to discuss the role of oral pathology in forensic investigation.

Oral Pathology in Forensic Investigation

PubMed Central

Shamim, Thorakkal

2018-01-01

Forensic odontology is the subdiscipline of dentistry which analyses dental evidence in the interest of justice. Oral pathology is the subdiscipline of dentistry that deals with the pathology affecting the oral and maxillofacial regions. This subdiscipline is utilized for identification through oral and maxillofacial pathologies with associated syndromes, enamel rod patterns, sex determination using exfoliative cytology, identification from occlusal morphology of teeth, and deoxyribonucleic acid profiling from teeth. This subdiscipline is also utilized for age estimation studies which include Gustafson's method, incremental lines of Retzius, perikymata, natal line formation in teeth, neonatal line, racemization of collagen in dentin, cemental incremental lines, thickness of the cementum, and translucency of dentin. Even though the expertise of an oral pathologist is not taken in forensic investigations, this paper aims to discuss the role of oral pathology in forensic investigation. PMID:29629322

Raman spectroscopy-based identification of nosocomial outbreaks of the clonal bacterium Escherichia coli.

PubMed

Kusters, J G; van Leeuwen, W B; Maquelin, K; Blok, H E M; Willemse, H F M; de Graaf-Miltenburg, L A M; Fluit, A C; Troelstra, A

2016-01-01

DNA-based techniques are frequently used to confirm the relatedness of putative outbreak isolates. These techniques often lack the discriminatory power when analyzing closely related microbes such as E. coli. Here the value of Raman spectroscopy as a typing tool for E. coli in a clinical setting was retrospectively evaluated.

Identification of quantitative trait loci controlling gene expression during the innate immunity response of soybean

USDA-ARS?s Scientific Manuscript database

Microbe associated molecular pattern (MAMP)-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. However, most of our knowledge of MTI comes from studies of model systems with relatively little work done with crop plants. In this work, we re...

Identification of novel mimicry epitopes for cardiac myosin heavy chain-α that induce autoimmune myocarditis in A/J mice.

PubMed

Massilamany, Chandirasegaran; Gangaplara, Arunakumar; Steffen, David; Reddy, Jay

2011-01-01

Myocarditis is one cause of sudden cardiac death in young adolescents, and individuals affected with myocarditis can develop dilated cardiomyopathy, a frequent reason for heart transplantation. Exposure to environmental microbes has been suspected in the initiation of heart autoimmunity, but the direct causal link is lacking. We report here identification of novel mimicry epitopes that bear sequences similar to those in cardiac myosin heavy chain (MYHC)-α 334-352. These epitopes represent Bacillus spp., Magnetospirillum gryphiswaldense, Cryptococcus neoformans and Zea mays. The mimicry peptides induced varying degrees of myocarditis in A/J mice reminiscent of the disease induced with MYHC-α 334-352. We demonstrate that the mimics induce cross-reactive T cell responses for MYHC-α 334-352 as verified by MHC class II IA(k)/tetramer staining and Th-1 and Th-17 cytokines similar to those of MYHC-α 334-352. The data suggest that exposure to environmental microbes which are otherwise innocuous can predispose to heart autoimmunity by molecular mimicry. Copyright © 2011 Elsevier Inc. All rights reserved.

Investigation of detection conditions of captured microbes in space with PCR Microbes capture experiment on ISS proposed in "Tanpopo" mission

NASA Astrophysics Data System (ADS)

Kawaguchi, Yuko; Sugino, Tomohiro; Yang, Yinjie; Yoshimura, Yoshitaka; Tsuji, Takashi; Kobayashi, Kensei; Tabata, Makoto; Hashimoto, Hirofumi; Mita, Hajime; Imai, Eiichi; Kawai, Hideyuki; Okudaira, Kyoko; Hasegawa, Sunao; Yamashita, Masamichi; Yano, Hajime; Yokobori, Shin-Ichi; Yamagishi, Akihiko

Terrestrial life may fly off into outer space by volcanic eruption meteorological impacts, and so on. Microbes have been collected from high altitude up to 70 km since 1936 [1]. We also isolated microbes at high altitude up to 35 km using an airplane and balloons [2, 3]. The two isolates of these microbes are new species, one of which shows higher UV ray tolerance than Deinococcus radiodurans [2, 3]. On the other hand, there is a hypothesis on the origin of terrestrial life called panspermia [4, 5], in which terrestrial life is thought to have come from space (or astronomical bodies other than Earth). This hypothesis suggests that life may migrate between Earth and other planets. If microbes were to exist at the high altitude of low earth orbit (400 km), it would endorse the possibility of interplanetary migration of terrestrial lifeWe proposed, the Tanpopo mission to examine interplanetary migration of microbes and organic compounds on Japan Experimental Module (JEM) of the International Space Station (ISS). We will capture micro-particles including microbes and micro-meteoroids at the altitude of ISS orbit (400 km) with ultra low-density aerogel exposed to space for a given period of time. After retreaving the aerogel, we will investigate captured micro particles and tracks followed by microbiological, organic chemical and mineralogical analyses.Captured particles will be analyzed after the initial curation of the aerogel and tracks. Particles potentially containing microbes will be used for PCR amplification of small subunit (ss) rRNA gene followed by DNA sequencing. Comparision between the determined sequences and known ss rRNA gene sequences of terrestrial organisms will suggest the origin and properties of the organism.The density of microbes at the ISS altitude might be quite low, and microbe cell number on each captured particle may be quite limited. Therefore, it is necessary to establish the effective PCR procedure for quite small amount of DNA template in the presence of other materials such as clay and aerogel.We will report current status of the PCR identification of microbes from test samples. The PCR conditions to amplify ss rRNA gene from quite small number of cells and quite low concentration of genomic DNA with/without clay and aerogel are examined. References. [1] Y. Yang et al. (2009) Biol. Sci. in Space, 23, 151-163[2] Y. Yang et al. (2009) Int. J. Syst. Evol. Microbiol, 59, 1862-1866[3] Y. Yang et al. (2010) Int. J. Syst. Evol. Microbiol, (in press)[4] S. Arrhenius (1908) Worlds in the Making-the Evolution of the Universe. Harper and Brothers Publishers.[5] F. Crick (1981) Life Itself. Simon Schuster.

The quality of microorganism on coal bed methane processing with various livestock waste in laboratory scale

NASA Astrophysics Data System (ADS)

Marlina, E. T.; Kurnani, Tb. B. A.; Hidayati, Y. A.; Rahmah, K. N.; Joni, I. M.; Harlia, E.

2018-02-01

Coal-bed Methane (CBM) is a form of natural gas extracted from coal and has been developed as future energy source. Organic materials are required as nutrition source for methanogenic microbes. The addition of cattle waste in the formation of CBM on coal media can be utilized as organic materials as well as methanogenic microbe sources. This research covered study of total amount of anaerobic microbes, methane production, protozoa, fungi and endoparasites. Descriptive approach is conducted for this study. Media used for culturing methanogens is Nutrient Agar in powder form and Lactose Broth with the addition of rumen fluid. The technique for counting microbes is through Total Plate Count in anaerobic Hungate tube, methane was analyzed using Gas Chromatography (GC), while identification of protozoa, fungi and endoparasites based on its morphology is conducted before and after anaerobic fermentation process. Incubation period is 30 days. The results showed that growth of anaerobic microbes from dairy cattle waste i.e. biogas sludge is 3.57×103 CFU/ml and fresh feces is 3.38 × 104 CFU/ml, growth of anaerobic microbes from beef cattle waste i.e. biogas sludge is 7.0 × 105 CFU/ml; fresh feces is 7.5 x 104 CFU/ml; and rumen contents of about 1.33 × 108 CFU/ml. Methane production in dairy cattle waste in sludge and fresh feces amounted to 10.57% and 2.39%, respectively. Methane production in beef cattle waste in sludge accounted for 5.95%; in fresh feces it is about 0.41%; and rumen contents of 4.92%. Decreasing of protozoa during fermentation to 84.27%, dominated by Eimeria sp. Decreasing of fungi to 16%, dominated by A. Niger, A. Flavus, A. Fumigatus and Monilia sitophila. Decreasing of endoparasitic worms to 15%, dominated by Strongylus sp. and Fasciola sp. The growth of anaerobic microbes and methane production indicated that dairy cattle waste and beef cattle waste have potential as source of methanogenic microbes, meanwhile the decreasing amount of protozoa, fungi and endoparasites indicated that CBM formation process can reduce pollutants from microorganism in the environment.

Treatment of Oral Biofilms by a D-Enantiomeric Peptide.

PubMed

Zhang, Tian; Wang, Zhejun; Hancock, Robert E W; de la Fuente-Núñez, César; Haapasalo, Markus

2016-01-01

Almost all dental diseases are caused by biofilms that consist of multispecies communities. DJK-5, which is a short D-enantiomeric, protease-resistant peptide with broad-spectrum anti-biofilm activity, was tested for its effect on oral multispecies biofilms. Peptide DJK-5 at 10 μg/mL effectively prevented the growth of these microbes in culture media in a time-dependent manner. In addition to the prevention of growth, peptide DJK-5 completely killed both Streptococcus mutans and Enterococcus faecalis suspended from biofilms after 30 minutes of incubation in liquid culture media. DJK-5 also led to the effective killing of microbes in plaque biofilm. The proportion of bacterial cells killed by 10 μg/mL of DJK-5 was similar after 1 and 3 days, both exceeding 85%. DJK-5 was able to significantly prevent biofilm formation over 3 days (P = 0.000). After 72 hours of exposure, DJK-5 significantly reduced and almost completely prevented plaque biofilm production by more than 90% of biovolume compared to untreated controls (P = 0.000). The proportion of dead biofilm bacteria at the 10 μg/mL DJK-5 concentration was similar for 1- and 3-day-old biofilms, whereby >86% of the bacteria were killed. DJK-5 was also able to kill >79% and >85% of bacteria, respectively, after one-time and three brief treatments of 3-day-old biofilms. The combination of DJK-5 and chlorhexidine showed the best bacterial killing among all treatments, with ~83% and >88% of bacterial cells killed after 1 and 3 minutes, respectively. No significant difference was found in the percentage of biofilm killing amongst three donor plaque samples after DJK-5 treatment. In particular, DJK-5 showed strong performance in inhibiting biofilm development and eradicating pre-formed oral biofilms compared to L-enantiomeric peptide 1018. DJK-5 was very effective against oral biofilms when used alone or combined with chlorhexidine, and may be a promising agent for use in oral anti-biofilm strategies in the future.

Oral pathogens change proliferation properties of oral tumor cells by affecting gene expression of human defensins.

PubMed

Hoppe, T; Kraus, D; Novak, N; Probstmeier, R; Frentzen, M; Wenghoefer, M; Jepsen, S; Winter, J

2016-10-01

The impact of oral pathogens onto the generation and variability of oral tumors has only recently been investigated. To get further insights, oral cancer cells were treated with pathogens and additionally, as a result of this bacterial cellular infection, with human defensins, which are as anti-microbial peptide members of the innate immune system. After cell stimulation, proliferation behavior, expression analysis of oncogenic relevant defensin genes, and effects on EGFR signaling were investigated. The expression of oncogenic relevant anti-microbial peptides was analyzed with real-time PCR and immunohistochemistry. Cell culture experiments were performed to examine cellular impacts caused by stimulation, i.e., altered gene expression, proliferation rate, and EGF receptor-dependent signaling. Incubation of oral tumor cells with an oral pathogen (Porphyromonas gingivalis) and human α-defensins led to an increase in cell proliferation. In contrast, another oral bacterium used, Aggregatibacter actinomycetemcomitans, enhanced cell death. The bacteria and anti-microbial peptides exhibited diverse effects on the transcript levels of oncogenic relevant defensin genes and epidermal growth factor receptor signaling. These two oral pathogens exhibited opposite primary effects on the proliferation behavior of oral tumor cells. Nevertheless, both microbe species led to similar secondary impacts on the proliferation rate by modifying expression levels of oncogenic relevant α-defensin genes. In this respect, oral pathogens exerted multiplying effects on tumor cell proliferation. Additionally, human defensins were shown to differently influence epidermal growth factor receptor signaling, supporting the hypothesis that these anti-microbial peptides serve as ligands of EGFR, thus modifying the proliferation behavior of oral tumor cells.

Water swallow screening test for patients after surgery for head and neck cancer: early identification of dysphagia, aspiration and limitations of oral intake.

PubMed

Hey, Christiane; Lange, Benjamin P; Eberle, Silvia; Zaretsky, Yevgen; Sader, Robert; Stöver, Timo; Wagenblast, Jens

2013-09-01

Patients with head and neck cancer (HNC) are at high risk for oropharyngeal dysphagia (OD) following surgical therapy. Early identification of OD can improve outcomes and reduce economic burden. This study aimed to evaluate the validity of a water screening test using increasing volumes postsurgically for patients with HNC (N=80) regarding the early identification of OD in general, and whether there is a need for further instrumental diagnostics to investigate the presence of aspiration as well as to determine the limitations of oral intake as defined by fiberoptic endoscopic evaluation of swallowing. OD in general was identified in 65%, with aspiration in 49%, silent aspiration in 21% and limitations of oral intake in 56%. Despite a good sensitivity, for aspiration of 100% and for limitations of oral intake of 97.8%, the presented water screening test did not satisfactorily predict either of these reference criteria due to its low positive likelihood ratio (aspiration=2.6; limitations of oral intake=3.1). However, it is an accurate tool for the early identification of OD in general, with a sensitivity of 96.2% and a positive likelihood ratio of 5.4 in patients after surgery for HNC.

A systems biology perspective on plant-microbe interactions: biochemical and structural targets of pathogen effectors.

PubMed

Pritchard, Leighton; Birch, Paul

2011-04-01

Plants have biochemical defences against stresses from predators, parasites and pathogens. In this review we discuss the interaction of plant defences with microbial pathogens such as bacteria, fungi and oomycetes, and viruses. We examine principles of complex dynamic networks that allow identification of network components that are differentially and predictably sensitive to perturbation, thus making them likely effector targets. We relate these principles to recent developments in our understanding of known effector targets in plant-pathogen systems, and propose a systems-level framework for the interpretation and modelling of host-microbe interactions mediated by effectors. We describe this framework briefly, and conclude by discussing useful experimental approaches for populating this framework. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Current state of coenzyme Q(10) production and its applications.

PubMed

Jeya, Marimuthu; Moon, Hee-Jung; Lee, Jeong-Lim; Kim, In-Won; Lee, Jung-Kul

2010-02-01

Coenzyme Q(10) (CoQ(10)), an obligatory cofactor in the aerobic respiratory electron transfer for energy generation, is formed from the conjugation of a benzoquinone ring with a hydrophobic isoprenoid chain. CoQ(10) is now used as a nutritional supplement because of its antioxidant properties and is beneficial in the treatment of several human diseases when administered orally. Bioprocesses have been developed for the commercial production of CoQ(10) because of its increased demand, and these bioprocesses depend on microbes that produce high levels of CoQ(10) naturally. However, as knowledge of the biosynthetic enzymes and the regulatory mechanisms modulating CoQ(10) production increases, approaches arise for the genetic engineering of CoQ(10) production in Escherichia coli and Agrobacterium tumefaciens. This review focused on approaches for CoQ(10) production, strategies used to engineer CoQ(10) production in microbes, and potential applications of CoQ(10).

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

Forensic dentistry in human identification: A review of the literature.

PubMed

Ata-Ali, Javier; Ata-Ali, Fadi

2014-04-01

An update is provided of the literature on the role of odontology in human identification, based on a PubMed-Medline search of the last 5 years and using the terms: "forensic dentistry" (n = 464 articles), "forensic odontology" (n = 141 articles) and "forensic dentistry identification" (n = 169 articles). Apart from these initial 774 articles, others considered to be important and which were generated by a manual search and cited as references in review articles were also included. Forensic dentistry requires interdisciplinary knowledge, since the data obtained from the oral cavity can contribute to identify an individual or provide information needed in a legal process. Furthermore, the data obtained from the oral cavity can narrow the search range of an individual and play a key role in the victim identification process following mass disasters or catastrophes. This literature search covering the last 5 years describes the novelties referred to buccodental studies in comparative identification, buccodental evaluation in reconstructive identification, human bites as a method for identifying the aggressor, and the role of DNA in dental identification. The oral cavity is a rich and noninvasive source of DNA, and can be used to solve problems of a social, economic or legal nature. Key words:Forensic identification, DNA, forensic dentistry, rugoscopy, cheiloscopy, saliva.

Identification of microbes from the surfaces of food-processing lines based on the flow cytometric evaluation of cellular metabolic activity combined with cell sorting.

PubMed

Juzwa, W; Duber, A; Myszka, K; Białas, W; Czaczyk, K

2016-09-01

In this study the design of a flow cytometry-based procedure to facilitate the detection of adherent bacteria from food-processing surfaces was evaluated. The measurement of the cellular redox potential (CRP) of microbial cells was combined with cell sorting for the identification of microorganisms. The procedure enhanced live/dead cell discrimination owing to the measurement of the cell physiology. The microbial contamination of the surface of a stainless steel conveyor used to process button mushrooms was evaluated in three independent experiments. The flow cytometry procedure provided a step towards monitoring of contamination and enabled the assessment of microbial food safety hazards by the discrimination of active, mid-active and non-active bacterial sub-populations based on determination of their cellular vitality and subsequently single cell sorting to isolate microbial strains from discriminated sub-populations. There was a significant correlation (r = 0.97; p < 0.05) between the bacterial cell count estimated by the pour plate method and flow cytometry, despite there being differences in the absolute number of cells detected. The combined approach of flow cytometric CRP measurement and cell sorting allowed an in situ analysis of microbial cell vitality and the identification of species from defined sub-populations, although the identified microbes were limited to culturable cells.

[Recent achievements in the microbiological etiology of dental caries].

PubMed

Jing, Chen; Lei, Cheng; Xuedong, Zhou; Xian, Peng

2018-02-01

Dental caries is the most common chronic infectious disease of the oral cavity. The bacterium Streptococcus mutans is the sole pathogen that causes this disease. However, substantial evidence suggests that prevention and treatment strategies developed from traditional "cariogenic pathogen theory" are inefficient in reducing the prevalence of dental caries. An increasing number of individuals adopt the ecological view of the microbiota in the pathogenesis of dental caries. Recent technological improvements have enabled the detection and analysis of oral microorganisms, and many studies have focused on this area. The core microbiota is defined as a cluster of microbes playing critical roles in the initial and development phases of dental caries and may provide future direction for microorganism-related etiological studies.

Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe

USDA-ARS?s Scientific Manuscript database

Background: We recently reported the identification of Bacillus sp. NRRL B-14911 that induces heart autoimmunity by generating cardiac-reactive T cells through molecular mimicry. This marine bacterium was originally isolated from the Gulf of Mexico, but no associations with human diseases were rep...

Principal Component Analysis of Microbial Community Data from an Accelerated Decay Cellar Test

Treesearch

Grant T. Kirker; Patricia K. Lebow

2014-01-01

Analysis of microbial communities is a valuable tool for characterization and identification of microbes in a myriad of environments. We are currently using the molecular method terminal restriction fragment length polymorphism (T-RFLP) analysis to characterize changes in bacterial and fungal communities on treated and untreated wood in soil. T-RFLP uses fluorescently...

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.

Microbial Communities in Produced Water of the Green River Basin in Southeast Wyoming.

NASA Astrophysics Data System (ADS)

Wawrousek, K.; Drogos, D. L.; Urynowicz, M. A.; Nye, C.; Quillinan, S.

2017-12-01

Despite the prevalence of hydraulic fracturing for natural gas production, little is understood about the downhole microbial ecosystems encountered. Illumina MiSeq 16S rRNA sequencing has been performed on waters collected from the water-gas separator of five hydraulically fractured wells in the Green River Basin in southeast Wyoming, and identification of bacteria and archaea reveal the presence of several microbes. Well depths ranged from approximately 9,500ft to 11,500ft. Correlations between inorganic chemistry, such as pH, salinity, and metals naturally present in the groundwater, as well as biocides used during fracturing and production were made when analyzing different microbial communities. Preliminary results identify several microbial families including: Clostridiales, Thermoanaerobacterales, Synergistales, Alteromonadales, and Thermotogales. Of the 5 sampled oil wells in the Greater Green River Basin, 16 microbes were identified in all samples. These included microbes such as Anaerobaculum, Thermovirga, and an unclassified Clostridiaceae. Ongoing work includes matching unclassified 16S sequences present in multiple samples and correlating microbial populations across wells to understand better the microbial communities present in these exotic environmental conditions.

T Cell Epitope Mimicry between Sjögren’s Syndrome Antigen A (SSA)/Ro60 and Oral, Gut, Skin and Vaginal Bacteria.

PubMed Central

Szymula, Agnieszka; Rosenthal, Jacob; Szczerba, Barbara M; Bagavant, Harini; Fu, Shu Man; Deshmukh, Umesh S.

2014-01-01

This study was undertaken to test the hypothesis that Sjogren’s syndrome Antigen A (SSA)/Ro60-reactive T cells are activated by peptides originating from oral and gut bacteria. T cell hybridomas generated from HLA-DR3 transgenic mice recognized 3 regions on Ro60, with core epitopes mapped to amino acids 228-238, 246-256 and 371-381. BLAST analysis identified several mimicry peptides, originating from human oral, intestinal, skin and vaginal bacteria, as well as environmental bacteria. Amongst these, a peptide from the von Willebrand factor type A domain protein (vWFA) from the oral microbe Capnocytphaga ochracea was the most potent activator. Further, Ro60-reactive T cells were activated by recombinant vWFA protein and whole E. coli expressing this protein. These results demonstrate that peptides derived from normal human microbiota can activate Ro60-reactive T cells. Thus, immune responses to commensal microbiota and opportunistic pathogens should be explored as potential triggers for initiating autoimmunity in SLE and Sjögren’s syndrome. PMID:24576620

Microbiomes of Site-Specific Dental Plaques from Children with Different Caries Status.

PubMed

Richards, Vincent P; Alvarez, Andres J; Luce, Amy R; Bedenbaugh, Molly; Mitchell, Mary Lyn; Burne, Robert A; Nascimento, Marcelle M

2017-08-01

The oral microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. The Human Oral Microbe Identification Using Next-Generation Sequencing (HOMI NGS ) approach was used to analyze the microbiomes of site-specific supragingival dental plaques from children with different caries status. Fifty-five children (2 to 7 years of age) were assessed at baseline and at 12 months and grouped as caries free (CF), caries active with enamel lesions (CAE), and caries active with dentin carious lesions (CA). Plaque samples from caries-free tooth surfaces (PF) and from enamel carious lesions (PE) and dentin carious lesions (PD) were collected. 16S community profiles were obtained by HOMI NGS , and 408 bacterial species and 84 genus probes were assigned. Plaque bacterial communities showed temporal stability, as there was no significant difference in beta diversity values between the baseline and 12-month samples. Irrespective of collection time points, the microbiomes of healthy tooth surfaces differed substantially from those found during caries activity. All pairwise comparisons of beta diversity values between groups were significantly different ( P < 0.05), except for comparisons between the CA-PF, CAE-PE, and CA-PE groups. Streptococcus genus probe 4 and Neisseria genus probe 2 were the most frequently detected taxa across the plaque groups, followed by Streptococcus sanguinis , which was highly abundant in CF-PF. Well-known acidogenic/aciduric species such as Streptococcus mutans , Scardovia wiggsiae , Parascardovia denticolens , and Lactobacillus salivarius were found almost exclusively in CA-PD. The microbiomes of supragingival dental plaque differ substantially among tooth surfaces and children of different caries activities. In support of the ecological nature of caries etiology, a steady transition in community species composition was observed with disease progression. Copyright © 2017 American Society for Microbiology.

Microbiomes of Site-Specific Dental Plaques from Children with Different Caries Status

PubMed Central

Alvarez, Andres J.; Luce, Amy R.; Bedenbaugh, Molly; Mitchell, Mary Lyn

2017-01-01

ABSTRACT The oral microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. The Human Oral Microbe Identification Using Next-Generation Sequencing (HOMINGS) approach was used to analyze the microbiomes of site-specific supragingival dental plaques from children with different caries status. Fifty-five children (2 to 7 years of age) were assessed at baseline and at 12 months and grouped as caries free (CF), caries active with enamel lesions (CAE), and caries active with dentin carious lesions (CA). Plaque samples from caries-free tooth surfaces (PF) and from enamel carious lesions (PE) and dentin carious lesions (PD) were collected. 16S community profiles were obtained by HOMINGS, and 408 bacterial species and 84 genus probes were assigned. Plaque bacterial communities showed temporal stability, as there was no significant difference in beta diversity values between the baseline and 12-month samples. Irrespective of collection time points, the microbiomes of healthy tooth surfaces differed substantially from those found during caries activity. All pairwise comparisons of beta diversity values between groups were significantly different (P < 0.05), except for comparisons between the CA-PF, CAE-PE, and CA-PE groups. Streptococcus genus probe 4 and Neisseria genus probe 2 were the most frequently detected taxa across the plaque groups, followed by Streptococcus sanguinis, which was highly abundant in CF-PF. Well-known acidogenic/aciduric species such as Streptococcus mutans, Scardovia wiggsiae, Parascardovia denticolens, and Lactobacillus salivarius were found almost exclusively in CA-PD. The microbiomes of supragingival dental plaque differ substantially among tooth surfaces and children of different caries activities. In support of the ecological nature of caries etiology, a steady transition in community species composition was observed with disease progression. PMID:28507066

Microbiomes of Endodontic-Periodontal Lesions before and after Chemomechanical Preparation.

PubMed

Gomes, Brenda P F A; Berber, Vanessa B; Kokaras, Alexis S; Chen, Tsute; Paster, Bruce J

2015-12-01

This study was conducted to evaluate the microbiomes of endodontic-periodontal lesions before and after chemomechanical preparation (CMP). Clinical samples were taken from 15 root canals (RCs) with necrotic pulp tissues and from their associated periodontal pockets (PPs) (n = 15) of teeth with endodontic-periodontal lesions before and after CMP. The Human Oral Microbe Identification using Next Generation Sequencing (NGS) protocol and viable culture were used to analyze samples from RCs and PPs. The Mann-Whitney U test and Benjamini-Hochberg corrections were performed to correlate the clinical and radiographic findings with microbial findings (P < .05). Bacteria were detected in 100% of the samples in both sites (15/15) using NGS. Firmicutes was the most predominant phylum in both sites using both methods. The most frequently detected species in the RCs before and after CMP using NGS were Enterococcus faecalis, Parvimonas micra, Mogibacterium timidum, Filifactor alocis, and Fretibacterium fastidiosum. The species most frequently detected in the PPs before and after CMP using NGS were P. micra, E. faecalis, Streptococcus constellatus, Eubacterium brachy, Tannerella forsythia, and F. alocis. Associations were found between periapical lesions ≤ 2 mm and Desulfobulbus sp oral taxon 041 and with periodontal pockets ≥ 6 mm and Dialister invisius and Peptostreptococcus stomatis (all P < .05, found in the RCs before CMP). It is concluded that the microbial community present in combined endodontic-periodontal lesions is complex and more diverse than previously reported. It is important to note that bacteria do survive in some root canals after CMP. Finally, the similarity between the microbiota of both sites, before and after CMP, suggests there may be a pathway of infection between the pulp and periodontium. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

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

Forensic dentistry in human identification: A review of the literature

PubMed Central

Ata-Ali, Fadi

2014-01-01

An update is provided of the literature on the role of odontology in human identification, based on a PubMed-Medline search of the last 5 years and using the terms: “forensic dentistry” (n = 464 articles), “forensic odontology” (n = 141 articles) and “forensic dentistry identification” (n = 169 articles). Apart from these initial 774 articles, others considered to be important and which were generated by a manual search and cited as references in review articles were also included. Forensic dentistry requires interdisciplinary knowledge, since the data obtained from the oral cavity can contribute to identify an individual or provide information needed in a legal process. Furthermore, the data obtained from the oral cavity can narrow the search range of an individual and play a key role in the victim identification process following mass disasters or catastrophes. This literature search covering the last 5 years describes the novelties referred to buccodental studies in comparative identification, buccodental evaluation in reconstructive identification, human bites as a method for identifying the aggressor, and the role of DNA in dental identification. The oral cavity is a rich and noninvasive source of DNA, and can be used to solve problems of a social, economic or legal nature. Key words:Forensic identification, DNA, forensic dentistry, rugoscopy, cheiloscopy, saliva. PMID:24790717

Microbial Analysis of Australian Dry Lake Cores; Analogs For Biogeochemical Processes

NASA Astrophysics Data System (ADS)

Nguyen, A. V.; Baldridge, A. M.; Thomson, B. J.

2014-12-01

Lake Gilmore in Western Australia is an acidic ephemeral lake that is analogous to Martian geochemical processes represented by interbedded phyllosilicates and sulfates. These areas demonstrate remnants of a global-scale change on Mars during the late Noachian era from a neutral to alkaline pH to relatively lower pH in the Hesperian era that continues to persist today. The geochemistry of these areas could possibly be caused by small-scale changes such as microbial metabolism. Two approaches were used to determine the presence of microbes in the Australian dry lake cores: DNA analysis and lipid analysis. Detecting DNA or lipids in the cores will provide evidence of living or deceased organisms since they provide distinct markers for life. Basic DNA analysis consists of extraction, amplification through PCR, plasmid cloning, and DNA sequencing. Once the sequence of unknown DNA is known, an online program, BLAST, will be used to identify the microbes for further analysis. The lipid analysis approach consists of phospholipid fatty acid analysis that is done by Microbial ID, which will provide direct identification any microbes from the presence of lipids. Identified microbes are then compared to mineralogy results from the x-ray diffraction of the core samples to determine if the types of metabolic reactions are consistent with the variation in composition in these analog deposits. If so, it provides intriguing implications for the presence of life in similar Martian deposits.

[The role of the human microbiom in the pathogenesis of rheumatoid arthritis - a literature review].

PubMed

Krajewska-Włodarczyk, Magdalena

Rheumatoid arthritis is a chronic, progressive, autoimmune disease with numerous articular, extra-articular and systemic manifestations. The cause of rheumatoid arthritis is multifactorial including genetic and environmental factors. Recent advantages in sequencing techniques have allowed the deep characterization of the human microbiota. Available evidence confirms the existence of an association between dysbiosis and rheumatoid arthritis but it still remains unclear whether alterations in the microbiome are a pathogenic cause or an effect of autoimmune disease. In patients with rheumatoid arthritis the most supported association between disease and microbiota is with the oral dysbiosis usually observed in patients with periodontitis. Given the strong variability and abundance of microbes living in close relation with human host, it becomes a difficult task to define what should be considered the favorable microbiome. There is need for broader studies to establish how the human microbiome contributes to disease susceptibility, and to characterize the role of microbial diversity in the pathogenesis of rheumatoid arthritis, disease manifestation, and progression. The identification of dysbiosis specific for rheumatoid arthritis and the understanding of the dynamic interaction between microbiota and their host may help in establishing an individualized management for each patient with rheumatoid arthritis, and achieve a better efficacy of the therapy.

Salivary microbiota and caries occurrence in Mutans Streptococci-positive school children.

PubMed

ElSalhy, M; Söderling, E; Honkala, E; Fontana, M; Flannagan, S; Kokaras, A; Paster, B J; Varghese, A; Honkala, S

2016-09-01

To compare the composition of the salivary microbiota in caries-affected vs. caries-free mutans streptococci (MS)- positive children with mixed dentition. Twenty eight healthy, 11-12-year-old schoolchildren with high MS counts (>10⊃5 CFU/mL) were included in this study. The children were screened with the Dentocult SM Strip Mutans test (Orion Diagnostica, Espoo, Finland) and examined using the International Caries Detection and Assessment System (ICDAS). The microbial composition of the saliva was assessed using the Human Oral Microbe Identification Microarray (HOMIM). Microbial differences between caries-affected (n=18) and caries-free children (n=10) were compared by Mann-Whitney analysis. The microbiota of the caries-affected vs. caries-free children was rather similar. Abiotrophia defectiva and Actinomyces meyeri/A. odontolyticus were significantly higher in caries-affected than in caries-free children (p=0.006, 0.046, respectively). Shuttleworthia satelles was significantly higher in caries-free compared to caries-affected children (p=0.031). A. defectiva and A. meyeri/A. odontolyticus correlated positively with caries severity measured by ICDAS Caries Index (p = 0.494, 0.454, 0.400 respectively) while S. satelles was negatively correlated with caries severity (p= -0.489). Salivary A. defectiva and A. meyeri/A. odontolyticus and are associated with caries occurrence in MS-positive children with mixed dentition.

Does the buck stop with the bugs?: an overview of microbial dysbiosis in rheumatoid arthritis.

PubMed

Sandhya, Pulukool; Danda, Debashish; Sharma, Disha; Scaria, Vinod

2016-01-01

The human body is an environmental niche which is home to diverse co-habiting microbes collectively referred as the human microbiome. Recent years have seen the in-depth characterization of the human microbiome and associations with diseases. Linking of the composition or number of the human microbiota with diseases and traits date back to the original work of Elie Metchnikoff. Recent advances in genomic technologies have opened up finer details and dynamics of this new science with higher precision. Microbe-rheumatoid arthritis connection, largely related to the gut and oral microbiomes, has showed up as a result - apart from several other earlier, well-studied candidate autoimmune diseases. Although evidence favouring roles of specific microbial species, including Porphyromonas, Prevotella and Leptotricha, has become clearer, mechanistic insights still continue to be enigmatic. Manipulating the microbes by traditional dietary modifications, probiotics, and antibiotics and by currently employed disease-modifying agents seems to modulate the disease process and its progression. In the present review, we appraise the existing information as well as the gaps in knowledge in this challenging field. We also discuss the future directions for potential clinical applications, including prevention and management of rheumatoid arthritis using microbial modifications. © 2015 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

Identification of secreted bacterial proteins by noncanonical amino acid tagging

PubMed Central

Mahdavi, Alborz; Szychowski, Janek; Ngo, John T.; Sweredoski, Michael J.; Graham, Robert L. J.; Hess, Sonja; Schneewind, Olaf; Mazmanian, Sarkis K.; Tirrell, David A.

2014-01-01

Pathogenic microbes have evolved complex secretion systems to deliver virulence factors into host cells. Identification of these factors is critical for understanding the infection process. We report a powerful and versatile approach to the selective labeling and identification of secreted pathogen proteins. Selective labeling of microbial proteins is accomplished via translational incorporation of azidonorleucine (Anl), a methionine surrogate that requires a mutant form of the methionyl-tRNA synthetase for activation. Secreted pathogen proteins containing Anl can be tagged by azide-alkyne cycloaddition and enriched by affinity purification. Application of the method to analysis of the type III secretion system of the human pathogen Yersinia enterocolitica enabled efficient identification of secreted proteins, identification of distinct secretion profiles for intracellular and extracellular bacteria, and determination of the order of substrate injection into host cells. This approach should be widely useful for the identification of virulence factors in microbial pathogens and the development of potential new targets for antimicrobial therapy. PMID:24347637

Identification of ovine ruminal microbes capable of biotransforming hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)

USDA-ARS?s Scientific Manuscript database

Bioremediation is of great interest in the detoxification of soil contaminated with residues from explosives such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Although there are numerous forms of in situ and ex situ bioremediation, ruminants would provide the option of an in situ bioreactor tha...

Isolation and Identification of Microorganisms in JSC Mars-1 Simulant Soil

NASA Technical Reports Server (NTRS)

Mendez, Claudia; Garza, Elizabeth; Gulati, Poonam; Morris, Penny A.; Allen, Carlton C.

2005-01-01

Microorganisms were isolated and identified in samples of JSC Mars-1, a Mars simulant soil. JSC Mars-1 is an altered volcanic ash from a cinder cone south of Mauna Kea, Hawaii. This material was chosen because of its similarity to the Martian soil in physical and chemical composition. The soil was obtained by excavating 40 cm deep in a vegetated area to prevent contamination. In previous studies, bacteria from this soil has been isolated by culturing on different types of media, including minimal media, and using biochemical techniques for identification. Isolation by culturing is successful only for a small percentage of the population. As a result, molecular techniques are being employed to identify microorganisms directly from the soil without culturing. In this study, bacteria were identified by purifying and sequencing the DNA encoding the 16s ribosomal RNA (16s rDNA). This gene is well conserved in species and demonstrates species specificity. In addition, biofilm formation, an indicator of microbial life, was studied with this soil. Biofilms are microbial communities consisting of microbes and exopolysaccharides secreted by them. This is a protective way of life for the microbes as they are more resistant to environmental pressures.

[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.

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

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

PubMed Central

Agler, Matthew T.; Ruhe, Jonas; Kroll, Samuel; Morhenn, Constanze; Kim, Sang-Tae; Weigel, Detlef; Kemen, Eric M.

2016-01-01

Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial “hubs” and their importance in phyllosphere microbiome structuring has crucial implications for plant–pathogen and microbe–microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via “hub” microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome “keystone” pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes. PMID:26788878

A 100-Year Review: Microbiology and safety of milk handling.

PubMed

Boor, Kathryn J; Wiedmann, Martin; Murphy, Sarah; Alcaine, Sam

2017-12-01

Microbes that may be present in milk can include pathogens, spoilage organisms, organisms that may be conditionally beneficial (e.g., lactic acid bacteria), and those that have not been linked to either beneficial or detrimental effects on product quality or human health. Although milk can contain a full range of organisms classified as microbes (i.e., bacteria, viruses, fungi, and protozoans), with few exceptions (e.g., phages that affect fermentations, fungal spoilage organisms, and, to a lesser extent, the protozoan pathogens Cryptosporidium and Giardia) dairy microbiology to date has focused predominantly on bacteria. Between 1917 and 2017, our understanding of the microbes present in milk and the tools available for studying those microbes have changed dramatically. Improved microbiological tools have enabled enhanced detection of known microbes in milk and dairy products and have facilitated better identification of pathogens and spoilage organisms that were not known or well recognized in the early 20th century. Starting before 1917, gradual introduction and refinement of pasteurization methods throughout the United States and many other parts of the world have improved the safety and quality of milk and dairy products. In parallel to pasteurization, others strategies for reducing microbial contamination throughout the dairy chain (e.g., improved dairy herd health, raw milk tests, clean-in-place technologies) also played an important role in improving microbial milk quality and safety. Despite tremendous advances in reducing microbial food safety hazards and spoilage issues, the dairy industry still faces important challenges, including but not limited to the need for improved science-based strategies for safety of raw milk cheeses, control of postprocessing contamination, and control of sporeforming pathogens and spoilage organisms. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

21 CFR 330.3 - Imprinting of solid oral dosage form drug products.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Imprinting of solid oral dosage form drug products... AS SAFE AND EFFECTIVE AND NOT MISBRANDED General Provisions § 330.3 Imprinting of solid oral dosage form drug products. A requirement to imprint an identification code on solid oral dosage form drug...

21 CFR 872.5580 - Oral rinse to reduce the adhesion of dental plaque.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Oral rinse to reduce the adhesion of dental plaque... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Therapeutic Devices § 872.5580 Oral rinse to reduce the adhesion of dental plaque. (a) Identification. The device is assigned the generic name oral rinse to reduce...

21 CFR 872.5580 - Oral rinse to reduce the adhesion of dental plaque.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Oral rinse to reduce the adhesion of dental plaque... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Therapeutic Devices § 872.5580 Oral rinse to reduce the adhesion of dental plaque. (a) Identification. The device is assigned the generic name oral rinse to reduce...

21 CFR 872.5580 - Oral rinse to reduce the adhesion of dental plaque.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Oral rinse to reduce the adhesion of dental plaque... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Therapeutic Devices § 872.5580 Oral rinse to reduce the adhesion of dental plaque. (a) Identification. The device is assigned the generic name oral rinse to reduce...

21 CFR 872.5580 - Oral rinse to reduce the adhesion of dental plaque.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Oral rinse to reduce the adhesion of dental plaque... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Therapeutic Devices § 872.5580 Oral rinse to reduce the adhesion of dental plaque. (a) Identification. The device is assigned the generic name oral rinse to reduce...

21 CFR 872.5580 - Oral rinse to reduce the adhesion of dental plaque.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Oral rinse to reduce the adhesion of dental plaque... SERVICES (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Therapeutic Devices § 872.5580 Oral rinse to reduce the adhesion of dental plaque. (a) Identification. The device is assigned the generic name oral rinse to reduce...

21 CFR 330.3 - Imprinting of solid oral dosage form drug products.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 5 2011-04-01 2011-04-01 false Imprinting of solid oral dosage form drug products... AS SAFE AND EFFECTIVE AND NOT MISBRANDED General Provisions § 330.3 Imprinting of solid oral dosage form drug products. A requirement to imprint an identification code on solid oral dosage form drug...

21 CFR 872.6650 - Massaging pick or tip for oral hygiene.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Massaging pick or tip for oral hygiene. 872.6650... (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Miscellaneous Devices § 872.6650 Massaging pick or tip for oral hygiene. (a) Identification. A massaging pick or tip for oral hygiene is a rigid, pointed device intended...

Development and utility of the FDA 'GutProbe' DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics.

PubMed

Patro, J N; Ramachandran, P; Lewis, J L; Mammel, M K; Barnaba, T; Pfeiler, E A; Elkins, C A

2015-06-01

Lactic acid bacteria are beneficial microbes added to many food products and dietary supplements for their purported health benefits. Proper identification of bacteria is important to assess safety as well as proper product labelling. A custom microarray (FDA GutProbe) was developed to verify accurate labelling in commercial dietary supplements. Strain-specific attribution was achieved with GutProbe array which contains genes from the most commonly found species in probiotic supplements and food ingredients. Applied utility of the array was assessed with direct from product DNA hybridization to determine (i) if identification of multiple strains in one sample can be conducted and (ii) if any lot-to-lot variations exist with eight probiotics found on the US market. GutProbe is a useful tool in identifying a mixture of microbials in probiotics and did reveal some product variations. In addition, the array is able to identify lot-to-lot differences in these products. These strain level attribution may be useful for routine monitoring of batch variation as part of a 'Good Manufacturing Practices' process. The FDA GutProbe is an efficient and reliable platform to identify the presence of microbial ingredients and determining microbe differences in dietary supplements. The GutProbe is a fast, rapid method for direct community profiling or food matrix sampling. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

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

PCR detection and identification of oral streptococci in saliva samples using gtf genes.

PubMed

Hoshino, Tomonori; Kawaguchi, Mamoru; Shimizu, Noriko; Hoshino, Naoko; Ooshima, Takashi; Fujiwara, Taku

2004-03-01

Oral streptococci are major constituents of dental plaque, and their prevalence is implicated in various pathologies. Therefore, accurate identification of oral streptococci would be valuable for studies of cariogenic plaque and for diagnostic use in infective endocarditis. Many oral streptococci possess glucosyltransferase enzymes that synthesize glucan, which is an obligate component of dental plaque. We established a rapid and precise method to identify oral streptococci by PCR using the species-specific region from the glucosyltransferase gene. With the species-specific primers, Streptococcus mutans, S. sobrinus, S. salivarius, S. sanguinis, S. oralis, and S. gordonii could be successfully distinguished. Further, we developed a simple method to extract the bacterial DNA from saliva. Using the resultant DNA as a template, the proposed PCR detection was performed. Their distribution was in accord with results of conventional biochemical tests. These findings indicate that the present PCR method is useful for the analysis of oral streptococci and can be successfully used in clinical applications to identify pathogenic bacteria associated with oral infectious disease and/or endocarditis.

Quantification of oral palatine Langerhans cells in HIV/AIDS associated oral Kaposi sarcoma with and without oral candidiasis.

PubMed

Jivan, Vibha; Meer, Shabnum

2016-01-01

Langerhans cells (LCs) are effective antigen-presenting cells that function as "custodians" of mucosa, modifying the immune system to pathogen entry, and tolerance to self-antigen and commensal microbes. A reduction in number of LCs in human immunodeficiency virus (HIV)-positive individuals may predispose to local mucosal infections. To quantitatively determine the number of oral mucosal LCs in HIV/acquired immunodeficiency syndrome HIV/acquired immunodeficiency syndrome (AIDS) associated oral Kaposi sarcoma (KS) with/without oral candidiasis (OC) and to define in situ interrelationships between the cells, OC, and HIV infection. Thirty-two periodic acid-Schiff. (PAS) stained histologic sections of palatal HIV/AIDS associated KS with intact oral epithelium were examined for Candida and divided into two groups: . (1) KS coinfected with Candida and. (2) KS noninfected with Candida. Sections were immunohistochemically stained with CD1a. The standard length of surface epithelium was measured and number of positively stained LCs counted per unit length. Control cases included non-Candida infected palatal mucosa overlying pleomorphic adenoma. (PA) and oral mucosa infected with Candida in otherwise healthy individuals. LC number per unit length of surface epithelium was statistically significantly greatest in uninfected PA mucosa and lowest in KS coinfected with Candida (P = 0.0001). A statistically significant difference was also noted between uninfected PA mucosa and non-Candida infected KS (P = 0.0014), in KS coinfected with Candida and non-infected KS (P = 0.0035), between OC and PA (P = 0.0001), and OC and KS coinfected with Candida (P = 0.0247). LC numbers are significantly reduced in oral tissues of HIV/AIDS infected patients by Candida infection when compared to oral tissues without.

Efficacy of Dentaq® Oral and ENT Health Probiotic Complex on Clinical Parameters of Gingivitis in Patients Undergoing Fixed Orthodontic Treatment: A Pilot Study.

PubMed

Kolip, Duygu; Yılmaz, Nuray; Gökkaya, Berna; Kulan, Pinar; Kargul, Betul; MacDonald, Kyle W; Cadieux, Peter A; Burton, Jeremy P; James, Kris M

2016-09-01

Probiotics act as a unique approach to maintaining oral health by supplementing the endogenous oral bacteria with additional naturally occurring beneficial microbes to provide defense against pathogens harmful to teeth and gingiva. The aim of this pilot study was to clinically evaluate the effects of probiotics on plaque accumulation and gingival inflammation in subjects with fixed orthodontics. The pilot study was comprised of 15 healthy patients, aged 11 to 18 years, undergoing fixed orthodontic treatment. Patients used an all-natural, dissolving lozenge containing six proprietary probiotic strains (Dentaq® Oral and ENT Health Probiotic Complex)for 28 days. Gingival Index (GI) according to Löe-Silness and Plaque Index (PI) according to Quigley-Hein for all teeth were measured at baseline (Day Zero) and at the end of the probiotic regimen (Day 28). The mean baseline GI and PI scores within each patient decreased by 28.4% and 35.8%, respectively, by Day 28. Patients reported decreased tooth and gingival pain, decreased oral bleeding, and increased motivation to maintain proper oral hygiene over the course of the study. This pilot study provided preliminary support for the use of Dentaq Oral and ENT Health Probiotic Complex as a safe and effective natural health product for the reduction of plaque accumulation and gingival inflammation. The results demonstrate its potential therapeutic value and open the door for larger scale placebo-controlled clinical studies to verify these findings.

The Microbiome and the Respiratory Tract

PubMed Central

Dickson, Robert P.; Erb-Downward, John R.; Martinez, Fernando J.; Huffnagle, Gary B.

2016-01-01

Although the notion that “the normal lung is free from bacteria” remains common in textbooks, it is virtually always stated without citation or argument. The lungs are constantly exposed to diverse communities of microbes from the oropharynx and other sources, and over the past decade, novel culture-independent techniques of microbial identification have revealed that the lungs, previously considered sterile in health, harbor diverse communities of microbes. In this review, we describe the topography and population dynamics of the respiratory tract, both in health and as altered by acute and chronic lung disease. We provide a survey of current techniques of sampling, sequencing, and analysis of respiratory microbiota and review technical challenges and controversies in the field. We review and synthesize what is known about lung microbiota in various diseases and identify key lessons learned across disease states. PMID:26527186

Receptor-like kinases in plant innate immunity.

PubMed

Wu, Ying; Zhou, Jian-Min

2013-12-01

Plants employ a highly effective surveillance system to detect potential pathogens, which is critical for the success of land plants in an environment surrounded by numerous microbes. Recent efforts have led to the identification of a number of immune receptors and components of immune receptor complexes. It is now clear that receptor-like kinases (RLKs) and receptor-like proteins (RLPs) are key pattern-recognition receptors (PRRs) for microbe- and plant-derived molecular patterns that are associated with pathogen invasion. RLKs and RLPs involved in immune signaling belong to large gene families in plants and have undergone lineage specific expansion. Molecular evolution and population studies on phytopathogenic molecular signatures and their receptors have provided crucial insight into the co-evolution between plants and pathogens. [Figure: see text] Jian-Min Zhou (Corresponding author). © 2013 Institute of Botany, Chinese Academy of Sciences.

Clinical and mycological analysis of dog’s oral cavity

PubMed Central

Santin, Rosema; Mattei, Antonella Souza; Waller, Stefanie Bressan; Madrid, Isabel Martins; Cleff, Marlete Brum; Xavier, Melissa Orzechowski; de Oliveira Nobre, Márcia; Nascente, Patrícia da Silva; de Mello, João Roberto Braga; Meireles, Mário Carlos Araújo

2013-01-01

The oral microbiota of humans and animals is made up of a wide variety of yeasts and bacteria, but microbiota of dogs is not totally described. Although such identification is an important step to establish the etiopathogenesis and adequate therapy for the periodontal disease The aim of this study was to evaluate and correlate oral alterations with the presence of yeasts in oral cavity of female dogs. After clinical evaluation samples from healthy and from dogs with oral diseases were obtained from three different oral sites by swabs, curettes, millimeter periodontal probes and HA membrane tip in cellulose ester. Yeast identification was performed through macroscopic and microscopic colony features and biochemical tests. Dental calculus was the most prevalent occurrence in the oral cavity of 59 females. However, the isolation of yeasts was significantly higher (p < 0.05) in animals suffering from halitosis. Eleven yeast species were identified, namely: Malassezia pachydermatis, Rhodotorula spp., Candida albicans, C. catenulata, C. famata, C. guilliermondii, C. parapsilosis, C. intermedia, Trichosporon asahii, T. mucoides and Cryptococcus albidus. It could be concluded that the yeasts are part of the microbiota from the different sites of the oral cavity of the female canines studied without causing any significant alterations except halitosis. PMID:24159296

Microfluidics and microbial engineering.

PubMed

Kou, Songzi; Cheng, Danhui; Sun, Fei; Hsing, I-Ming

2016-02-07

The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.

Cluster formation in liverwort-associated methylobacteria and its implications.

PubMed

Kutschera, U; Thomas, J; Hornschuh, M

2007-08-01

Pink-pigmented methylotropic bacteria of the genus Methylobacterium inhabit the surfaces of plant organs. In bryophytes, these methylobacteria enhance cell growth, but the nature of this plant-microbe interaction is largely unknown. In this study, methylobacteria were isolated from the upper surface of the free-living thalli of the liverwort Marchantia polymorpha L. Identification of one strain by 16S ribosomal RNA (rRNA) gene-targeted polymerase chain reaction (PCR) and other data show that these microbes represent an undescribed species of the genus Methylobacterium (Methylobacterium sp.). The growth-promoting activity of these wild-type methylobacteria was tested and compared with that of the type strain Methylobacterium mesophilicum. Both types of methylobacteria stimulated surface expansion of isolated gemmae from Marchantia polymorpha by about 350%. When suspended in water, the liverwort-associated bacteria (Methylobacterium sp.) formed dense clusters of up to 600 cells. In liquid cultures of Methylobacterium mesophilicum, single cells were observed, but no clustering occurred. We suggest that the liverwort-associated methylobacteria are co-evolved symbionts of the plants: Cluster formation may be a behavior that enhances the survival of the epiphytic microbes during periods of drought of these desiccation-tolerant lower plants.

Cluster formation in liverwort-associated methylobacteria and its implications

NASA Astrophysics Data System (ADS)

Kutschera, U.; Thomas, J.; Hornschuh, M.

2007-08-01

Pink-pigmented methylotropic bacteria of the genus Methylobacterium inhabit the surfaces of plant organs. In bryophytes, these methylobacteria enhance cell growth, but the nature of this plant-microbe interaction is largely unknown. In this study, methylobacteria were isolated from the upper surface of the free-living thalli of the liverwort Marchantia polymorpha L. Identification of one strain by 16S ribosomal RNA (rRNA) gene-targeted polymerase chain reaction (PCR) and other data show that these microbes represent an undescribed species of the genus Methylobacterium ( Methylobacterium sp.). The growth-promoting activity of these wild-type methylobacteria was tested and compared with that of the type strain Methylobacterium mesophilicum. Both types of methylobacteria stimulated surface expansion of isolated gemmae from Marchantia polymorpha by about 350%. When suspended in water, the liverwort-associated bacteria ( Methylobacterium sp.) formed dense clusters of up to 600 cells. In liquid cultures of Methylobacterium mesophilicum, single cells were observed, but no clustering occurred. We suggest that the liverwort-associated methylobacteria are co-evolved symbionts of the plants: Cluster formation may be a behavior that enhances the survival of the epiphytic microbes during periods of drought of these desiccation-tolerant lower plants.

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.

Intestinal alkaline phosphatase preserves the normal homeostasis of gut microbiota.

PubMed

Malo, M S; Alam, S Nasrin; Mostafa, G; Zeller, S J; Johnson, P V; Mohammad, N; Chen, K T; Moss, A K; Ramasamy, S; Faruqui, A; Hodin, S; Malo, P S; Ebrahimi, F; Biswas, B; Narisawa, S; Millán, J L; Warren, H S; Kaplan, J B; Kitts, C L; Hohmann, E L; Hodin, R A

2010-11-01

The intestinal microbiota plays a critical role in maintaining human health; however, the mechanisms governing the normal homeostatic number and composition of these microbes are largely unknown. Previously it was shown that intestinal alkaline phosphatase (IAP), a small intestinal brush border enzyme, functions as a gut mucosal defence factor limiting the translocation of gut bacteria to mesenteric lymph nodes. In this study the role of IAP in the preservation of the normal homeostasis of the gut microbiota was investigated. Bacterial culture was performed in aerobic and anaerobic conditions to quantify the number of bacteria in the stools of wild-type (WT) and IAP knockout (IAP-KO) C57BL/6 mice. Terminal restriction fragment length polymorphism, phylogenetic analyses and quantitative real-time PCR of subphylum-specific bacterial 16S rRNA genes were used to determine the compositional profiles of microbiotas. Oral supplementation of calf IAP (cIAP) was used to determine its effects on the recovery of commensal gut microbiota after antibiotic treatment and also on the colonisation of pathogenic bacteria. IAP-KO mice had dramatically fewer and also different types of aerobic and anaerobic microbes in their stools compared with WT mice. Oral supplementation of IAP favoured the growth of commensal bacteria, enhanced restoration of gut microbiota lost due to antibiotic treatment and inhibited the growth of a pathogenic bacterium (Salmonella typhimurium). IAP is involved in the maintenance of normal gut microbial homeostasis and may have therapeutic potential against dysbiosis and pathogenic infections.

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

PubMed Central

Libkind, Diego; Hittinger, Chris Todd; Valério, Elisabete; Gonçalves, Carla; Dover, Jim; Johnston, Mark; Gonçalves, Paula; Sampaio, José Paulo

2011-01-01

Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement. PMID:21873232

Rapid Screening and Characterization of Acetylcholinesterase Inhibitors from Yinhuang Oral Liquid Using Ultrafiltration-liquid Chromatography-electrospray Ionization Tandem Mass Spectrometry

PubMed Central

Zhang, Haomin; Guo, Yinan; Meng, Lingwen; Sun, Hui; Yang, Yinping; Gao, Ying; Sun, Jiaming

2018-01-01

Background: At present, approximately 17–25 million people in the world suffer from Alzheimer's disease (AD). The most efficacious and acceptable therapeutic drug clinically are the acetylcholinesterase inhibitors (AChEIs). Yinhuang oral liquid is a Chinese medicine preparation which contains AChEIs according to the literatures. However, no strategy has been presented for rapid screening and identification of AChEIs from Yinhuang oral liquid. Objective: To develop a method for rapid screening and identification of AChEIs from Yinhuang oral liquid using ultrafiltration–liquid chromatography–electrospray ionization tandem mass spectrometry (UF-LC-ESI-MS/MS). Materials and Methods: In this study, UF incubation conditions such as enzyme concentration, incubation time, and incubation temperature were optimized so as to get better screening results. The AChEIs from Yinhuang oral liquid were identified by high-performance liquid chromatography-ESI-MS and the improved Ellman method was used for the AChE inhibitory activity test in vitro. Results: The results showed that Yinhuang oral liquid can inhibit the activity of AChE. We screened and identified seven compounds with potential AChE inhibitory activity from Yinhuang oral liquid, which provided experimental basis for the treatment and prevention of AD. Conclusion: The current technique was used to directly screen the active ingredients with acetylcholinesterase inhibition from complex traditional Chinese medicine, which was simple, rapid, accurate, and suitable for high-throughput screening of AChEI from complex systems. SUMMARY A UF-LC-ESI-MS/MS method for rapid screening and identification of AChEIs from Yinhuang oral liquid was developedSeven compounds were screened and identified with potential AChE inhibitory activity from Yinhuang oral liquidIt provided experimental basis of Yinhuang oral liquid for the treating and preventing AD. Abbreviations used: (AD): Alzheimer's disease; (UF-LC-ESI-MS/MS): ultrafiltration–liquid chromatography–electrospray ionization tandem mass spectrometry; (AChEIs): acetylcholinesterase inhibitors. PMID:29720840

Oral Rehabilitation and Management of Mentally Retarded

PubMed Central

Khetan, Jitendra; Gupta, Sarika; Tomar, Deepak; Singh, Meenakshi

2015-01-01

High level of periodontal problems of dental caries are frequently observed in mentally handicapped children. This group of patients presents various problems when they face dental treatments. Identification of such population and providing them affordable oral health care is the new concept. A systematic method for identification and screening of persons with mental retardation has been developed and is being followed. Cost and fear are the most commonly cited barriers to dental care. Physical or mental may lead to deterioration in self-care, and oral care state have a low priority. Risk factors are inter-related and are often barriers to oral health. With advancements in today’s world sufficient information and support is available for each and every individual to lead a healthy life which include the access to the oral health care. Factors such as fear, anxiety and dental phobia plays a vital role in acceptance of dental care and also the delaying of dental care. Lack of knowledge of oral and dental disease, awareness or oral need, oral side-effects of medication and organization of dental services are highlighted in the literature. All health personnel should receive training to support the concept of primary oral health care. Training about dealing with such mentally handicapped people should be addressed urgently among the health professionals. PMID:25738098

Oral rehabilitation and management of mentally retarded.

PubMed

Solanki, Jitender; Khetan, Jitendra; Gupta, Sarika; Tomar, Deepak; Singh, Meenakshi

2015-01-01

High level of periodontal problems of dental caries are frequently observed in mentally handicapped children. This group of patients presents various problems when they face dental treatments. Identification of such population and providing them affordable oral health care is the new concept. A systematic method for identification and screening of persons with mental retardation has been developed and is being followed. Cost and fear are the most commonly cited barriers to dental care. Physical or mental may lead to deterioration in self-care, and oral care state have a low priority. Risk factors are inter-related and are often barriers to oral health. With advancements in today's world sufficient information and support is available for each and every individual to lead a healthy life which include the access to the oral health care. Factors such as fear, anxiety and dental phobia plays a vital role in acceptance of dental care and also the delaying of dental care. Lack of knowledge of oral and dental disease, awareness or oral need, oral side-effects of medication and organization of dental services are highlighted in the literature. All health personnel should receive training to support the concept of primary oral health care. Training about dealing with such mentally handicapped people should be addressed urgently among the health professionals.

Discrimination between Pseudogymnoascus destructans, other dermatophytes of cave-dwelling bats, and related innocuous keratinophilic fungi based on electronic-nose/GC signatures of VOC-metabolites produced in culture

Treesearch

Alphus Dan Wilson; Lisa Beth Forse

2017-01-01

White-nose syndrome (WNS), caused by the fungal dermatophyte (Pseudogymnoascus destructans), is considered the most important disease affecting hibernating bats in North America. The identification of dermatophytic fungi, isolated from the skins of cave-dwelling bat species, is necessary to distinguish pathogenic (disease-causing) microbes from those that are innocuous...

Microbial Monitoring of Common Opportunistic Pathogens by Comparing Multiple Real-time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Roman, Monserrate C.; Jones, Kathy U.; Oubre, Cherie M.; Castro, Victoria; Ott, Mark C.; Birmele, Michele; Venkateswaran, Kasthuri J.; Vaishampayan, Parag A.

2013-01-01

Current methods for microbial detection: a) Labor & time intensive cultivation-based approaches that can fail to detect or characterize all cells present. b) Requires collection of samples on orbit and transportation back to ground for analysis. Disadvantages to current detection methods: a) Unable to perform quick and reliable detection on orbit. b) Lengthy sampling intervals. c) No microbe identification.

Host-microbe interactions in distal airways: relevance to chronic airway diseases.

PubMed

Martin, Clémence; Burgel, Pierre-Régis; Lepage, Patricia; Andréjak, Claire; de Blic, Jacques; Bourdin, Arnaud; Brouard, Jacques; Chanez, Pascal; Dalphin, Jean-Charles; Deslée, Gaetan; Deschildre, Antoine; Gosset, Philippe; Touqui, Lhousseine; Dusser, Daniel

2015-03-01

This article is the summary of a workshop, which took place in November 2013, on the roles of microorganisms in chronic respiratory diseases. Until recently, it was assumed that lower airways were sterile in healthy individuals. However, it has long been acknowledged that microorganisms could be identified in distal airway secretions from patients with various respiratory diseases, including cystic fibrosis (CF) and non-CF bronchiectasis, chronic obstructive pulmonary disease, asthma and other chronic airway diseases (e.g. post-transplantation bronchiolitis obliterans). These microorganisms were sometimes considered as infectious agents that triggered host immune responses and contributed to disease onset and/or progression; alternatively, microorganisms were often considered as colonisers, which were considered unlikely to play roles in disease pathophysiology. These concepts were developed at a time when the identification of microorganisms relied on culture-based methods. Importantly, the majority of microorganisms cannot be cultured using conventional methods, and the use of novel culture-independent methods that rely on the identification of microorganism genomes has revealed that healthy distal airways display a complex flora called the airway microbiota. The present article reviews some aspects of current literature on host-microbe (mostly bacteria and viruses) interactions in healthy and diseased airways, with a special focus on distal airways. Copyright ©ERS 2015.

17 CFR 12.312 - Oral hearing.

Code of Federal Regulations, 2014 CFR

2014-04-01

... location of an oral hearing shall be in one of the following cities: Albuquerque, N.M.; Atlanta, Ga... issues to be tried at the hearing; (ii) An identification of each witness expected to be called by that..., which, unless modified to prevent injustice, shall control the scope of matters to be tried at the oral...

17 CFR 12.312 - Oral hearing.

Code of Federal Regulations, 2011 CFR

2011-04-01

... location of an oral hearing shall be in one of the following cities: Albuquerque, N.M.; Atlanta, Ga... issues to be tried at the hearing; (ii) An identification of each witness expected to be called by that..., which, unless modified to prevent injustice, shall control the scope of matters to be tried at the oral...

17 CFR 12.312 - Oral hearing.

Code of Federal Regulations, 2013 CFR

2013-04-01

... location of an oral hearing shall be in one of the following cities: Albuquerque, N.M.; Atlanta, Ga... issues to be tried at the hearing; (ii) An identification of each witness expected to be called by that..., which, unless modified to prevent injustice, shall control the scope of matters to be tried at the oral...

17 CFR 12.312 - Oral hearing.

Code of Federal Regulations, 2010 CFR

2010-04-01

... location of an oral hearing shall be in one of the following cities: Albuquerque, N.M.; Atlanta, Ga... issues to be tried at the hearing; (ii) An identification of each witness expected to be called by that..., which, unless modified to prevent injustice, shall control the scope of matters to be tried at the oral...

17 CFR 12.312 - Oral hearing.

Code of Federal Regulations, 2012 CFR

2012-04-01

... location of an oral hearing shall be in one of the following cities: Albuquerque, N.M.; Atlanta, Ga... issues to be tried at the hearing; (ii) An identification of each witness expected to be called by that..., which, unless modified to prevent injustice, shall control the scope of matters to be tried at the oral...

Isolation and Identification of the Antimicrobial Agent Beauvericin from the Endophytic Fusarium oxysporum 5-19 with NMR and ESI-MS/MS

PubMed Central

Ruan, Chuanfen; Bai, Xuelian; Zhang, Miao; Zhu, Shuangshuang; Jiang, Yingying

2016-01-01

Endophytic microbe has been proved to be one of rich sources of bioactive natural products with potential application for new drug and pesticide discovery. One cyclodepsipeptide, beauvericin, was firstly isolated from the fermentation broth of Fusarium oxysporum 5-19 endophytic on Edgeworthia chrysantha Linn. Its chemical structure was unambiguously identified by a combination of spectroscopic methods, such as HRESI-MS and 1H and 13C NMR. ESI-MS/MS was successfully used to elucidate the splitting decomposition route of the positive molecule ion of beauvericin. Antimicrobial results showed that this cyclodepsipeptide had inhibitory effect on three human pathogenic microbes, Candida albicans, Escherichia coli, and Staphylococcus aureus. In particular, beauvericin exhibited the strongest antimicrobial activity against S. aureus with MIC values of 3.91 μM, which had similar effect with that of the positive control amoxicillin. PMID:27413733

The influence of milk oligosaccharides on microbiota of infants: opportunities for formulas.

PubMed

Chichlowski, Maciej; German, J Bruce; Lebrilla, Carlito B; Mills, David A

2011-01-01

In addition to a nutritive role, human milk also guides the development of a protective intestinal microbiota in the infant. Human milk possesses an overabundance of complex oligosaccharides that are indigestible by the infant yet are consumed by microbial populations in the developing intestine. These oligosaccharides are believed to facilitate enrichment of a healthy infant gastrointestinal microbiota, often associated with bifidobacteria. Advances in glycomics have enabled precise determination of milk glycan structures as well as identification of the specific glycans consumed by various gut microbes. Furthermore, genomic analysis of bifidobacteria from infants has revealed specific genetic loci related to milk oligosaccharide import and processing, suggesting coevolution between the human host, milk glycans, and the microbes they enrich. This review discusses the current understanding of how human milk oligosaccharides interact with the infant microbiota and examines the opportunities for translating this knowledge to improve the functionality of infant formulas.

Identification of Quantitative Trait Loci Controlling Gene Expression during the Innate Immunity Response of Soybean1[W][OA

PubMed Central

Valdés-López, Oswaldo; Thibivilliers, Sandra; Qiu, Jing; Xu, Wayne Wenzhong; Nguyen, Tran H.N.; Libault, Marc; Le, Brandon H.; Goldberg, Robert B.; Hill, Curtis B.; Hartman, Glen L.; Diers, Brian; Stacey, Gary

2011-01-01

Microbe-associated molecular pattern-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. However, most of our knowledge of MTI comes from studies of model systems with relatively little work done with crop plants. In this work, we report on variation in both the microbe-associated molecular pattern-triggered oxidative burst and gene expression across four soybean (Glycine max) genotypes. Variation in MTI correlated with the level of pathogen resistance for each genotype. A quantitative trait locus analysis on these traits identified four loci that appeared to regulate gene expression during MTI in soybean. Likewise, we observed that both MTI variation and pathogen resistance were quantitatively inherited. The approach utilized in this study may have utility for identifying key resistance loci useful for developing improved soybean cultivars. PMID:21963820

Raman spectroscopic study of the photoprotection of extremophilic microbes against ultraviolet radiation

NASA Astrophysics Data System (ADS)

Edwards, H. G. M.; Moeller, R.; Jorge Villar, S. E.; Horneck, G.; Stackebrandt, E.

2006-12-01

Extremophiles use a range of pigments for protection against low-wavelength radiation in exposed terrestrial habitats and photoaccessory materials are synthesized for the effective harnessing of photosynthetically active radiation. Raman spectroscopy has been demonstrated to be a useful probe for information on the survival strategies employed by extremophilic bacteria through the identification of key biomolecular signatures of the suite of protective chemicals synthesized by the organisms in stressed environments. Raman spectroscopic analyses of Bacillus spp. spores, Bacillus atrophaeus (DSM 675: deep red) and Bacillus subtilis (DSM 5611: light grey and DSM 7264: dark grey), Deinococcus radiodurans (pink) and Natronomonas pharaonis (red), of visually different pigmentation showed the presence of different carotenoids and other protectant biomolecules, which assist microorganisms against UVA radiation. The implications for the survival of extremophilic microbes in extraterrestrial habitats and for the detection of the protectant biomolecules by remote, robotic Raman spectroscopic instrumentation in an astrobiological search for life context are discussed.

Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort

PubMed Central

Gonzalez, Antonio; Hyde, Embriette; Sangwan, Naseer; Gilbert, Jack A.; Viirre, Erik

2016-01-01

ABSTRACT Nitrates, such as cardiac therapeutics and food additives, are common headache triggers, with nitric oxide playing an important role. Facultative anaerobic bacteria in the oral cavity may contribute migraine-triggering levels of nitric oxide through the salivary nitrate-nitrite-nitric oxide pathway. Using high-throughput sequencing technologies, we detected observable and significantly higher abundances of nitrate, nitrite, and nitric oxide reductase genes in migraineurs versus nonmigraineurs in samples collected from the oral cavity and a slight but significant difference in fecal samples. IMPORTANCE Recent work has demonstrated a potentially symbiotic relationship between oral commensal bacteria and humans through the salivary nitrate-nitrite-nitric oxide pathway (C. Duncan et al., Nat Med 1:546–551, 1995, http://dx.doi.org/10.1038/nm0695-546). Oral nitrate-reducing bacteria contribute physiologically relevant levels of nitrite and nitric oxide to the human host that may have positive downstream effects on cardiovascular health (V. Kapil et al., Free Radic Biol Med 55:93–100, 2013, http://dx.doi.org/10.1016/j.freeradbiomed.2012.11.013). In the work presented here, we used 16S rRNA Illumina sequencing to determine whether a connection exists between oral nitrate-reducing bacteria, nitrates for cardiovascular disease, and migraines, which are a common side effect of nitrate medications (U. Thadani and T. Rodgers, Expert Opin Drug Saf 5:667–674, 2006, http://dx.doi.org/10.1517/14740338.5.5.667). PMID:27822557

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.

Probiotics: Healthy bugs and nourishing elements of diet.

PubMed

Pandey, Vijayendra; Berwal, Vikas; Solanki, Neeraj; Malik, Narender Singh

2015-01-01

The use of probiotics is based on the concept that adding the right live microbes to the complex human system can result in physiological benefits. The benefit of fermented milk in human diet has been acknowledged since Vedic times; however, the scientific interest in this field was evoked by Ellie Metchinkoff who recommended that people should consume fermented milk containing lactobacilli to prolong their lives, as accelerated aging is due to autointoxication caused by the toxins produced by the gut microflora. They have been used to improve gastrointestinal health and their attractiveness has evinced interest to study their role in the promotion of oral health also. Studies have been widely carried out to establish the role of intestinal lactobacilli as probiotic to treat various gastrointestinal disorders, but only limited studies are available on the oral use of probiotics. The probiotic products usually contain lactobacilli and bifidobacteria, and their demand in the market is growing day by day. This paper provides an overview of various studies in the literature that emphasize on the role of probiotics to combat oral diseases and encourages more research in this field.

Probiotics: Healthy bugs and nourishing elements of diet

PubMed Central

Pandey, Vijayendra; Berwal, Vikas; Solanki, Neeraj; Malik, Narender Singh

2015-01-01

The use of probiotics is based on the concept that adding the right live microbes to the complex human system can result in physiological benefits. The benefit of fermented milk in human diet has been acknowledged since Vedic times; however, the scientific interest in this field was evoked by Ellie Metchinkoff who recommended that people should consume fermented milk containing lactobacilli to prolong their lives, as accelerated aging is due to autointoxication caused by the toxins produced by the gut microflora. They have been used to improve gastrointestinal health and their attractiveness has evinced interest to study their role in the promotion of oral health also. Studies have been widely carried out to establish the role of intestinal lactobacilli as probiotic to treat various gastrointestinal disorders, but only limited studies are available on the oral use of probiotics. The probiotic products usually contain lactobacilli and bifidobacteria, and their demand in the market is growing day by day. This paper provides an overview of various studies in the literature that emphasize on the role of probiotics to combat oral diseases and encourages more research in this field. PMID:25992331

The oral microflora in obesity and type-2 diabetes.

PubMed

Shillitoe, Edward; Weinstock, Ruth; Kim, Taewan; Simon, Howard; Planer, Jessica; Noonan, Susan; Cooney, Robert

2012-01-01

Type 2 diabetes mellitus (T2DM) is prevalent in people with obesity. It has been proposed that these conditions are related to specific features of the microflora of the mouth and lower gastrointestinal (GI) tract. Hyperglycemia often resolves quickly after Roux-en-Y gastric bypass (RYGB) but the role of the GI microflora cannot be examined easily because of reduced intestinal mobility. We propose that the study of microorganisms present in the mouth of patients undergoing RYGB will contribute to our understanding of the role of bacteria in the pathogenesis of T2DM. To conduct a feasibility study to examine differences in oral microbes in obese patients with and without T2DM and to determine whether it is feasible to measure changes after gastric bypass surgery. Individuals with morbid obesity (n=29), of whom 13 had T2DM, were studied. Oral rinses, stool samples, and blood samples were obtained before RYGB, and oral rinses and blood samples were obtained at 2 and 12 weeks postsurgery. Prior to surgery, participants with T2DM had slightly higher total levels of oral bacteria than those without diabetes. Those with HbA1c > 6.5% had rather lower levels of Bifidobacteria in the mouth and stool. At 2 weeks post-RYGB, patients with T2DM were able to reduce or discontinue their hypoglycemic medications. Stool samples could not be obtained but oral rinses were readily available. The levels of oral Bifidobacteria had increased tenfold and levels of circulating endotoxin and tumor necrosis factor-alpha had decreased. The study of oral bacteria before and after RYGB is feasible and should be tested in larger patient populations to increase our understanding of the role of microorganisms in the pathogenesis of obesity and T2DM.

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat

PubMed Central

Hyde, Embriette R.; Navas-Molina, Jose A.; Kueneman, Jordan G.; Ackermann, Gail; Cardona, Cesar; Humphrey, Gregory; Boyer, Don; Weaver, Tom; Mendelson, Joseph R.; McKenzie, Valerie J.; Gilbert, Jack A.

2016-01-01

ABSTRACT Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon’s environment are similar to the Komodo dragon’s salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals’ environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions. PMID:27822543

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat.

PubMed

Hyde, Embriette R; Navas-Molina, Jose A; Song, Se Jin; Kueneman, Jordan G; Ackermann, Gail; Cardona, Cesar; Humphrey, Gregory; Boyer, Don; Weaver, Tom; Mendelson, Joseph R; McKenzie, Valerie J; Gilbert, Jack A; Knight, Rob

2016-01-01

Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon ( Varanus komodoensis ) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals' environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.

21 CFR 872.6650 - Massaging pick or tip for oral hygiene.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Massaging pick or tip for oral hygiene. 872.6650 Section 872.6650 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... hygiene. (a) Identification. A massaging pick or tip for oral hygiene is a rigid, pointed device intended...

Discovery of Tetrahydropyrazolopyridine as Sphingosine 1-Phosphate Receptor 3 (S1P3)-Sparing S1P1 Agonists Active at Low Oral Doses.

PubMed

Demont, Emmanuel H; Bailey, James M; Bit, Rino A; Brown, Jack A; Campbell, Colin A; Deeks, Nigel; Dowell, Simon J; Eldred, Colin; Gaskin, Pam; Gray, James R J; Haynes, Andrea; Hirst, David J; Holmes, Duncan S; Kumar, Umesh; Morse, Mary A; Osborne, Greg J; Renaux, Jessica F; Seal, Gail A L; Smethurst, Chris A; Taylor, Simon; Watson, Robert; Willis, Robert; Witherington, Jason

2016-02-11

FTY720 is the first oral small molecule approved for the treatment of people suffering from relapsing-remitting multiple sclerosis. It is a potent agonist of the S1P1 receptor, but its lack of selectivity against the S1P3 receptor has been linked to most of the cardiovascular side effects observed in the clinic. These findings have triggered intensive efforts toward the identification of a second generation of S1P3-sparing S1P1 agonists. We have recently disclosed a series of orally active tetrahydroisoquinoline (THIQ) compounds matching these criteria. In this paper we describe how we defined and implemented a strategy aiming at the discovery of selective structurally distinct follow-up agonists. This effort culminated with the identification of a series of orally active tetrahydropyrazolopyridines.

Identification of potent orally active factor Xa inhibitors based on conjugation strategy and application of predictable fragment recommender system.

PubMed

Ishihara, Tsukasa; Koga, Yuji; Iwatsuki, Yoshiyuki; Hirayama, Fukushi

2015-01-15

Anticoagulant agents have emerged as a promising class of therapeutic drugs for the treatment and prevention of arterial and venous thrombosis. We investigated a series of novel orally active factor Xa inhibitors designed using our previously reported conjugation strategy to boost oral anticoagulant effect. Structural optimization of anthranilamide derivative 3 as a lead compound with installation of phenolic hydroxyl group and extensive exploration of the P1 binding element led to the identification of 5-chloro-N-(5-chloro-2-pyridyl)-3-hydroxy-2-{[4-(4-methyl-1,4-diazepan-1-yl)benzoyl]amino}benzamide (33, AS1468240) as a potent factor Xa inhibitor with significant oral anticoagulant activity. We also reported a newly developed Free-Wilson-like fragment recommender system based on the integration of R-group decomposition with collaborative filtering for the structural optimization process. Copyright © 2014 Elsevier Ltd. All rights reserved.

Investigating the Endobacteria Which Thrive in Arbuscular Mycorrhizal Fungi.

PubMed

Desirò, Alessandro; Salvioli, Alessandra; Bonfante, Paola

2016-01-01

The study of the so-called unculturable bacteria is still considered a challenging task. However, given recent improvements in the sensitivity of culture-free approaches, the identification and characterization of such microbes in complex biological samples is now possible. In this chapter we report how endobacteria thriving inside arbuscular mycorrhizal fungi (AMF), which are themselves obligate biotrophs of plants, can be studied using a combination of in vitro culture, molecular biology, and microscopy techniques.

Species specific identification of spore-producing microbes using the gene sequence of small acid-soluble spore coat proteins for amplification based diagnostics

DOEpatents

McKinney, Nancy

2002-01-01

PCR (polymerase chain reaction) primers for the detection of certain Bacillus species, such as Bacillus anthracis. The primers specifically amplify only DNA found in the target species and can distinguish closely related species. Species-specific PCR primers for Bacillus anthracis, Bacillus globigii and Clostridium perfringens are disclosed. The primers are directed to unique sequences within sasp (small acid soluble protein) genes.

The antimicrobial and antiadhesion activities of micellar solutions of surfactin, CTAB and CPCl with terpinen-4-ol: applications to control oral pathogens.

PubMed

Bucci, Andreia R; Marcelino, Larissa; Mendes, Renata K; Etchegaray, Augusto

2018-06-06

The oral pathogen Streptococcus mutans is involved in tooth decay by a process that initiates with biofilm adhesion and caries development. The presence of other microbes such as Candida albicans may worsen the demineralization process. Since both microbes are virulent to the host and will proliferate under specific host immune deficiencies and systemic diseases, it is important to study antimicrobial substances and their effects on both pathogens. There are several antiseptic agents used to reduce plaque biofilm and its outcome (dental caries and/or periodontal disease). However, some of these have undesired effects. In the current study we investigated the antimicrobial and anti-adhesion properties of micellar solutions of surfactants and the plant natural product terpinen-4-ol (TP). The results revealed an increase in antimicrobial properties of the synthetic surfactants, cetylpyridinium chloride (CPC) and cetyltrimethylammonium bromide (CTAB), when mixed with TP. In addition, although surfactin, a biosurfactant, has little antimicrobial activity, it was demonstrated that it enhanced the effect of TP both as antimicrobial and anti-adhesion compound. Surfactin and the synthetic surfactants promote the antimicrobial activity of TP against S. mutans, the causal agent of tooth decay, suggesting specificity for membrane interactions that may be facilitated by surfactants. This is the first report on the successful use of surfactin in association with TP to inhibit the growth and adhesion of microbial pathogens. Surfactin has other beneficial properties besides being biodegradable, it has antiviral and anti-mycoplasma activities in addition to adjuvant properties and encapsulating capacity at low concentration.

A wide diversity of bacteria from the human gut produces and degrades biogenic amines.

PubMed

Pugin, Benoit; Barcik, Weronika; Westermann, Patrick; Heider, Anja; Wawrzyniak, Marcin; Hellings, Peter; Akdis, Cezmi A; O'Mahony, Liam

2017-01-01

Background : Biogenic amines (BAs) are metabolites produced by the decarboxylation of amino acids with significant physiological functions in eukaryotic and prokaryotic cells. BAs can be produced by bacteria in fermented foods, but little is known concerning the potential for microbes within the human gut microbiota to produce or degrade BAs. Objective : To isolate and identify BA-producing and BA-degrading microbes from the human gastrointestinal tract. Design : Fecal samples from human volunteers were screened on multiple growth media, under multiple growth conditions. Bacterial species were identified using 16S rRNA sequencing and BA production or degradation was assessed using ultra-performance liquid chromatography. Results : In total, 74 BA-producing or BA-degrading strains were isolated from the human gut. These isolates belong to the genera Bifidobacterium , Clostridium , Enterococcus , Lactobacillus , Pediococcus , Streptococcus , Enterobacter , Escherichia , Klebsiella , Morganella and Proteus . While differences in production or degradation of specific BAs were observed at the strain level, our results suggest that these metabolic activities are widely spread across different taxa present within the human gut microbiota. Conclusions : The isolation and identification of microbes from the human gut with BA-producing and BA-degrading metabolic activity is an important first step in developing a better understanding of how these metabolites influence health and disease.

Ancient DNA analysis of dental calculus.

PubMed

Weyrich, Laura S; Dobney, Keith; Cooper, Alan

2015-02-01

Dental calculus (calcified tartar or plaque) is today widespread on modern human teeth around the world. A combination of soft starchy foods, changing acidity of the oral environment, genetic pre-disposition, and the absence of dental hygiene all lead to the build-up of microorganisms and food debris on the tooth crown, which eventually calcifies through a complex process of mineralisation. Millions of oral microbes are trapped and preserved within this mineralised matrix, including pathogens associated with the oral cavity and airways, masticated food debris, and other types of extraneous particles that enter the mouth. As a result, archaeologists and anthropologists are increasingly using ancient human dental calculus to explore broad aspects of past human diet and health. Most recently, high-throughput DNA sequencing of ancient dental calculus has provided valuable insights into the evolution of the oral microbiome and shed new light on the impacts of some of the major biocultural transitions on human health throughout history and prehistory. Here, we provide a brief historical overview of archaeological dental calculus research, and discuss the current approaches to ancient DNA sampling and sequencing. Novel applications of ancient DNA from dental calculus are discussed, highlighting the considerable scope of this new research field for evolutionary biology and modern medicine. Copyright © 2014 Elsevier Ltd. All rights reserved.

Oral passive IgY-based immunotherapeutics

PubMed Central

Rahman, Shofiqur; Van Nguyen, Sa; Icatlo Jr., Faustino C.; Umeda, Kouji; Kodama, Yoshikatsu

2013-01-01

This commentary summarizes the laboratory investigations and clinical trials published recently involving per-oral application of IgY supplemented food for specific orogastrointestinal disease prevention and control purposes. The prolonged use and misuse of conventional antibacterial drugs has spawned antibiotic resistant microbes prompting scientists to search for other germ-killing options. In particular, the use of IgY as a novel mode of immunotherapy using oral chicken immunoglobulin (IgY) to confer passive immunity has gained much interest as an inexpensive non-antibiotic alternative for the prophylaxis and treatment of a wide variety of infectious diseases. The stability of IgY in the orogastrointestinal tract and its safety profile has been well-documented. IgY has been used in the treatment or prevention of dental caries, periodontitis and gingivitis, gastritis and gastric ulcer, oral thrush and infant rotavirus diarrhea. The recent clinical trials on IgY with encouraging results has catapulted into the market novel nutraceutical or health supplements for therapeutic or prophylactic intervention based on the consumption of mono-specific or mixed IgY formulations. With recent trends in consumer preference for natural materials to alleviate health concerns, the increasing healthcare costs and the recent advances in drug delivery systems, IgY is likely to shift from its mainly functional food status toward pharmaceuticalization in the foreseeable future. PMID:23319156

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

PubMed Central

Cross, Karissa L.; Chirania, Payal; Xiong, Weili; Elkins, James G.; Giannone, Richard J.; Griffen, Ann L.; Hettich, Robert L.; Joshi, Snehal S.; Mokrzan, Elaine M.; Martin, Roman K.; Leys, Eugene J.

2018-01-01

ABSTRACT The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis, the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives, D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury were also lost by D. oralis, a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. PMID:29535201

A Comprehensive Assessment of Biologicals Contained Within Commercial Airliner Cabin Air

NASA Technical Reports Server (NTRS)

LaDuc, Myron T.; Osman, Shariff; Dekas, Anne; Stuecker, Tara; Newcombe, Dave; Piceno, Yvette; Fuhrman, J.; Andersen, Gary; Venkateswaran, Kasthuri; Bearman, Greg

2006-01-01

Both culture-based and culture-independent, biomarker-targeted microbial enumeration and identification technologies were employed to estimate total microbial and viral burden and diversity within the cabin air of commercial airliners. Samples from each of twenty flights spanning three commercial carriers were collected via air-impingement. When the total viable microbial population was estimated by assaying relative concentrations of the universal energy carrier ATP, values ranged from below detection limits (BDL) to 4.1 x 106 cells/cubic m of air. The total viable microbial population was extremely low in both of Airline A (approximately 10% samples) and C (approximately 18% samples) compared to the samples collected aboard flights on Airline A and B (approximately 70% samples). When samples were collected as a function of time over the course of flights, a gradual accumulation of microbes was observed from the time of passenger boarding through mid-flight, followed by a sharp decline in microbial abundance and viability from the initiation of descent through landing. It is concluded in this study that only 10% of the viable microbes of the cabin air were cultivable and suggested a need to employ state-of-the art molecular assay that measures both cultivable and viable-but-non-cultivable microbes. Among the cultivable bacteria, colonies of Acinetobacter sp. were by far the most profuse in Phase I, and Gram-positive bacteria of the genera Staphylococcus and Bacillus were the most abundant during Phase II. The isolation of the human pathogens Acinetobacter johnsonii, A. calcoaceticus, Janibacter melonis, Microbacterium trichotecenolyticum, Massilia timonae, Staphylococcus saprophyticus, Corynebacterium lipophiloflavum is concerning, as these bacteria can cause meningitis, septicemia, and a handful of sometimes fatal diseases and infections. Molecular microbial community analyses exhibited presence of the alpha-, beta-, gamma-, and delta- proteobacteria, as well as Gram-positive bacteria, Fusobacteria, Cyanobacteria, Deinococci, Bacterioidetes, Spirochetes, and Planctomyces in varying abundance. Neisseria meningitidis rDNA sequences were retrieved in great abundance from Airline A followed by Streptococcus oralis/mitis sequences. Pseudomonas synxantha sequences dominated Airline B clone libraries, followed by those of N. meningitidis and S. oralis/mitis. In Phase II, Airline C, sequences representative of more than 113 species, enveloping 12 classes of bacteria, were retrieved. Proteobacterial sequences were retrieved in greatest frequency (58% of all clone sequences), followed in short order by those stemming from Gram-positives bacteria (31% of all clone sequences). As for overall phylogenetic breadth, Gram-positive and alpha-proteobacteria seem to have a higher affinity for international flights, whereas beta-and gamma-proteobacteria are far more common about domestic cabin air parcels in Airline C samples. Ultimately, the majority of microbial species circulating throughout the cabin airs of commercial airliners are commensal, infrequently pathogenic normal flora of the human nasopharynx and respiratory system. Many of these microbes likely originate from the oral and nasal cavities, and lungs of passengers and flight crew and are disseminated unknowingly via routine conversation, coughing, sneezing, and stochastic passing of fomites. The data documented in this study will be useful to generate a baseline microbial population database and can be utilized to develop biosensor instrumentation for monitoring microbial quality of cabin or urban air.

Evaluation of oral stereognostic ability after rehabilitating patients with complete dentures: in vivo study.

PubMed

Meenakshi, S; Gujjari, Anil Kumar; Thippeswamy, H N; Raghunath, N

2014-12-01

Stereognosis has been defined as the appreciation of the form of objects by palpation. Whilst this definition holds good for the manual exploration of objects, it is possible for the shape of objects to be explored intra orally referred to as oral stereognosis. To better understand patients' relative satisfaction with complete dentures, differences in oral stereognostic perception, based on the identification of 6 edible objects was analyzed in a group of 30 edentulous individuals at 3 stages, namely, just before (pre-treatment), 30 min after (30 min post-treatment) and 1 month after (1 month post-treatment) the insertion of new dentures. The time required to identify each object was recorded and the correctness of identification of each object was scored using oral stereognostic score. Descriptive statistics, Wilcoxon signed rank test, Spearman's rank correlation test, Pearson Chi square test was used to statistically analyze the data obtained. OSA scores was significantly increased 1 month post-treatment compared to 30 min post-treatment (p < 0.05). It was found that Oral stereognostic test is reliable for measuring patients' oral stereognostic perception and may be used as one of the clinical aids in appreciating the functional limitations imposed by the prostheses.

In vivo Raman spectroscopic identification of premalignant lesions in oral buccal mucosa

NASA Astrophysics Data System (ADS)

Singh, S. P.; Deshmukh, Atul; Chaturvedi, Pankaj; Murali Krishna, C.

2012-10-01

Cancers of oral cavities are one of the most common malignancies in India and other south-Asian countries. Tobacco habits are the main etiological factors for oral cancer. Identification of premalignant lesions is required for improving survival rates related to oral cancer. Optical spectroscopy methods are projected as alternative/adjunct for cancer diagnosis. Earlier studies have demonstrated the feasibility of classifying normal, premalignant, and malignant oral ex-vivo tissues. We intend to evaluate potentials of Raman spectroscopy in detecting premalignant conditions. Spectra were recorded from premalignant patches, contralateral normal (opposite to tumor site), and cancerous sites of subjects with oral cancers and also from age-matched healthy subjects with and without tobacco habits. A total of 861 spectra from 104 subjects were recorded using a fiber-optic probe-coupled HE-785 Raman spectrometer. Spectral differences in the 1200- to 1800-cm-1 region were subjected to unsupervised principal component analysis and supervised linear discriminant analysis followed by validation with leave-one-out and an independent test data set. Results suggest that premalignant conditions can be objectively discriminated with both normal and cancerous sites as well as from healthy controls with and without tobacco habits. Findings of the study further support efficacy of Raman spectroscopic approaches in oral-cancer applications.

Evolutionary Ecology of Multitrophic Interactions between Plants, Insect Herbivores and Entomopathogens.

PubMed

Shikano, Ikkei

2017-06-01

Plants play an important role in the interactions between insect herbivores and their pathogens. Since the seminal review by Cory and Hoover (2006) on plant-mediated effects on insect-pathogen interactions, considerable progress has been made in understanding the complexity of these tritrophic interactions. Increasing interest in the areas of nutritional and ecological immunology over the last decade have revealed that plant primary and secondary metabolites can influence the outcomes of insect-pathogen interactions by altering insect immune functioning and physical barriers to pathogen entry. Some insects use plant secondary chemicals and nutrients to prevent infections (prophylactic medication) and medicate to limit the severity of infections (therapeutic medication). Recent findings suggest that there may be selectable plant traits that enhance entomopathogen efficacy, suggesting that entomopathogens could potentially impose selection pressure on plant traits that improve both pathogen and plant fitness. Moreover, plants in nature are inhabited by diverse communities of microbes, in addition to entomopathogens, some of which can trigger immune responses in insect herbivores. Plants are also shared by numerous other herbivorous arthropods with different modes of feeding that can trigger different defensive responses in plants. Some insect symbionts and gut microbes can degrade ingested defensive phytochemicals and be orally secreted onto wounded plant tissue during herbivory to alter plant defenses. Since non-entomopathogenic microbes and other arthropods are likely to influence the outcomes of plant-insect-entomopathogen interactions, I discuss a need to consider these multitrophic interactions within the greater web of species interactions.

Molecular Epidemiologic Source Tracking of Orally Transmitted Chagas Disease, Venezuela

PubMed Central

Segovia, Maikell; Martínez, Clara E.; Messenger, Louisa A.; Nessi, Anaibeth; Londoño, Juan C.; Espinosa, Raul; Martínez, Cinda; Alfredo, Mijares; Bonfante-Cabarcas, Rafael; Lewis, Michael D.; de Noya, Belkisyolé A.; Miles, Michael A.; Llewellyn, Martin S.

2013-01-01

Oral outbreaks of Chagas disease are increasingly reported in Latin America. The transitory presence of Trypanosoma cruzi parasites within contaminated foods, and the rapid consumption of those foods, precludes precise identification of outbreak origin. We report source attribution for 2 peri-urban oral outbreaks of Chagas disease in Venezuela via high resolution microsatellite typing. PMID:23768982

Rapid Electrochemical Detection and Identification of Microbiological and Chemical Contaminants for Manned Spaceflight Project

NASA Technical Reports Server (NTRS)

Pierson, Duane; Botkin, Douglas; Gazda, Daniel

2014-01-01

Microbial control in the spacecraft environment is a daunting task, especially in the presence of human crew members. Currently, assessing the potential crew health risk associated with a microbial contamination event requires return of representative environmental samples that are analyzed in a ground-based laboratory. It is therefore not currently possible to quickly identify microbes during spaceflight. This project addresses the unmet need for spaceflight-compatible microbial identification technology. The electrochemical detection and identification platform is expected to provide a sensitive, specific, and rapid sample-to-answer capability for in-flight microbial monitoring that can distinguish between related microorganisms (pathogens and non-pathogens) as well as chemical contaminants. This will dramatically enhance our ability to monitor the spacecraft environment and the health risk to the crew. Further, the project is expected to eliminate the need for sample return while significantly reducing crew time required for detection of multiple targets. Initial work will focus on the optimization of bacterial detection and identification. The platform is designed to release nucleic acids (DNA and RNA) from microorganisms without the use of harmful chemicals. Bacterial DNA or RNA is captured by bacteria-specific probe molecules that are bound to a microelectrode, and that capture event can generate a small change in the electrical current (Lam, et al. 2012. Anal. Chem. 84(1): 21-5.). This current is measured, and a determination is made whether a given microbe is present in the sample analyzed. Chemical detection can be accomplished by directly applying a sample to the microelectrode and measuring the resulting current change. This rapid microbial and chemical detection device is designed to be a low-cost, low-power platform anticipated to be operated independently of an external power source, characteristics optimal for manned spaceflight and areas where power and computing resources are scarce.

Antimicrobial proteins in human unstimulated whole saliva in relation to each other, and to measures of health status, dental plaque accumulation and composition.

PubMed

Rudney, J D; Krig, M A; Neuvar, E K; Soberay, A H; Iverson, L

1991-01-01

Saliva antimicrobial proteins may interact in a common system to influence the oral ecology. Clinical studies of antimicrobial protein action thus may require a multiple-protein approach. Multivariate statistical methods have been used to describe possible patterns of interaction for lysozyme, lactoferrin, salivary peroxidase and secretory IgA in stimulated parotid saliva. However, oral microbes are most likely to encounter antimicrobial proteins in mixed resting saliva. Relationships among levels of lysozyme, lactoferrin, salivary peroxidase, and secretory IgA therefore were investigated in whole saliva from 216 subjects, and an attempt made to relate interperson variation in those proteins to differences in health and status, and dental plaque accumulation and composition. All proteins were significantly (alpha = 0.05) correlated with each other (r = 0.38-0.52, p less than 0.001). There was only one axis of common variation among proteins, and that axis was significantly correlated (p less than 0.001) with total protein (r = 0.84) and flow rate (r = -0.56). That pattern deviated from the previous finding that proteins of acinar origin tended to vary independently from proteins of ductal origin in stimulated parotid saliva. The difference between parotid and whole saliva may reflect constitutive secretion of all proteins at low levels of stimulation. Common variation of unstimulated saliva proteins suggests that antimicrobial actions can be compared in subjects at population extremes. There were no significant associations between antimicrobial proteins in whole saliva and measures of health status or plaque accumulation. However, the proportions of Streptococcus sanguis were significantly correlated with lysozyme (r = -0.26), lactoferrin (r = -0.34), peroxidase (r = -0.30), total protein (r = -0.37), flow rate (r = 0.24) and principal-components scores (r = -0.33) in a subset of subjects (n = 85) where commercial biochemical tests were used to supplement species identification by colony morphology. Those findings may indicate that saliva antimicrobial proteins can affect the composition of dental plaque.

US Army Institute of Dental Research Annual Progress Report Fiscal Year 1981 (1 October 1980 - 30 September 1981)

DTIC Science & Technology

1981-10-01

Oral Biology) DA OF 6024 Identification and Control of Orofacial Infections 9 of Military Importance (Oral Biology) DA OG 8676 The Secondary Effect of...I. -SA h ImS-CII1 CIAN.IIIC..Ia CAR I 23. (U) Emiergency dental restorative work in the field often involves pulpal pain , inflamma~tion and infection...are being considered for field use. --. A D, ’-07-A49 PROJE1JT NUMBER 31161102BS10 IDENTIFICATION AND CDNTWOL OF OROFACIAL INFECfIONS OF MILITARY

Polymerase chain reaction-based denaturing gradient gel electrophoresis in the evaluation of oral microbiota.

PubMed

Li, Y; Saxena, D; Barnes, V M; Trivedi, H M; Ge, Y; Xu, T

2006-10-01

Clinical evaluation of oral microbial reduction after a standard prophylactic treatment has traditionally been based on bacterial cultivation methods. However, not all microbes in saliva or dental plaque can be cultivated. Polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE) is a cultivation-independent molecular fingerprinting technique that allows the assessment of the predominant bacterial species present in the oral cavity. This study sought to evaluate the oral microbial changes that occurred after a standard prophylactic treatment with a conventional oral care product using PCR-DGGE. Twelve healthy adults participated in the study. Pooled plaque samples were collected at baseline, 24 h after prophylaxis (T1), and 4 days after toothbrushing with fluoride toothpaste (T4). The total microbial genomic DNA of the plaque was isolated. PCR was performed with a set of universal bacterial 16S rDNA primers. The PCR-amplified 16S rDNA fragments were separated by DGGE. The effects of the treatment and of dental brushing were assessed by comparing the PCR-DGGE fingerprinting profiles. The mean numbers of detected PCR amplicons were 22.3 +/- 6.1 for the baseline group, 13.0 +/- 3.1 for the T1 group, and 13.5 +/- 4.3 for the T4 group; the differences among the three groups were statistically significant (P < 0.01). The study also found a significant difference in the mean similarities of microbial profiles between the baseline and the treatment groups (P < 0.001). PCR-based DGGE has been shown to be an excellent means of rapidly and accurately assessing oral microbial changes in this clinical study.

Understanding Caries From the Oral Microbiome Perspective.

PubMed

Tanner, Anne C R; Kressirer, Christine A; Faller, Lina L

2016-07-01

Dental caries is a major disease of the oral cavity with profound clinical significance. Caries results from a transition of a healthy oral microbiome into an acidogenic community of decreased microbial diversity in response to excessive dietary sugar intake. Microbiological cultivation, molecular identification, gene expression and metabolomic analyses show the importance of the entire microbial community in understanding the role of the microbiome in the pathology of caries.

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.

Oral Lactobacilli and Dental Caries

PubMed Central

Caufield, P.W.; Schön, C.N.; Saraithong, P.; Li, Y.; Argimón, S.

2015-01-01

Lactobacilli have been associated with dental caries for over a century. Here, we review the pertinent literature along with findings from our own study to formulate a working hypothesis about the natural history and role of lactobacilli. Unlike most indigenous microbes that stably colonize a host, lactobacilli appear to be planktonic, opportunistic settlers that can gather and multiply only in certain restrictive niches of the host, at least within the oral cavity. We postulate that the following essential requirements are necessary for sustained colonization of lactobacilli in humans: 1) a stagnant, retentive niche that is mostly anaerobic; 2) a low pH milieu; and 3) ready access to carbohydrates. Three sites on the human body meet these specifications: caries lesions, the stomach, and the vagina. Only a handful of Lactobacillus species is found in caries lesions, but they are largely absent in caries-free children. Lactobacilli present in caries lesions represent both a major contributor to caries progression and a major reservoir to the gastrointestinal (GI) tract. We extend the assertion from other investigators that lactobacilli found in the GI tract originate in the oral cavity by proposing that lactobacilli in the oral cavity arise from caries lesions. This, in turn, leads us to reflect on the health implications of the lactobacilli in the mouth and downstream GI and to ponder whether these or any of the Lactobacillus species are truly indigenous to the human GI tract or the oral cavity. PMID:25758458

Targeting of Streptococcus mutans Biofilms by a Novel Small Molecule Prevents Dental Caries and Preserves the Oral Microbiome.

PubMed

Garcia, S S; Blackledge, M S; Michalek, S; Su, L; Ptacek, T; Eipers, P; Morrow, C; Lefkowitz, E J; Melander, C; Wu, H

2017-07-01

Dental caries is a costly and prevalent disease characterized by the demineralization of the tooth's enamel. Disease outcome is influenced by host factors, dietary intake, cariogenic bacteria, and other microbes. The cariogenic bacterial species Streptococcus mutans metabolizes sucrose to initiate biofilm formation on the tooth surface and consequently produces lactic acid to degrade the tooth's enamel. Persistence of S. mutans biofilms in the oral cavity can lead to tooth decay. To date, no anticaries therapies that specifically target S. mutans biofilms but do not disturb the overall oral microbiome are available. We screened a library of 2-aminoimidazole antibiofilm compounds with a biofilm dispersion assay and identified a small molecule that specifically targets S. mutans biofilms. At 5 µM, the small molecule annotated 3F1 dispersed 50% of the established S. mutans biofilm but did not disperse biofilms formed by the commensal species Streptococcus sanguinis or Streptococcus gordonii. 3F1 dispersed S. mutans biofilms independently of biofilm-related factors such as antigen I/II and glucosyltransferases. 3F1 treatment effectively prevented dental caries by controlling S. mutans in a rat caries model without perturbing the oral microbiota. Our study demonstrates that selective targeting of S. mutans biofilms by 3F1 was able to effectively reduce dental caries in vivo without affecting the overall oral microbiota shaped by the intake of dietary sugars, suggesting that the pathogenic biofilm-specific treatment is a viable strategy for disease prevention.

Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study.

PubMed

Fan, Xiaozhou; Alekseyenko, Alexander V; Wu, Jing; Peters, Brandilyn A; Jacobs, Eric J; Gapstur, Susan M; Purdue, Mark P; Abnet, Christian C; Stolzenberg-Solomon, Rachael; Miller, George; Ravel, Jacques; Hayes, Richard B; Ahn, Jiyoung

2018-01-01

A history of periodontal disease and the presence of circulating antibodies to selected oral pathogens have been associated with increased risk of pancreatic cancer; however, direct relationships of oral microbes with pancreatic cancer have not been evaluated in prospective studies. We examine the relationship of oral microbiota with subsequent risk of pancreatic cancer in a large nested case-control study. We selected 361 incident adenocarcinoma of pancreas and 371 matched controls from two prospective cohort studies, the American Cancer Society Cancer Prevention Study II and the National Cancer Institute Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. From pre-diagnostic oral wash samples, we characterised the composition of the oral microbiota using bacterial 16S ribosomal RNA (16S rRNA) gene sequencing. The associations between oral microbiota and risk of pancreatic cancer, controlling for the random effect of cohorts and other covariates, were examined using traditional and L1-penalised least absolute shrinkage and selection operator logistic regression. Carriage of oral pathogens, Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans , were associated with higher risk of pancreatic cancer (adjusted OR for presence vs absence=1.60 and 95% CI 1.15 to 2.22; OR=2.20 and 95% CI 1.16 to 4.18, respectively). Phylum Fusobacteria and its genus Leptotrichia were associated with decreased pancreatic cancer risk (OR per per cent increase of relative abundance=0.94 and 95% CI 0.89 to 0.99; OR=0.87 and 95% CI 0.79 to 0.95, respectively). Risks related to these phylotypes remained after exclusion of cases that developed within 2 years of sample collection, reducing the likelihood of reverse causation in this prospective study. This study provides supportive evidence that oral microbiota may play a role in the aetiology of pancreatic cancer. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

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

Clinically Detectable Dental Identifiers Observed in Intra-oral Photographs and Extra-oral Radiographs, Validated for Human Identification Purposes.

PubMed

Angelakopoulos, Nikolaos; Franco, Ademir; Willems, Guy; Fieuws, Steffen; Thevissen, Patrick

2017-07-01

Screening the prevalence and pattern of dental identifiers contributes toward the process of human identification. This research investigated the uniqueness of clinical dental identifiers in photographs and radiographs. Panoramic and lateral cephalometric radiographs and five intra-oral photographs of 1727 subjects were used. In a target set, two observers examined different subjects. In a subset, both observers examined the same subjects (source set). The distance between source and target subjects was quantified for each identifier. The percentage of subjects in the target set being at least as close as the correct subject was assessed. The number of molars (34.6%), missing teeth (42%), and displaced teeth (59.9%) were the most unique identifiers in photographs and panoramic and lateral cephalometric radiographs, respectively. The pattern of rotated teeth (14.9%) was the most unique in photographs, while displaced teeth was in panoramic (37.6%) and lateral cephalometric (54.8%) radiographs. Morphological identifiers were the most unique, highlighting their importance for human identifications. © 2016 American Academy of Forensic Sciences.

Identification of Candida species in the oral cavity of diabetic patients

PubMed Central

Mohammadi, F; Javaheri, MR; Nekoeian, S; Dehghan, P

2016-01-01

Background and Purpose: Diabetic patients are more susceptible to oral candidiasis infection than non-diabetics due to the factors promoting oral carriage of Candida. Several factors can increase colonization of Candida species in the oral cavity such as xerostomia, which reduces the salivary flow and is a salivary pH disorder. In the current study, we aimed to identify and compare the colonization level of Candida spp. in the oral cavity of diabetic and non-diabetic groups. Materials and Methods: Swabs were taken from the mouth of 106 participants and were cultured on Sabouraud dextrose agar (SDA) medium. Likewise, the saliva samples were collected for salivary glucose and pH measurements. The study was performed during June 2014-September 2015 on two groups of diabetic patients (n=58) and non-diabetics (n=48) as the control group. The Candida spp. were identified with PCR-restriction fragment length polymorphism (RFLP) using the restriction enzymes HinfI and MspI and were differentiated by culture on CHROMagar Candida medium. Results: The frequency of Candida spp. was higher in diabetic patients compared to non-diabetics. The most frequent Candida spp. in the diabetic patients were Candida albicans (%36.2), C. Krusei (%10.4), C. Glabrata (%5.1), and C. tropcalis .(%3.4)Likewise, C. albicans was the most frequent species (%27) in the non-diabetic individuals. In this study, the results of both methods for identification of the isolates were consistent with each other. Conclusion: Xerostomia and disturbance of physiological factors including pH and glucose can promote overgrowth of Candida flora in the oral cavity. These factors are considered important predisposing factors for oral candidiasis in diabetic patients. In the present study, it was observed that application of CHROMagar Candida and PCR-RFLP methods at the same time contributes to more accurate identification of isolates. PMID:28681013

Oral Delivery of Protein Drugs Bioencapsulated in Plant Cells.

PubMed

Kwon, Kwang-Chul; Daniell, Henry

2016-08-01

Plants cells are now approved by the FDA for cost-effective production of protein drugs (PDs) in large-scale current Good Manufacturing Practice (cGMP) hydroponic growth facilities. In lyophilized plant cells, PDs are stable at ambient temperature for several years, maintaining their folding and efficacy. Upon oral delivery, PDs bioencapsulated in plant cells are protected in the stomach from acids and enzymes but are subsequently released into the gut lumen by microbes that digest the plant cell wall. The large mucosal area of the human intestine offers an ideal system for oral drug delivery. When tags (receptor-binding proteins or cell-penetrating peptides) are fused to PDs, they efficiently cross the intestinal epithelium and are delivered to the circulatory or immune system. Unique tags to deliver PDs to human immune or nonimmune cells have been developed recently. After crossing the epithelium, ubiquitous proteases cleave off tags at engineered sites. PDs are also delivered to the brain or retina by crossing the blood-brain or retinal barriers. This review highlights recent advances in PD delivery to treat Alzheimer's disease, diabetes, hypertension, Gaucher's or ocular diseases, as well as the development of affordable drugs by eliminating prohibitively expensive purification, cold chain and sterile delivery.

The Biofilm Community-Rebels with a Cause.

PubMed

Aruni, A Wilson; Dou, Yuetan; Mishra, Arunima; Fletcher, Hansel M

2015-03-01

Oral Biofilms are one of the most complex and diverse ecosystem developed by successive colonization of more than 600 bacterial taxa. Development starts with the attachment of early colonizers such as Actinomyces species and oral streptococci on the acquired pellicle and tooth enamel. These bacteria not only adhere to tooth surface but also interact with each other and lay foundation for attachment of bridging colonizer such as Fusobacterium nucleatum followed by late colonizers including the red complex species: Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola -the founders of periodontal disease. As the biofilm progresses from supragingival sites to subgingival sites, the environment changes from aerobic to anaerobic thus favoring the growth of mainly Gram-negative obligate anaerobes while restricting the growth of the early Gram-positive facultative aerobes. Microbes present at supragingival level are mainly related to gingivitis and root-caries whereas subgingival species advance the destruction of teeth supporting tissues and thus causing periodontitis. This review summarizes our present understanding and recent developments on the characteristic features of supra- and subgingival biofilms, interaction between different genera and species of bacteria constituting these biofilms and draws our attention to the role of some of the recently discovered members of the oral community.

The Biofilm Community-Rebels with a Cause

PubMed Central

Aruni, A. Wilson; Dou, Yuetan; Mishra, Arunima; Fletcher, Hansel M.

2015-01-01

Oral Biofilms are one of the most complex and diverse ecosystem developed by successive colonization of more than 600 bacterial taxa. Development starts with the attachment of early colonizers such as Actinomyces species and oral streptococci on the acquired pellicle and tooth enamel. These bacteria not only adhere to tooth surface but also interact with each other and lay foundation for attachment of bridging colonizer such as Fusobacterium nucleatum followed by late colonizers including the red complex species: Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola-the founders of periodontal disease. As the biofilm progresses from supragingival sites to subgingival sites, the environment changes from aerobic to anaerobic thus favoring the growth of mainly Gram-negative obligate anaerobes while restricting the growth of the early Gram-positive facultative aerobes. Microbes present at supragingival level are mainly related to gingivitis and root-caries whereas subgingival species advance the destruction of teeth supporting tissues and thus causing periodontitis. This review summarizes our present understanding and recent developments on the characteristic features of supra- and subgingival biofilms, interaction between different genera and species of bacteria constituting these biofilms and draws our attention to the role of some of the recently discovered members of the oral community. PMID:26120510

IL-22 mediates the oral mucosal wound healing via STAT3 in keratinocytes.

PubMed

Yu, Ran; Ding, Yumei; Zhu, Lijuan; Qu, Yinying; Zhang, Chenguang; Liu, Lin; Chen, Lili

2016-12-01

Wounds are common in the oral cavity. During wound healing, several cytokines are released, which are probably helpful in providing wound debridement, removal of damaged tissues and microbes. Most of the target cells of IL-22 are epithelial cells, which play an important role in mucosa immunity. The function of IL-22 in oral diseases is not well understood. We investigated the expression level of IL-22, collagen I and p-stat3 (Tyr705) via a mice tongue wound model in vivo and detected the effect of IL-22 on the expression of MMP-1, type I collagen and p-stat3 in keratinocytes. IL-22 and p-stat3 were associated with wound healing, and STAT3 was activated when the keratinocytes or the tongue tissue were stimulated by IL-22. In addition, IL-22 could mediate gene expression involved in wounds involving keratinocytes, such as type I collagen and MMP-1, which may contribute to scarless healing. Our study suggests that IL-22 mediates wound healing via STAT3 in keratinocytes. This study reveals a new role for IL-22 in mediating wound healing. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular markers associated with development and progression of potentially premalignant oral epithelial lesions: Current knowledge and future implications.

PubMed

Nikitakis, Nikolaos G; Pentenero, Monica; Georgaki, Maria; Poh, Catherine F; Peterson, Douglas E; Edwards, Paul; Lingen, Mark; Sauk, John J

2018-06-01

Identification and management of potentially premalignant oral epithelial lesions (PPOELs) at highest risk of malignant transformation holds great promise for successful secondary prevention of oral squamous cell carcinoma, potentially reducing oral cancer morbidity and mortality. However, to date, neither clinical nor histopathologic validated risk predictors that can reliably predict which PPOELs will definitively progress to malignancy have been identified. In addition, the management of PPOELs remains a major challenge. Arguably, progress in the prevention and treatment of oral premalignancy and cancer will require improved understanding of the underlying molecular mechanisms, facilitating the discovery of diagnostic, prognostic, and predictive markers, as well as the identification of novel targeted therapeutics. This review provides a synopsis of the molecular biomarkers that have been studied in PPOELs and have been correlated with the presence and grade of dysplasia and/or their propensity to undergo malignant transformation to oral squamous cell carcinoma. The emphasis is on highlighting new emerging research fields, particularly epigenetic events, including methylation and micro-RNA regulation. Several promising biomarkers are highlighted. Current limitations and challenges are discussed. Recommendations for future focused research areas, to validate and promote clinically useful applications, are offered. Copyright © 2018 Elsevier Inc. All rights reserved.

Microbiota in Allergy and Asthma and the Emerging Relationship with the Gut Microbiome

PubMed Central

Fujimura, Kei E.; Lynch, Susan V.

2015-01-01

Asthma and atopy, classically associated with hyper-activation of the T helper 2 (Th2) arm of adaptive immunity, are amongst the most common chronic illnesses worldwide. Emerging evidence relates atopy and asthma to the composition and function of the human microbiome, the collection of microbes that reside in and on and interact with the human body. The ability to interrogate microbial ecology of the human host is due in large part to recent technological developments that permit identification of microbes and their products using culture-independent molecular detection techniques. In this review we explore the roles of respiratory, gut and environmental microbiomes in asthma and allergic disease development, manifestation and attenuation. Though still a relatively nascent field of research, evidence to date suggests that the airway and/or gut microbiome may represent fertile targets for prevention or management of allergic asthma and other diseases in which adaptive immune dysfunction is a prominent feature. PMID:25974301

Assessment of microorganisms from Indonesian Oil Fields

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

Kadarwati, S.; Udiharto, M.; Rahman, M.

1995-12-31

Petroleum resources have been the mainstay of the national development in Indonesia. However, resources are being depleted after over a century of exploitation, while the demand continues to grow with the rapid economic development of the country. In facing the problem, EOR has been applied in Indonesia, such as the steamflooding project in Duri field, but a more energy efficient technology would be preferable. Therefore, MEOR has been recommended as a promising solution. Our study, aimed at finding indigenous microorganisms which can be developed for application in MEOR, has isolated microbes from some oil fields of Indonesia. These microorganisms havemore » been identified, their activities studied, and the effects of their metabolisms examined. This paper describes the research carried out by LEMIGAS in this respect, giving details on the methods of sampling, incubation, identification, and activation of the microbes as well as tests on the effects of their metabolites, with particular attention to those with potential for application in MEOR.« less

Microbiota in allergy and asthma and the emerging relationship with the gut microbiome.

PubMed

Fujimura, Kei E; Lynch, Susan V

2015-05-13

Asthma and atopy, classically associated with hyper-activation of the T helper 2 (Th2) arm of adaptive immunity, are among the most common chronic illnesses worldwide. Emerging evidence relates atopy and asthma to the composition and function of the human microbiome, the collection of microbes that reside in and on and interact with the human body. The ability to interrogate microbial ecology of the human host is due in large part to recent technological developments that permit identification of microbes and their products using culture-independent molecular detection techniques. In this review we explore the roles of respiratory, gut, and environmental microbiomes in asthma and allergic disease development, manifestation, and attenuation. Though still a relatively nascent field of research, evidence to date suggests that the airway and/or gut microbiome may represent fertile targets for prevention or management of allergic asthma and other diseases in which adaptive immune dysfunction is a prominent feature. Copyright © 2015 Elsevier Inc. All rights reserved.

Sequencing of the Cheese Microbiome and Its Relevance to Industry.

PubMed

Yeluri Jonnala, Bhagya R; McSweeney, Paul L H; Sheehan, Jeremiah J; Cotter, Paul D

2018-01-01

The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.

An Orthogonal and pH-Tunable Sensor-Selector for Muconic Acid Biosynthesis in Yeast.

PubMed

Snoek, Tim; Romero-Suarez, David; Zhang, Jie; Ambri, Francesca; Skjoedt, Mette L; Sudarsan, Suresh; Jensen, Michael K; Keasling, Jay D

2018-04-20

Microbes offer enormous potential for production of industrially relevant chemicals and therapeutics, yet the rapid identification of high-producing microbes from large genetic libraries is a major bottleneck in modern cell factory development. Here, we develop and apply a synthetic selection system in Saccharomyces cerevisiae that couples the concentration of muconic acid, a plastic precursor, to cell fitness by using the prokaryotic transcriptional regulator BenM driving an antibiotic resistance gene. We show that the sensor-selector does not affect production nor fitness, and find that tuning pH of the cultivation medium limits the rise of nonproducing cheaters. We apply the sensor-selector to selectively enrich for best-producing variants out of a large library of muconic acid production strains, and identify an isolate that produces more than 2 g/L muconic acid in a bioreactor. We expect that this sensor-selector can aid the development of other synthetic selection systems based on allosteric transcription factors.

Gene-Based Detection of Microorganisms in Environmental Samples Using PCR

NASA Technical Reports Server (NTRS)

Glass, John I.; Lefkowitz, Elliot J.; Cassell, Gail H.; Wechser, Mark; Taylor, Theresa B.; Albin, Michael; Paszko-Kolva, Christine; Roman, Monsi C.

1997-01-01

Contaminating microorganisms pose a serious potential risk to the crew's well being and water system integrity aboard the International Space Station (ISS). We are developing a gene-based microbial monitor that functions by replicating specific segments of DNA as much as 10(exp 12) x. Thus a single molecule of DNA can be replicated to detectable levels, and the kinetics of that molecule's accumulation can be used to determine the original concentration of specific microorganisms in a sample. Referred to as the polymerase chain reaction (PCR), this enzymatic amplification of specific segments of the DNA or RNA from contaminating microbes offers the promise of rapid, sensitive, quantitative detection and identification of bacteria, fungi, viruses, and parasites. We envision a small instrument capable of assaying an ISS water sample for 48 different microbes in a 24 hour period. We will report on both the developments in the chemistry necessary for the PCR assays to detect microbial contaminants in ISS water, and on progress towards the miniaturization and automation of the instrumentation.

Hardy Bacterium Isolated From Two Geographically Distinct Spacecraft Assembly Cleanroom Facilities

NASA Technical Reports Server (NTRS)

Vaisham-payan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra; Moissl-Eichinger, Christine

2012-01-01

Earlier studies have confirmed that a tenacious hardy bacterial population manages to persist and survive throughout a spacecraft assembly process. The widespread detection of these organisms underscores the challenges in eliminating them completely. Only comprehensive and repetitive microbial diversity studies of geographically distinct cleanroom facilities will bolster the understanding of planetary protection relevant microbes. Extensive characterizations of the physiological traits demonstrated by cleanroom microbes will aid NASA in gauging the forward contamination risk that hardy bacteria (such as Tersicoccus phoenicis) pose to spacecraft. This study reports on the isolation and identification of two gram-positive, non-motile, non-spore-forming bacterial strains from the spacecraft assembly facilities at Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana. DNA-DNA relatedness values between the novel strains indicates that these novel strains were indeed members of a same species. Phylogenetic evidence derived from a 16S ribosomal DNA analysis indicated that both the novel strains are less closely related to all other Arthrobacter species.

Rhizobium–legume symbiosis shares an exocytotic pathway required for arbuscule formation

PubMed Central

Ivanov, Sergey; Fedorova, Elena E.; Limpens, Erik; De Mita, Stephane; Genre, Andrea; Bonfante, Paola; Bisseling, Ton

2012-01-01

Endosymbiotic interactions are characterized by the formation of specialized membrane compartments, by the host in which the microbes are hosted, in an intracellular manner. Two well-studied examples, which are of major agricultural and ecological importance, are the widespread arbuscular mycorrhizal symbiosis and the Rhizobium–legume symbiosis. In both symbioses, the specialized host membrane that surrounds the microbes forms a symbiotic interface, which facilitates the exchange of, for example, nutrients in a controlled manner and, therefore, forms the heart of endosymbiosis. Despite their key importance, the molecular and cellular mechanisms underlying the formation of these membrane interfaces are largely unknown. Recent studies strongly suggest that the Rhizobium–legume symbiosis coopted a signaling pathway, including receptor, from the more ancient arbuscular mycorrhizal symbiosis to form a symbiotic interface. Here, we show that two highly homologous exocytotic vesicle-associated membrane proteins (VAMPs) are required for formation of the symbiotic membrane interface in both interactions. Silencing of these Medicago VAMP72 genes has a minor effect on nonsymbiotic plant development and nodule formation. However, it blocks symbiosome as well as arbuscule formation, whereas root colonization by the microbes is not affected. Identification of these VAMP72s as common symbiotic regulators in exocytotic vesicle trafficking suggests that the ancient exocytotic pathway forming the periarbuscular membrane compartment has also been coopted in the Rhizobium–legume symbiosis. PMID:22566631

Contemporary issues: diseases with a food vector.

PubMed

Archer, D L; Young, F E

1988-10-01

Foodborne disease has become a contemporary issue. Several large, well-publicized outbreaks of foodborne disease have heightened public awareness that harmful microorganisms may be present in food and that chronic as well as acute disease may be caused by foodborne microbes. The field of food microbiology has likewise experienced a resurgence of interest. New tools, such as recombinant deoxyribonucleic acid technology and monoclonal antibody production, used to elucidate microbial virulence factors have facilitated identification of disease-causing microbes once thought to be harmless and demonstrated the complexity of individual virulence mechanisms previously considered to be well understood. Foodborne pathogens are also causing disease via some surprising food vectors, such as chopped, bottled garlic and sauteed onions. In addition to acute gastrointestinal disturbances, certain microorganisms may, through complex interactions with the human immune response, cause chronic diseases that affect several major organ systems. These microbes are serving as models in studies of molecular mimicry and genetic interrelatedness of procaryotes and eucaryotes. Other recently recognized attributes of foodborne microorganisms, such as the heat shock phenomenon and the possible nonculturability of some bacteria, may affect their ability to cause disease in humans. Because foodborne disease is a major cause of morbidity and mortality, the study of these diseases and their causative microorganisms presents a unique challenge to many professionals in the subdisciplines of microbiology, epidemiology, and clinical medicine.

Psychrotrophic bacteria in milk: How much do we really know?

PubMed Central

de Oliveira, Gislene B.; Favarin, Luciana; Luchese, Rosa H.; McIntosh, Douglas

2015-01-01

The occurrence of psychrotrophic bacteria in raw milk is studied worldwide due to the difficulties associated with controlling their growth during cold storage and the consequent negative effects upon fluid milk or dairy products. Among the psychrotrophic bacteria, the genus Pseudomonas (represented primarily by P. fluorescens) has been highlighted as the cause of numerous defects in dairy products. In light of its perceived predominance, this species has frequently been chosen as a model organism to assess the effects of psychrotrophic bacteria on milk or to evaluate the efficacy of control measures. However, recent findings derived from the application of molecular biological techniques have exposed a number of deficiencies in our knowledge of the biology of milk-associated psychrotrophs. Furthermore, it has been revealed that microbe to microbe communication plays a significant role in determining both the identities and the extent to which different groups of microbes develop during cold storage. The application of molecular identification methods has exposed errors in the classification of members of the genus Pseudomonas isolated from cold stored milk and has stimulated a reevaluation of the presumed status of P. fluorescens as the predominant milk-associated psychrotrophic species. This article presents a succinct review of data from studies on psychrotrophic bacteria in milk, some of which contest established theories in relation to the microbiology of cold stored raw milk, and poses the question: how much do we really know? PMID:26273245

Contemporary issues: diseases with a food vector.

PubMed Central

Archer, D L; Young, F E

1988-01-01

Foodborne disease has become a contemporary issue. Several large, well-publicized outbreaks of foodborne disease have heightened public awareness that harmful microorganisms may be present in food and that chronic as well as acute disease may be caused by foodborne microbes. The field of food microbiology has likewise experienced a resurgence of interest. New tools, such as recombinant deoxyribonucleic acid technology and monoclonal antibody production, used to elucidate microbial virulence factors have facilitated identification of disease-causing microbes once thought to be harmless and demonstrated the complexity of individual virulence mechanisms previously considered to be well understood. Foodborne pathogens are also causing disease via some surprising food vectors, such as chopped, bottled garlic and sauteed onions. In addition to acute gastrointestinal disturbances, certain microorganisms may, through complex interactions with the human immune response, cause chronic diseases that affect several major organ systems. These microbes are serving as models in studies of molecular mimicry and genetic interrelatedness of procaryotes and eucaryotes. Other recently recognized attributes of foodborne microorganisms, such as the heat shock phenomenon and the possible nonculturability of some bacteria, may affect their ability to cause disease in humans. Because foodborne disease is a major cause of morbidity and mortality, the study of these diseases and their causative microorganisms presents a unique challenge to many professionals in the subdisciplines of microbiology, epidemiology, and clinical medicine. PMID:3069199

Psychrotrophic bacteria in milk: How much do we really know?

PubMed

de Oliveira, Gislene B; Favarin, Luciana; Luchese, Rosa H; McIntosh, Douglas

2015-06-01

The occurrence of psychrotrophic bacteria in raw milk is studied worldwide due to the difficulties associated with controlling their growth during cold storage and the consequent negative effects upon fluid milk or dairy products. Among the psychrotrophic bacteria, the genus Pseudomonas (represented primarily by P. fluorescens) has been highlighted as the cause of numerous defects in dairy products. In light of its perceived predominance, this species has frequently been chosen as a model organism to assess the effects of psychrotrophic bacteria on milk or to evaluate the efficacy of control measures. However, recent findings derived from the application of molecular biological techniques have exposed a number of deficiencies in our knowledge of the biology of milk-associated psychrotrophs. Furthermore, it has been revealed that microbe to microbe communication plays a significant role in determining both the identities and the extent to which different groups of microbes develop during cold storage. The application of molecular identification methods has exposed errors in the classification of members of the genus Pseudomonas isolated from cold stored milk and has stimulated a reevaluation of the presumed status of P. fluorescens as the predominant milk-associated psychrotrophic species. This article presents a succinct review of data from studies on psychrotrophic bacteria in milk, some of which contest established theories in relation to the microbiology of cold stored raw milk, and poses the question: how much do we really know?

Identification of quinazoline based inhibitors of IRAK4 for the treatment of inflammation

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

Smith, Graham F.; Altman, Michael D.; Andresen, Brian

Interleukin-1 receptor associated kinase 4 (IRAK4) has been implicated in IL-1R and TLR based signaling. Therefore selective inhibition of the kinase activity of this protein represents an attractive target for the treatment of inflammatory diseases. Medicinal chemistry optimization of high throughput screening (HTS) hits with the help of structure based drug design led to the identification of orally-bioavailable quinazoline based IRAK4 inhibitors with excellent pharmacokinetic profile and kinase selectivity. These highly selective IRAK4 compounds show activity in vivo via oral dosing in a TLR7 driven model of inflammation.

A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities

PubMed Central

Leung, Kaston; Zahn, Hans; Leaver, Timothy; Konwar, Kishori M.; Hanson, Niels W.; Pagé, Antoine P.; Lo, Chien-Chi; Chain, Patrick S.; Hallam, Steven J.; Hansen, Carl L.

2012-01-01

We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with the sample compartmentalization and dispersion-free transport that is inherent to droplets. The device allows for the execution of user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging programmable sequences of picoliter-volume droplets containing reagents or cells. This functionality is enabled by “flow-controlled wetting,” a droplet docking and merging mechanism that exploits the physics of droplet flow through a channel to control the precise location of droplet wetting. The device also allows for automated cross-contamination-free recovery of reaction products from individual chambers into standard microfuge tubes for downstream analysis. The combined features of programmability, addressability, and selective recovery provide a general hardware platform that can be reprogrammed for multiple applications. We demonstrate this versatility by implementing multiple single-cell experiment types with this device: bacterial cell sorting and cultivation, taxonomic gene identification, and high-throughput single-cell whole genome amplification and sequencing using common laboratory strains. Finally, we apply the device to genome analysis of single cells and microbial consortia from diverse environmental samples including a marine enrichment culture, deep-sea sediments, and the human oral cavity. The resulting datasets capture genotypic properties of individual cells and illuminate known and potentially unique partnerships between microbial community members. PMID:22547789

Efficacy of chlorhexidine digluconate-containing formulations and other mouthrinses against periodontopathogenic microorganisms.

PubMed

Eick, Sigrun; Goltz, Susann; Nietzsche, Sandor; Jentsch, Holger; Pfister, Wolfgang

2011-09-01

To determine in vitro the action of chlorhexidine digluconate and different commercially available mouthrinses on oral microorganisms. Minimal inhibitory concentrations and possible induction of resistance by chlorhexidine digluconate, an essential oil-containing mouthwash and an amine fluoride/stannous fluoride solution, were determined against microorganisms normally found in the oral cavity (10 streptococci, 2 enterobacteria, 1 Candida albicans, 8 Porphyromonas gingivalis, 6 Aggregatibacter actinomycetemcomitans, and 1 Fusobacterium nucleatum). Further, the effect of a 1-minute exposure on cell and bacterial viability was studied. The susceptibility of the oral microorganisms to chlorhexidine digluconate ranged from 0.01% to 0.50%. Passages on agar plates containing subinhibitory concentrations of chlorhexidine digluconate resulted in a transitory moderate increase in the tolerance to chlorhexidine digluconate in five of the 24 isolates. After 1 minute of exposure, chlorhexidine digluconate solutions as well as the essential oil and the amine/stannous fluoride-containing solutions showed a high activity against the tested microorganisms. Commercially available chlorhexidine digluconate formulations (ie, those with antidiscoloration systems) were partly less efficient than the corresponding manually prepared chlorhexidine digluconate preparation. The determination of MTT resulted in a strong cytotoxicity of all tested preparations to gingival fibroblasts. The results indicate that most of the chlorhexidine digluconate formulations as well as essential oil and the amine fluoride/stannous fluoride solutions are active against oral microbes. Long-term use of these agents would not result in emergent antimicrobial resistance.

Magnetic Resonance Angiography Using Fresh Blood Imaging in Oral and Maxillofacial Regions

PubMed Central

Oda, Masafumi; Tanaka, Tatsurou; Kito, Shinji; Habu, Manabu; Kodama, Masaaki; Kokuryo, Shinya; Miyamoto, Ikuya; Yoshiga, Daigo; Yamauchi, Kensuke; Nogami, Shinnosuke; Wakasugi-Sato, Nao; Matsumoto-Takeda, Shinobu; Ishikawa, Ayataka; Nishida, Ikuko; Saeki, Katsura; Morikawa, Kazumasa; Matsuo, Kou; Seta, Yuji; Yamashita, Yoshihiro; Maki, Kenshi; Tominaga, Kazuhiro; Morimoto, Yasuhiro

2012-01-01

The present paper provides general dentists with an introduction to the clinical applications and significance of magnetic resonance angiography (MRA) in the oral and maxillofacial regions. Specifically, the method and characteristics of MRA are first explained using the relevant MR sequences. Next, clinical applications to the oral and maxillofacial regions, such as identification of hemangiomas and surrounding vessels by MRA, are discussed. Moreover, the clinical significance of MRA for other regions is presented to elucidate future clinical applications of MRA in the oral and maxillofacial regions. PMID:23118751

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

PubMed Central

Singhal, Neelja; Kumar, Manish; Kanaujia, Pawan K.; Virdi, Jugsharan S.

2015-01-01

Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi. PMID:26300860

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis.

PubMed

Singhal, Neelja; Kumar, Manish; Kanaujia, Pawan K; Virdi, Jugsharan S

2015-01-01

Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.

Impact of formal training on agreement of videofluoroscopic swallowing study interpretation across and within disciplines.

PubMed

Silbergleit, Alice K; Cook, Diana; Kienzle, Scott; Boettcher, Erica; Myers, Daniel; Collins, Denise; Peterson, Edward; Silbergleit, Matthew A; Silbergleit, Richard

2018-04-04

Formal agreement studies on interpretation of the videofluoroscopic swallowing study (VFSS) procedure among speech-language pathologists, radiology house officers, and staff radiologists have not been pursued. Each of these professions participates in the procedure, interprets the examination, and writes separate reports on the findings. The aim of this study was to determine reliability of interpretation between and within the disciplines and to determine if structured training improved reliability. Thirteen speech-language pathologists (SLPs), ten diagnostic radiologists (RADs) and twenty-one diagnostic radiology house officers (HOs) participated in this study. Each group viewed 24 VFSS samples and rated the presence or absence of seven aberrant swallowing features as well as the presence of dysphagia and identification of oral dysphagia, pharyngeal dysphagia, or both. During part two, the groups were provided with a training session on normal and abnormal swallowing, using different VFSS samples from those in part one, followed by re-rating of the original 24 VFSS samples. A generalized estimating equations (GEE) approach with a binomial link function was used to examine each question separately. For each cluster of tests, as example, all pairwise comparisons between the three groups in the pretraining period, a Hochberg's correction for multiple testing was used to determine significance. A GEE approach with a binomial link function was used to compare the premeasure to postmeasure for each of the three groups of raters stratified by experience. The primary result revealed that the HO group scored significantly lower than the SLP and RAD group on identification of the presence of dysphagia (p = 0.008; p = 0.001, respectively), identification of oral phase dysphagia (p = 0.003; p = 0.001, respectively), and identification of both oral and pharyngeal phase dysphagia, (p = 0.014, p = 0.001, respectively) pretraining. Post training there was no statistically significant difference between the three groups on identification of dysphagia and identification of combined oral and pharyngeal dysphagia. Formal training to identify oropharyngeal dysphagia characteristics appears to improve accuracy of interpretation of the VFSS procedure for radiology house officers. Consideration to include formal training in this area for radiology residency training programs is recommended.

Design Aspects of a Case-Control Clinical Investigation of the Effect of HIV on Oral and Gastrointestinal Soluble Innate Factors and Microbes

PubMed Central

Phelan, Joan A.; Abrams, William R.; Norman, Robert G.; Li, Yihong; Laverty, Maura; Corby, Patricia M.; Nembhard, Jason; Neri, Dinah; Barber, Cheryl A.; Aberg, Judith A.; Fisch, Gene S.; Poles, Michael A.; Malamud, Daniel

2014-01-01

Introduction The impaired host defense system in HIV infection impacts the oral and gastrointestinal microbiota and associated opportunistic infections. Antiretroviral treatment is predicted to partially restore host defenses and decrease the oral manifestation of HIV/AIDS. Well-designed longitudinal studies are needed to better understand the interactions of soluble host defense proteins with bacteria and virus in HIV/AIDS. “Crosstalk” was designed as a longitudinal study of host responses along the gastrointestinal (GI) tract and interactions between defense molecules and bacteria in HIV infection and subsequent therapy. Purpose The clinical core formed the infrastructure for the study of the interactions between the proteome, microbiome and innate immune system. The core recruited and retained study subjects, scheduled visits, obtained demographic and medical data, assessed oral health status, collected samples, and guided analysis of the hypotheses. This manuscript presents a well-designed clinical core that may serve as a model for studies that combine clinical and laboratory data. Methods Crosstalk was a case-control longitudinal clinical study an initial planned enrollment of 170 subjects. HIV+ antiretroviral naïve subjects were followed for 9 visits over 96 weeks and HIV uninfected subjects for 3 visits over 24 weeks. Clinical prevalence of oral mucosal lesions, dental caries and periodontal disease were assessed. Results During the study, 116 subjects (47 HIV+, 69 HIV-) were enrolled. Cohorts of HIV+ and HIV- were demographically similar except for a larger proportion of women in the HIV- group. The most prevalent oral mucosal lesions were oral candidiasis and hairy leukoplakia in the HIV+ group. Discussion The clinical core was essential to enable the links between clinical and laboratory data. The study aims to determine specific differences between oral and GI tissues that account for unique patterns of opportunistic infections and to delineate the differences in their susceptibility to infection by HIV and their responses post-HAART. PMID:25409430

The oral microflora in obesity and type-2 diabetes

PubMed Central

Shillitoe, Edward; Weinstock, Ruth; Kim, Taewan; Simon, Howard; Planer, Jessica; Noonan, Susan; Cooney, Robert

2012-01-01

Background Type 2 diabetes mellitus (T2DM) is prevalent in people with obesity. It has been proposed that these conditions are related to specific features of the microflora of the mouth and lower gastrointestinal (GI) tract. Hyperglycemia often resolves quickly after Roux-en-Y gastric bypass (RYGB) but the role of the GI microflora cannot be examined easily because of reduced intestinal mobility. We propose that the study of microorganisms present in the mouth of patients undergoing RYGB will contribute to our understanding of the role of bacteria in the pathogenesis of T2DM. Objective To conduct a feasibility study to examine differences in oral microbes in obese patients with and without T2DM and to determine whether it is feasible to measure changes after gastric bypass surgery. Methods Individuals with morbid obesity (n=29), of whom 13 had T2DM, were studied. Oral rinses, stool samples, and blood samples were obtained before RYGB, and oral rinses and blood samples were obtained at 2 and 12 weeks postsurgery. Results Prior to surgery, participants with T2DM had slightly higher total levels of oral bacteria than those without diabetes. Those with HbA1c > 6.5% had rather lower levels of Bifidobacteria in the mouth and stool. At 2 weeks post-RYGB, patients with T2DM were able to reduce or discontinue their hypoglycemic medications. Stool samples could not be obtained but oral rinses were readily available. The levels of oral Bifidobacteria had increased tenfold and levels of circulating endotoxin and tumor necrosis factor-alpha had decreased. Conclusions The study of oral bacteria before and after RYGB is feasible and should be tested in larger patient populations to increase our understanding of the role of microorganisms in the pathogenesis of obesity and T2DM. PMID:23119124

Design aspects of a case-control clinical investigation of the effect of HIV on oral and gastrointestinal soluble innate factors and microbes.

PubMed

Phelan, Joan A; Abrams, William R; Norman, Robert G; Li, Yihong; Laverty, Maura; Corby, Patricia M; Nembhard, Jason; Neri, Dinah; Barber, Cheryl A; Aberg, Judith A; Fisch, Gene S; Poles, Michael A; Malamud, Daniel

2014-01-01

The impaired host defense system in HIV infection impacts the oral and gastrointestinal microbiota and associated opportunistic infections. Antiretroviral treatment is predicted to partially restore host defenses and decrease the oral manifestation of HIV/AIDS. Well-designed longitudinal studies are needed to better understand the interactions of soluble host defense proteins with bacteria and virus in HIV/AIDS. "Crosstalk" was designed as a longitudinal study of host responses along the gastrointestinal (GI) tract and interactions between defense molecules and bacteria in HIV infection and subsequent therapy. The clinical core formed the infrastructure for the study of the interactions between the proteome, microbiome and innate immune system. The core recruited and retained study subjects, scheduled visits, obtained demographic and medical data, assessed oral health status, collected samples, and guided analysis of the hypotheses. This manuscript presents a well-designed clinical core that may serve as a model for studies that combine clinical and laboratory data. Crosstalk was a case-control longitudinal clinical study an initial planned enrollment of 170 subjects. HIV+ antiretroviral naïve subjects were followed for 9 visits over 96 weeks and HIV uninfected subjects for 3 visits over 24 weeks. Clinical prevalence of oral mucosal lesions, dental caries and periodontal disease were assessed. During the study, 116 subjects (47 HIV+, 69 HIV-) were enrolled. Cohorts of HIV+ and HIV- were demographically similar except for a larger proportion of women in the HIV- group. The most prevalent oral mucosal lesions were oral candidiasis and hairy leukoplakia in the HIV+ group. The clinical core was essential to enable the links between clinical and laboratory data. The study aims to determine specific differences between oral and GI tissues that account for unique patterns of opportunistic infections and to delineate the differences in their susceptibility to infection by HIV and their responses post-HAART.

Evaluation of behavior change goal-setting action plan on oral health activity and status.

PubMed

Lepore, Lindsay M; Yoon, Richard K; Chinn, Courtney H; Chussid, Steven

2011-11-01

This experimental study determined if a "report card-like" oral health action plan was effective in improving oral health behaviors in a sample of 69 patients, ages 1 to 6 years. Participants were divided randomly into control and intervention groups. Data collected included dmft, plaque score, Streptococcus mutans levels and oral health behaviors. Participants in the intervention group received an oral health action plan that included: 1. child's current caries-risk status; 2. identification issues of concern; and 3. one "goal" to improve on for the next visit. All participants returned after two months for follow-up examination and data collection.

Review of nanomaterials in dentistry: interactions with the oral microenvironment, clinical applications, hazards, and benefits.

PubMed

Besinis, Alexandros; De Peralta, Tracy; Tredwin, Christopher J; Handy, Richard D

2015-03-24

Interest in the use of engineered nanomaterials (ENMs) as either nanomedicines or dental materials/devices in clinical dentistry is growing. This review aims to detail the ultrafine structure, chemical composition, and reactivity of dental tissues in the context of interactions with ENMs, including the saliva, pellicle layer, and oral biofilm; then describes the applications of ENMs in dentistry in context with beneficial clinical outcomes versus potential risks. The flow rate and quality of saliva are likely to influence the behavior of ENMs in the oral cavity, but how the protein corona formed on the ENMs will alter bioavailability, or interact with the structure and proteins of the pellicle layer, as well as microbes in the biofilm, remains unclear. The tooth enamel is a dense crystalline structure that is likely to act as a barrier to ENM penetration, but underlying dentinal tubules are not. Consequently, ENMs may be used to strengthen dentine or regenerate pulp tissue. ENMs have dental applications as antibacterials for infection control, as nanofillers to improve the mechanical and bioactive properties of restoration materials, and as novel coatings on dental implants. Dentifrices and some related personal care products are already available for oral health applications. Overall, the clinical benefits generally outweigh the hazards of using ENMs in the oral cavity, and the latter should not prevent the responsible innovation of nanotechnology in dentistry. However, the clinical safety regulations for dental materials have not been specifically updated for ENMs, and some guidance on occupational health for practitioners is also needed. Knowledge gaps for future research include the formation of protein corona in the oral cavity, ENM diffusion through clinically relevant biofilms, and mechanistic investigations on how ENMs strengthen the tooth structure.

Sequencing the Unknown

NASA Image and Video Library

2017-12-19

Being able to identify microbes in real time aboard the International Space Station, without having to send them back to Earth for identification first, would be revolutionary for the world of microbiology and space exploration, and the Genes in Space-3 team turned that possibility into a reality this year when it completed the first-ever sample-to-sequence process entirely aboard the space station. This advance could aid in the ability to diagnose and treat astronaut ailments in real time, as well as assisting in the identification of DNA-based life on other planets. It could also benefit other experiments aboard the orbiting laboratory. HD Download: https://archive.org/details/jsc2017m001160_Sequencing_the_Unknown _______________________________________ FOLLOW THE SPACE STATION! Twitter: https://twitter.com/Space_Station Facebook: https://www.facebook.com/ISS Instagram: https://instagram.com/iss/

The evidence of the rugoscopy effectiveness as a human identification method in patients submitted to rapid palatal expansion.

PubMed

Barbieri, Ana A; Scoralick, Raquel A; Naressi, Suely C M; Moraes, Mari E L; Daruge, Eduardo; Daruge, Eduardo

2013-01-01

The objective of this study was to demonstrate the effectiveness of rugoscopy as a human identification method, even when the patient is submitted to rapid palatal expansion, which in theory would introduce doubt. With this intent, the Rugoscopic Identity was obtained for each subject using the classification formula proposed by Santos based on the intra-oral casts made before and after treatment from patients who were subjected to palatal expansion. The casts were labeled with the patients' initials and randomly arranged for studying. The palatine rugae kept the same patterns in every case studied. The technical error of the intra-evaluator measurement provided a confidence interval of 95%, making rugoscopy a reliable identification method for patients who were submitted to rapid palatal expansion, because even in the presence of intra-oral changes owing to the use of palatal expanders, the palatine rugae retained the biological and technical requirements for the human identification process. © 2012 American Academy of Forensic Sciences.

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

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer.

PubMed

Dominguez-Bello, Maria G; De Jesus-Laboy, Kassandra M; Shen, Nan; Cox, Laura M; Amir, Amnon; Gonzalez, Antonio; Bokulich, Nicholas A; Song, Se Jin; Hoashi, Marina; Rivera-Vinas, Juana I; Mendez, Keimari; Knight, Rob; Clemente, Jose C

2016-03-01

Exposure of newborns to the maternal vaginal microbiota is interrupted with cesarean birthing. Babies delivered by cesarean section (C-section) acquire a microbiota that differs from that of vaginally delivered infants, and C-section delivery has been associated with increased risk for immune and metabolic disorders. Here we conducted a pilot study in which infants delivered by C-section were exposed to maternal vaginal fluids at birth. Similarly to vaginally delivered babies, the gut, oral and skin bacterial communities of these newborns during the first 30 d of life was enriched in vaginal bacteria--which were underrepresented in unexposed C-section-delivered infants--and the microbiome similarity to those of vaginally delivered infants was greater in oral and skin samples than in anal samples. Although the long-term health consequences of restoring the microbiota of C-section-delivered infants remain unclear, our results demonstrate that vaginal microbes can be partially restored at birth in C-section-delivered babies.

Commensal microbes provide first line defense against Listeria monocytogenes infection

PubMed Central

Littmann, Eric R.; Kim, Sohn G.; Morjaria, Sejal M.; Ling, Lilan; Gyaltshen, Yangtsho; Taur, Ying; Leiner, Ingrid M.

2017-01-01

Listeria monocytogenes is a foodborne pathogen that causes septicemia, meningitis and chorioamnionitis and is associated with high mortality. Immunocompetent humans and animals, however, can tolerate high doses of L. monocytogenes without developing systemic disease. The intestinal microbiota provides colonization resistance against many orally acquired pathogens, and antibiotic-mediated depletion of the microbiota reduces host resistance to infection. Here we show that a diverse microbiota markedly reduces Listeria monocytogenes colonization of the gut lumen and prevents systemic dissemination. Antibiotic administration to mice before low dose oral inoculation increases L. monocytogenes growth in the intestine. In immunodeficient or chemotherapy-treated mice, the intestinal microbiota provides nonredundant defense against lethal, disseminated infection. We have assembled a consortium of commensal bacteria belonging to the Clostridiales order, which exerts in vitro antilisterial activity and confers in vivo resistance upon transfer into germ free mice. Thus, we demonstrate a defensive role of the gut microbiota against Listeria monocytogenes infection and identify intestinal commensal species that, by enhancing resistance against this pathogen, represent potential probiotics. PMID:28588016

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

Isolation, identification and screening of antimicrobial thermophilic Streptomyces sp. Al-Dhabi-1 isolated from Tharban hot spring, Saudi Arabia.

PubMed

Al-Dhabi, Naif Abdullah; Esmail, Galal Ali; Duraipandiyan, Veeramuthu; Valan Arasu, Mariadhas; Salem-Bekhit, Mounir M

2016-01-01

The strain Streptomyces sp. Al-Dhabi-1 was isolated from soil sediments collected from Tharban hot spring in the southern west of Saudi Arabia using actinomycetes isolation agar and starch casein agar at 55 °C. Identification of the isolate was done according to morphological, physiological and biochemical characteristics and 16S rRNA sequence similarity as well. 16S rRNA sequence and blast analyses confirmed that the isolate belonging to the genus Streptomyces. The sequence was submitted to GenBank with accession number (KF815080). Ethyl acetate extract of Streptomyces sp. Al-Dhabi-1 showed good antimicrobial activities against tested pathogenic microbes. Minimum inhibitory concentration results showed that the best values were observed against S. agalactiae (<0.039 mg/ml) and Klebsiella pneumonia (0.125 mg/ml). Minimum inhibitory concentration of Al-Dhabi-1 against fungi; Cryptococcus neoformans (0.078 mg/ml), C. albicans (0.156 mg/ml), A. niger (0.625 mg/ml), and T. mentagrophytes (0.156 mg/ml). GC-MS analysis was used for the chemical profile of ethyl acetate extract. Benzeneacetic acid (16.02 %) and acetic acid 2-phenylethyl ester (10.35 %) were the major compounds among 31 substances found the ethyl acetate extract. According to the results of antimicrobial activity against pathogenic microbes, it is clear that the actinomycetes from hot springs with extreme environments are promising source for antimicrobial compounds.

Lung Microbiome for Clinicians. New Discoveries about Bugs in Healthy and Diseased Lungs

PubMed Central

Rom, William N.; Weiden, Michael D.

2014-01-01

Microbes are readily cultured from epithelial surfaces of the skin, mouth, and colon. In the last 10 years, culture-independent DNA-based techniques demonstrated that much more complex microbial communities reside on most epithelial surfaces; this includes the lower airways, where bacterial culture had failed to reliably demonstrate resident bacteria. Exposure to a diverse bacterial environment is important for adequate immunological development. The most common microbes found in the lower airways are also found in the upper airways. Increasing abundance of oral characteristic taxa is associated with increased inflammatory cells and exhaled nitric oxide, suggesting that the airway microbiome induces an immunological response in the lung. Furthermore, rhinovirus infection leads to outgrowth of Haemophilus in patients with chronic obstructive pulmonary disease, and human immunodeficiency virus–infected subjects have more Tropheryma whipplei in the lower airway, suggesting a bidirectional interaction in which the host immune defenses also influence the microbial niche. Quantitative and/or qualitative changes in the lung microbiome may be relevant for disease progression and exacerbations in a number of pulmonary diseases. Future investigations with longitudinal follow-up to understand the dynamics of the lung microbiome may lead to the development of new therapeutic targets. PMID:24460444

A dielectrophoretic method of discrimination between normal oral epithelium, and oral and oropharyngeal cancer in a clinical setting.

PubMed

Graham, K A; Mulhall, H J; Labeed, F H; Lewis, M P; Hoettges, K F; Kalavrezos, N; McCaul, J; Liew, C; Porter, S; Fedele, S; Hughes, M P

2015-08-07

Despite the accessibility of the oral cavity to clinical examination, delays in diagnosis of oral and oropharyngeal carcinoma (OOPC) are observed in a large majority of patients, with negative impact on prognosis. Diagnostic aids might help detection and improve early diagnosis, but there remains little robust evidence supporting the use of any particular diagnostic technology at the moment. The aim of the present feasibility first-in-human study was to evaluate the preliminary diagnostic validity of a novel technology platform based on dielectrophoresis (DEP). DEP does not require labeling with antibodies or stains and it is an ideal tool for rapid analysis of cell properties. Cells from OOPC/dysplasia tissue and healthy oral mucosa were collected from 57 study participants via minimally-invasive brush biopsies and tested with a prototype DEP platform using median membrane midpoint frequency as main analysis parameter. Results indicate that the current DEP platform can discriminate between brush biopsy samples from cancerous and healthy oral tissue with a diagnostic sensitivity of 81.6% and a specificity of 81.0%. The present ex vivo results support the potential application of DEP testing for identification of OOPC. This result indicates that DEP has the potential to be developed into a low-cost, rapid platform as an assistive tool for the early identification of oral cancer in primary care; given the rapid, minimally-invasive and non-expensive nature of the test, dielectric characterization represents a promising platform for cost-effective early cancer detection.

Oral iron supplementation: Potential implications for the gut microbiome and metabolome in patients with CKD.

PubMed

Kortman, Guus A M; Reijnders, Dorien; Swinkels, Dorine W

2017-06-01

Patients with chronic kidney disease (CKD) and loss of kidney function are at increased risk for morbidity and mortality. The risks of CKD are attributed to "uremia," an increased concentration of uremic retention solutes (toxins) in the plasma. Recently, a colo-renal axis became clearly apparent and uremia has been associated with an altered gut microbiome composition and metabolism. There is a high prevalence of anemia in patients with CKD, for which patients are often treated with oral or intravenous iron. Recent in vivo and in vitro studies have reported adverse effects of oral iron supplementation on the gut microbiota composition, gut metabolome, and intestinal health, which in turn may result in an increased production of uremic toxins. It may also affect circulating levels of other microbe-derived molecules, that can act as mediators of immune regulation. Changes in body iron levels have also been reported to exert subtle effects on host immune function by modulating immune cell proliferation and differentiation, and by directly regulating cytokine formation and antimicrobial immune effector mechanisms. Based on the foregoing it is conceivable that oral iron supplementation in iron deficient predialysis CKD patients adversely changes gut microbiota composition, the gut and systemic metabolome, and host immunity and infection. Future studies are needed to confirm these hypotheses and to assess whether, compared to IV iron supplementation, oral iron supplementation negatively impacts on morbidity of CKD, and whether these adverse effects depend on the iron bioavailability of the iron formulation to the microbiota. © 2017 International Society for Hemodialysis.

Peri-Implant Tissue Findings in Bone Grafted Oral Cancer Patients Compared to non Bone Grafted Patients without Oral Cancer

PubMed Central

Agata, Hideki; Sándor, George K.; Haimi, Suvi

2011-01-01

ABSTRACT Objectives The aim of this study was to compare microbiological, histological, and mechanical findings from tissues around osseointergrated dental implants in patients who had undergone tumour resection and subsequent bone grafting with non bone grafted patients without a history of oral cancer and to develop an effective tool for the monitoring of the peri-implant tissues. A third aim was to assess and compare the masticatory function of the two patient groups after reconstruction with dental implants. Material and Methods A total of 20 patients were divided into 2 groups. The first group was edentulous and treated with dental implants without the need for bone grafting. The second edentulous group, with a history of oral cancer involving the mandible, received onlay bone grafts with concurrent placement of dental implants. Microbiological, histological, mechanical and biochemical assessment methods, crevicular fluid flow rate, hygiene-index, implant mobility, and the masticatory function were analysed and compared in both patient groups. Results The microbiological examinations showed no evidence of the three most common pathogenic bacteria: Porphyromonas gingivalis, Prevotella intermedius, Actinobacillus actinomycetencomitans. A causal relationship between specific microbes and peri-implant inflammation could not be found. All biopsies in both patient groups revealed early signs of soft tissue peri-implant inflammation. Conclusions The crevicular fluid volume and grade of gingival inflammation around the dental implants were related. Peri-implant tissue findings were similar in the two patient groups despite the history of oral cancer and the need for bone grafting at the time of dental implant placement. PMID:24421999

Crystal violet stain as a selective stain for the assessment of mitotic figures in oral epithelial dysplasia and oral squamous cell carcinoma.

PubMed

Jadhav, Kiran B; Ahmed Mujib, B R; Gupta, Nidhi

2012-01-01

Assessment of mitotic figures (MFs) is routinely practiced as prognostic indicator in oral epithelial dysplasia (OED) and oral squamous cell carcinoma (OSCC), but identification of MFs poses a problem in terms of staining characteristics. To evaluate effectiveness of crystal violet stain for staining of MFs and its comparison with hematoxylin and eosin (H and E) stain. Study sample includes archival tissues embedded in paraffin blocks diagnosed as OED (n = 30) and OSCC (n = 30). The control group comprised of tissue specimen from oral mucosa of healthy volunteers (n = 30). Two serial sections of each tissue specimen were stained separately with H and E stain and 1% crystal violet stain. The stained sections were observed under microscope for identification and counting of MFs. Data obtained was statistically analyzed by using the Man-Whitney U test. A significant increase in number of MFs was observed in OED and OSCC in comparison with normal oral mucosa. There was a highly significant increase in number of MFs in crystal violet stained tissue sections when compared with H and E stain. Metaphase is the most commonly observed phase of mitosis in crystal violet stain when compared with H and E stain for all three groups. Crystal violet stain can be considered as selective stain for mitotic figures.

Oral enzyme therapy for celiac sprue

PubMed Central

Bethune, Michael T; Khosla, Chaitan

2012-01-01

Celiac sprue is an inflammatory disease of the small intestine caused by dietary gluten and treated by adherence to a lifelong gluten-free diet. The recent identification of immunodominant gluten peptides, the discovery of their cogent properties, and the elucidation of the mechanisms by which they engender immunopathology in genetically-susceptible individuals have advanced our understanding of the molecular pathogenesis of this complex disease, enabling the rational design of new therapeutic strategies. The most clinically advanced of these is oral enzyme therapy, in which enzymes capable of proteolyzing gluten (i.e. glutenases) are delivered to the alimentary tract of a celiac sprue patient to detoxify ingested gluten in situ. In this chapter, we discuss the key challenges for discovery and preclinical development of oral enzyme therapies for celiac sprue. Methods for lead identification, assay development, gram-scale production and formulation, and lead optimization for next-generation proteases are described and critically assessed. PMID:22208988

Retro-binding thrombin active site inhibitors: identification of an orally active inhibitor of thrombin catalytic activity.

PubMed

Iwanowicz, Edwin J; Kimball, S David; Lin, James; Lau, Wan; Han, W-C; Wang, Tammy C; Roberts, Daniel G M; Schumacher, W A; Ogletree, Martin L; Seiler, Steven M

2002-11-04

A series of retro-binding inhibitors of human alpha-thrombin was prepared to elucidate structure-activity relationships (SAR) and optimize in vivo performance. Compounds 9 and 11, orally active inhibitors of thrombin catalytic activity, were identified to be efficacious in a thrombin-induced lethality model in mice.

Oral and Maxillofacial Anatomy.

PubMed

Sadrameli, Mitra; Mupparapu, Mel

2018-01-01

This article deals with identification and descriptions of intraoral and extraoral anatomy of the dental and maxillofacial structures. The anatomic landmarks are highlighted and described based on their radiographic appearance and their clinical significance is provided. Cone beam CT-based images are described in detail using the multiplanar reconstructions. The skull views are depicted via line diagrams in addition to their normal radiographic appearance to make identification of anatomic structures easier for clinicians. The authors cover most of the anatomic structures commonly noted via radiographs and their descriptions. This article serves as a clinician's guide to oral and maxillofacial radiographic anatomy. Copyright © 2017 Elsevier Inc. All rights reserved.

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis.

PubMed

Nowicki, Emily M; Shroff, Raghav; Singleton, Jacqueline A; Renaud, Diane E; Wallace, Debra; Drury, Julie; Zirnheld, Jolene; Colleti, Brock; Ellington, Andrew D; Lamont, Richard J; Scott, David A; Whiteley, Marvin

2018-04-17

Over half of adults experience gingivitis, a mild yet treatable form of periodontal disease caused by the overgrowth of oral microbes. Left untreated, gingivitis can progress to a more severe and irreversible disease, most commonly chronic periodontitis. While periodontal diseases are associated with a shift in the oral microbiota composition, it remains unclear how this shift impacts microbiota function early in disease progression. Here, we analyzed the transition from health to gingivitis through both 16S v4-v5 rRNA amplicon and metatranscriptome sequencing of subgingival plaque samples from individuals undergoing an experimental gingivitis treatment. Beta-diversity analysis of 16S rRNA reveals that samples cluster based on disease severity and patient but not by oral hygiene status. Significant shifts in the abundance of several genera occurred during disease transition, suggesting a dysbiosis due to development of gingivitis. Comparing taxonomic abundance with transcriptomic activity revealed concordance of bacterial diversity composition between the two quantification assays in samples originating from both healthy and diseased teeth. Metatranscriptome sequencing analysis indicates that during the early stages of transition to gingivitis, a number of virulence-related transcripts were significantly differentially expressed in individual and across pooled patient samples. Upregulated genes include those involved in proteolytic and nucleolytic processes, while expression levels of those involved in surface structure assembly and other general virulence functions leading to colonization or adaptation within the host are more dynamic. These findings help characterize the transition from health to periodontal disease and identify genes associated with early disease. IMPORTANCE Although more than 50% of adults have some form of periodontal disease, there remains a significant gap in our understanding of its underlying cause. We initiated this study in order to better characterize the progression from oral health to disease. We first analyzed changes in the abundances of specific microorganisms in dental plaque collected from teeth during health and gingivitis, the mildest form of periodontal disease. We found that the clinical score of disease and patient from whom the sample originated but not tooth brushing are significantly correlated with microbial community composition. While a number of virulence-related gene transcripts are differentially expressed in gingivitis samples relative to health, not all are increased, suggesting that the overall activity of the microbiota is dynamic during disease transition. Better understanding of which microbes are present and their function during early periodontal disease can potentially lead to more targeted prophylactic approaches to prevent disease progression. Copyright © 2018 Nowicki et al.

Identification and Remediation of Learning Disability Subtypes: Preliminary Findings.

ERIC Educational Resources Information Center

Lyon, G. Reid

1985-01-01

Current literature on identification and instructional remediation of subtypes of learning-disabled readers (LDR) are reviewed. Preliminary findings suggest that not all LDR children manifest the same oral language, memory, and perceptual deficits that impede decoding accuracy and efficiency and all do not respond equally well (or poorly) to the…

Dental Evidence in Forensic Identification - An Overview, Methodology and Present Status.

PubMed

Krishan, Kewal; Kanchan, Tanuj; Garg, Arun K

2015-01-01

Forensic odontology is primarily concerned with the use of teeth and oral structures for identification in a legal context. Various forensic odontology techniques help in the identification of the human remains in incidents such as terrorists' attacks, airplane, train and road accidents, fires, mass murders, and natural disasters such as tsunamis, earth quakes and floods, etc. (Disaster Victim Identification-DVI). Dental structures are the hardest and well protected structures in the body. These structures resist decomposition and high temperatures and are among the last ones to disintegrate after death. The principal basis of the dental identification lies in the fact that no two oral cavities are alike and the teeth are unique to an individual. The dental evidence of the deceased recovered from the scene of crime/occurrence is compared with the ante-mortem records for identification. Dental features such as tooth morphology, variations in shape and size, restorations, pathologies, missing tooth, wear patterns, crowding of the teeth, colour and position of the tooth, rotations and other peculiar dental anomalies give every individual a unique identity. In absence of ante-mortem dental records for comparison, the teeth can help in the determination of age, sex, race/ethnicity, habits, occupations, etc. which can give further clues regarding the identity of the individuals. This piece of writing gives an overview of dental evidence, its use in forensic identification and its limitations.

Dental Evidence in Forensic Identification – An Overview, Methodology and Present Status

PubMed Central

Krishan, Kewal; Kanchan, Tanuj; Garg, Arun K

2015-01-01

Forensic odontology is primarily concerned with the use of teeth and oral structures for identification in a legal context. Various forensic odontology techniques help in the identification of the human remains in incidents such as terrorists’ attacks, airplane, train and road accidents, fires, mass murders, and natural disasters such as tsunamis, earth quakes and floods, etc. (Disaster Victim Identification-DVI). Dental structures are the hardest and well protected structures in the body. These structures resist decomposition and high temperatures and are among the last ones to disintegrate after death. The principal basis of the dental identification lies in the fact that no two oral cavities are alike and the teeth are unique to an individual. The dental evidence of the deceased recovered from the scene of crime/occurrence is compared with the ante-mortem records for identification. Dental features such as tooth morphology, variations in shape and size, restorations, pathologies, missing tooth, wear patterns, crowding of the teeth, colour and position of the tooth, rotations and other peculiar dental anomalies give every individual a unique identity. In absence of ante-mortem dental records for comparison, the teeth can help in the determination of age, sex, race/ethnicity, habits, occupations, etc. which can give further clues regarding the identity of the individuals. This piece of writing gives an overview of dental evidence, its use in forensic identification and its limitations. PMID:26312096

A Robust Framework for Microbial Archaeology

PubMed Central

Warinner, Christina; Herbig, Alexander; Mann, Allison; Yates, James A. Fellows; Weiβ, Clemens L.; Burbano, Hernán A.; Orlando, Ludovic; Krause, Johannes

2017-01-01

Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field. PMID:28460196

Rapid identification of microorganisms for biodegradation of alkylphenols and alkylphenol ethercarboxylates

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

Hemming, B.; Williams, J.B.

1995-12-31

Alkylphenols, especially nonylphenol and octylphenol, are used in a wide variety of applications. These compounds, and alkylphenol ethercarboxylates, are also believed to be formed during the biodegradation of alkylphenol ethoxylates in activated sludge wastewater treatment systems. Microbe Inotech Laboratories has developed a rapid assay to identify the microorganisms present in activated sludge wastewater treatment systems (GC-FAME) and a screening assay to measure the biodegradation of compounds. These assays were used to show that alkylphenols and their corresponding ethercarboxylates were degraded aerobically even when these compounds were the sole carbon source.

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

PubMed Central

Berry, David; Mader, Esther; Lee, Tae Kwon; Woebken, Dagmar; Wang, Yun; Zhu, Di; Palatinszky, Marton; Schintlmeister, Arno; Schmid, Markus C.; Hanson, Buck T.; Shterzer, Naama; Mizrahi, Itzhak; Rauch, Isabella; Decker, Thomas; Bocklitz, Thomas; Popp, Jürgen; Gibson, Christopher M.; Fowler, Patrick W.; Huang, Wei E.; Wagner, Michael

2015-01-01

Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics. PMID:25550518

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.

Design and Optimization of Renin Inhibitors: Orally Bioavailable Alkyl Amines

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

Tice, C.; Xu, Z; Yuan, J

2009-01-01

Structure-based drug design led to the identification of a novel class of potent, low MW alkylamine renin inhibitors. Oral administration of lead compound 21l, with MW of 508 and IC{sub 50} of 0.47 nM, caused a sustained reduction in mean arterial blood pressure in a double transgenic rat model of hypertension.

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

Tracking Polymicrobial Metabolism in Cystic Fibrosis Airways: Pseudomonas aeruginosa Metabolism and Physiology Are Influenced by Rothia mucilaginosa-Derived Metabolites.

PubMed

Gao, Bei; Gallagher, Tara; Zhang, Ying; Elbadawi-Sidhu, Mona; Lai, Zijuan; Fiehn, Oliver; Whiteson, Katrine L

2018-04-25

Due to a lack of effective immune clearance, the airways of cystic fibrosis patients are colonized by polymicrobial communities. One of the most widespread and destructive opportunistic pathogens is Pseudomonas aeruginosa ; however, P. aeruginosa does not colonize the airways alone. Microbes that are common in the oral cavity, such as Rothia mucilaginosa , are also present in cystic fibrosis patient sputum and have metabolic capacities different from those of P. aeruginosa Here we examine the metabolic interactions of P. aeruginosa and R. mucilaginosa using stable-isotope-assisted metabolomics. Glucose-derived 13 C was incorporated into glycolysis metabolites, namely, lactate and acetate, and some amino acids in R. mucilaginosa grown aerobically and anaerobically. The amino acid glutamate was unlabeled in the R. mucilaginosa supernatant but incorporated the 13 C label after P. aeruginosa was cross-fed the R. mucilaginosa supernatant in minimal medium and artificial-sputum medium. We provide evidence that P. aeruginosa utilizes R. mucilaginosa -produced metabolites as precursors for generation of primary metabolites, including glutamate. IMPORTANCE Pseudomonas aeruginosa is a dominant and persistent cystic fibrosis pathogen. Although P. aeruginosa is accompanied by other microbes in the airways of cystic fibrosis patients, few cystic fibrosis studies show how P. aeruginosa is affected by the metabolism of other bacteria. Here, we demonstrate that P. aeruginosa generates primary metabolites using substrates produced by another microbe that is prevalent in the airways of cystic fibrosis patients, Rothia mucilaginosa These results indicate that P. aeruginosa may get a metabolic boost from its microbial neighbor, which might contribute to its pathogenesis in the airways of cystic fibrosis patients.

Infection caused by thymidine-requiring, trimethoprim-resistant bacteria.

PubMed Central

King, C H; Shlaes, D M; Dul, M J

1983-01-01

We first noted the appearance of thymidine-requiring, gram-negative bacilli in clinical specimens 2 years ago. Since then we have seen 10 patients colonized or infected with these organisms. These strains do not grow on Mueller-Hinton media, growth on MacConkey agar is variable, and growth in API 20E (Analytab Products) and Enterobacteriaceae-Plus Cards (AutoMicrobic system; Vitek Systems Inc.) is inadequate for reliable identifications. Thymidine-requiring organisms are routinely resistant to sulfonamides and trimethoprim. Infection or colonization is associated with previous sulfamethoxazole-trimethoprim therapy in most cases. Of 10 patients, 1 had septicemia of urinary tract origin, 5 had urinary tract colonization or infection, 2 had wound colonization, and two had colonization of respiratory secretions. Thymidine-requiring, gram-negative bacilli can be pathogens and present potential problems in diagnosis, identification, and susceptibility testing. PMID:6604070

Identification of aldolase and ferredoxin reductase within the dbt operon of Burkholderia fungorum DBT1.

PubMed

Piccoli, Stefano; Andreolli, Marco; Giorgetti, Alejandro; Zordan, Fabio; Lampis, Silvia; Vallini, Giovanni

2014-05-01

Burkholderia fungorum DBT1, first isolated from settling particulate matter of an oil refinery wastewater, is a bacterial strain which has been shown capable of utilizing several polycyclic aromatic hydrocarbons (PAHs) including dibenzothiophene (DBT). In particular, this microbe is able to efficiently degrade DBT through the Kodama pathway. Previous investigations have lead to the identification of six genes, on a total of eight, required for DBT degradation. In the present study, a combined experimental/computational approach was adopted to identify and in silico characterize the two missing genes, namely a ferredoxin reductase and a hydratase-aldolase. Thus, the finding of all enzymatic components of the Kodama pathway in B. fungorum DBT1 makes this bacterial strain amenable for possible exploitation in soil bioremediation protocols. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of non-streptococcal organisms from human dental plaque grown on the Streptococcus-selective medium mitis-salivarius agar.

PubMed

Kim, Yeon-Hee; Lee, Si Young

2015-02-01

Mitis-salivarius (MS) agar has been used widely in microbial epidemiological studies because oral viridans streptococci can be selectively grown on this medium. Even though the previous findings reported the limited selecting power of MS agar for streptococcus strains, the identities of non-streptococcal strains from human oral samples which can grow on this medium are not clear yet. In this study, we identified non-streptococcal organisms grown on MS agar plates by polymerase chain reaction (PCR) amplification and sequencing of the 16S ribosomal RNA (rRNA) gene. Eighty bacterial colonies on MS plates were isolated from plaque samples, and bacterial identification was achieved with the rapid ID 32 Strep system and mini API reader. The bacterial colonies identified as non-streptococci by the API system were selected for further identification. The 16S rRNA gene was amplified by PCR and verified using DNA sequencing analysis for identification. Sequences were compared with those of reference organisms in the genome database of the National Center for Biotechnology Information using the Basic Local Alignment Search Tool (BLAST). Among the 11 isolated non-streptococcal strains on MS plates, 3 strains were identified as Actinomyces naeslundii, 7 strains were identified as Actinomyces oris and 1 strain were identified as Actinomyces sp. using Blastn. In this study, we showed that some oral Actinomyces species can grow on Streptococcus-selective MS agar plates. Copyright © 2014 Elsevier Ltd. All rights reserved.

NEMiD: a web-based curated microbial diversity database with geo-based plotting.

PubMed

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/.

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics.

PubMed

Tarnecki, A M; Burgos, F A; Ray, C L; Arias, C R

2017-02-07

The gut microbiome of vertebrates plays an integral role in host health by stimulating development of the immune system, aiding in nutrient acquisition and outcompeting opportunistic pathogens. Development of next-generation sequencing technologies allows researchers to survey complex communities of microorganisms within the microbiome at great depth with minimal costs, resulting in a surge of studies investigating bacterial diversity of fishes. Many of these studies have focused on the microbial structure of economically significant aquaculture species with the goal of manipulating the microbes to increase feed efficiency and decrease disease susceptibility. The unravelling of intricate host-microbe symbioses and identification of core microbiome functions is essential to our ability to use the benefits of a healthy microbiome to our advantage in fish culture, as well as gain deeper understanding of bacterial roles in vertebrate health. This review aims to summarize the available knowledge on fish gastrointestinal communities obtained from metagenomics, including biases from sample processing, factors influencing assemblage structure, intestinal microbiology of important aquaculture species and description of the teleostean core microbiome. Journal of Applied Microbiology © 2017 The Society for Applied Microbiology.

Exploiting algal NADPH oxidase for biophotovoltaic energy

DOE PAGES

Anderson, Alexander; Laohavisit, Anuphon; Blaby, Ian K.; ...

2015-01-29

Photosynthetic microbes exhibit light-dependent electron export across the cell membrane, which can generate electricity in biological photovoltaic (BPV) devices. How electrons are exported remains to be determined; the identification of mechanisms would help selection or generation of photosynthetic microbes capable of enhanced electrical output. We show that plasma membrane NADPH oxidase activity is a significant component of light-dependent generation of electricity by the unicellular green alga Chlamydomonas reinhardtii. NADPH oxidases export electrons across the plasma membrane to form superoxide anion from oxygen. The C. reinhardtii mutant lacking the NADPH oxidase encoded by RBO1 is impaired in both extracellular superoxide anionmore » production and current generation in a BPV device. Complementation with the wild-type gene restores both capacities, demonstrating the role of the enzyme in electron export. Monitoring light-dependent extracellular superoxide production with a colorimetric assay is shown to be an effective way of screening for electrogenic potential of candidate algal strains. Furthermore, the results show that algal NADPH oxidases are important for superoxide anion production and open avenues for optimizing the biological component of these devices.« less

Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection.

PubMed

Chylewska, Agnieszka; Ogryzek, M; Makowski, Mariusz

2017-10-23

New analytical and molecular methods for microorganisms are being developed on various features of identification i.e. selectivity, specificity, sensitivity, rapidity and discrimination of the viable cell. The presented review was established following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis. This contribution also focuses on the development of analytical and biological methods in the analysis of microorganisms, with special attention paid to bio-samples containing microbes (blood, urine, lymph, wastewater). First, the paper discusses microbes characterization, their structure, surface, properties, size and then it describes pivotal points in the bacteria, viruses and fungi separation procedure obtained by researchers in the last 30 years. According to the above, detection techniques can be classified into three categories, which were, in our opinion, examined and modified most intensively during this period: electrophoretic, nucleic-acid-based, and immunological methods. The review covers also the progress, limitations and challenges of these approaches and emphasizes the advantages of new separative techniques in selective fractionating of microorganisms. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

PubMed Central

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/. PMID:24714636

A simple method for rapid microbial identification from positive monomicrobial blood culture bottles through matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Lin, Jung-Fu; Ge, Mao-Cheng; Liu, Tsui-Ping; Chang, Shih-Cheng; Lu, Jang-Jih

2017-06-30

Rapid identification of microbes in the bloodstream is crucial in managing septicemia because of its high disease severity, and direct identification from positive blood culture bottles through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) can shorten the turnaround time. Therefore, we developed a simple method for rapid microbiological identification from positive blood cultures by using MALDI-TOF MS. We modified previously developed methods to propose a faster, simpler and more economical method, which includes centrifugation and hemolysis. Specifically, our method comprises two-stage centrifugation with gravitational acceleration (g) at 600g and 3000g, followed by the addition of a lysis buffer and another 3000g centrifugation. In total, 324 monomicrobial bacterial cultures were identified. The success rate of species identification was 81.8%, which is comparable with other complex methods. The identification success rate was the highest for Gram-negative aerobes (85%), followed by Gram-positive aerobes (78.2%) and anaerobes (67%). The proposed method requires less than 10 min, costs less than US$0.2 per usage, and facilitates batch processing. We conclude that this method is feasible for clinical use in microbiology laboratories, and can serve as a reference for treatments or further complementary diagnostic testing. Copyright © 2017. Published by Elsevier B.V.

Progress in oral personalized medicine: contribution of 'omics'.

PubMed

Glurich, Ingrid; Acharya, Amit; Brilliant, Murray H; Shukla, Sanjay K

2015-01-01

Precision medicine (PM), representing clinically applicable personalized medicine, proactively integrates and interprets multidimensional personal health data, including clinical, 'omics', and environmental profiles, into clinical practice. Realization of PM remains in progress. The focus of this review is to provide a descriptive narrative overview of: 1) the current status of oral personalized medicine; and 2) recent advances in genomics and related 'omic' and emerging research domains contributing to advancing oral-systemic PM, with special emphasis on current understanding of oral microbiomes. A scan of peer-reviewed literature describing oral PM or 'omic'-based research conducted on humans/data published in English within the last 5 years in journals indexed in the PubMed database was conducted using mesh search terms. An evidence-based approach was used to report on recent advances with potential to advance PM in the context of historical critical and systematic reviews to delineate current state-of-the-art technologies. Special focus was placed on oral microbiome research associated with health and disease states, emerging research domains, and technological advances, which are positioning realization of PM. This review summarizes: 1) evolving conceptualization of personalized medicine; 2) emerging insight into roles of oral infectious and inflammatory processes as contributors to both oral and systemic diseases; 3) community shifts in microbiota that may contribute to disease; 4) evidence pointing to new uncharacterized potential oral pathogens; 5) advances in technological approaches to 'omics' research that will accelerate PM; 6) emerging research domains that expand insights into host-microbe interaction including inter-kingdom communication, systems and network analysis, and salivaomics; and 7) advances in informatics and big data analysis capabilities to facilitate interpretation of host and microbiome-associated datasets. Furthermore, progress in clinically applicable screening assays and biomarker definition to inform clinical care are briefly explored. Advancement of oral PM currently remains in research and discovery phases. Although substantive progress has been made in advancing the understanding of the role of microbiome dynamics in health and disease and is being leveraged to advance early efforts at clinical translation, further research is required to discern interpretable constituency patterns in the complex interactions of these microbial communities in health and disease. Advances in biotechnology and bioinformatics facilitating novel approaches to rapid analysis and interpretation of large datasets are providing new insights into oral health and disease, potentiating clinical application and advancing realization of PM within the next decade.

Supporting Fourth-Grade Students' Word Identification Using Application Software

ERIC Educational Resources Information Center

Moser, Gary P.; Morrison, Timothy G.; Wilcox, Brad

2017-01-01

A quasi-experimental study examined effects of a 10-week word structure intervention with fourth-grade students. During daily 10-15-minute practice periods, students worked individually with mobile apps focused on specific aspects of word identification. Pre- and post-treatment assessments showed no differences in rate and accuracy of oral reading…

Timetable for oral prevention in childhood--developing dentition and oral habits: a current opinion.

PubMed

Majorana, Alessandra; Bardellini, Elena; Amadori, Francesca; Conti, Giulio; Polimeni, Antonella

2015-01-01

As most of the etiologic factors of malocclusion are of genetic origin and thus cannot be prevented, environmental causative factors have become the focus for correction. Early interception of oral habits may be an important step in order to prevent occlusal disturbances in children. The identification of an abnormal habit and the assessment of its potential immediate and long-term effects on the dentition and potentially on the craniofacial complex should be made at an early stage. This paper focuses on the most common oral habits influencing dentofacial growth in childhood and management of these habits in the developing dentition.

Oral Language and Listening Comprehension: Same or Different Constructs?

PubMed

2017-05-24

The purpose of this study was to add to our understanding of the dimensionality of oral language in children and to determine whether oral language and listening comprehension are separate constructs in children enrolled in preschool (PK) through 3rd grade. In the spring of the school year, children from 4 states (N = 1,869) completed multiple measures of oral language (i.e., expressive and receptive vocabulary and grammar) and listening comprehension as part of a larger study of the language bases of reading comprehension. Initial confirmatory factor analysis found evidence that measures of oral language and listening comprehension loaded on two separate factors in PK through 3rd grade; however, these factors were highly correlated at all grades. These results suggest that oral language and listening comprehension are best characterized as a single oral language construct in PK through 3rd grade. The implications for early identification and intervention are discussed.

The human microbiota associated with overall health.

PubMed

Xu, Xiaofei; Wang, Zhujun; Zhang, Xuewu

2015-03-01

Human body harbors diverse microbes, the main components include bacteria, eukaryotes and viruses. Emerging evidences show that the human microbiota is intrinsically linked with overall health. The development of next-generation sequencing provides an unprecedented opportunity to investigate the complex microbial communities that are associated with the human body. Many factors like host genetics and environmental factors have a major impact on the composition and dynamic changes of human microbiota. The purpose of this paper is to present an overview of the relationship between human health and human microbiota (skin, nasal, throat, oral, vaginal and gut microbiota), then to focus on the factors modulating the composition of the microbiota and the future challenges to manipulate the microbiota for personalized health.

Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS

PubMed Central

Stingu, Catalina S.; Borgmann, Toralf; Rodloff, Arne C.; Vielkind, Paul; Jentsch, Holger; Schellenberger, Wolfgang; Eschrich, Klaus

2015-01-01

Background Actinomyces are a common part of the residential flora of the human intestinal tract, genitourinary system and skin. Isolation and identification of Actinomyces by conventional methods is often difficult and time consuming. In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has become a rapid and simple method to identify bacteria. Objective The present study evaluated a new in-house algorithm using MALDI-TOF-MS for rapid identification of different species of oral Actinomyces cultivated from subgingival biofilm. Design Eleven reference strains and 674 clinical strains were used in this study. All the strains were preliminarily identified using biochemical methods and then subjected to MALDI-TOF-MS analysis using both similarity-based analysis and classification methods (support vector machine [SVM]). The genotype of the reference strains and of 232 clinical strains was identified by sequence analysis of the 16S ribosomal RNA (rRNA). Results The sequence analysis of the 16S rRNA gene of all references strains confirmed their previous identification. The MALDI-TOF-MS spectra obtained from the reference strains and the other clinical strains undoubtedly identified as Actinomyces by 16S rRNA sequencing were used to create the mass spectra reference database. Already a visual inspection of the mass spectra of different species reveals both similarities and differences. However, the differences between them are not large enough to allow a reliable differentiation by similarity analysis. Therefore, classification methods were applied as an alternative approach for differentiation and identification of Actinomyces at the species level. A cross-validation of the reference database representing 14 Actinomyces species yielded correct results for all species which were represented by more than two strains in the database. Conclusions Our results suggest that a combination of MALDI-TOF-MS with powerful classification algorithms, such as SVMs, provide a useful tool for the differentiation and identification of oral Actinomyces. PMID:25597306

Development of hydrogel microtubes for microbe culture in open environment.

PubMed

Ogawa, M; Higashi, K; Miki, N

2015-08-01

This paper describes a microbe culture system in an open environment using hydrogel microtubes. In recent years, oil production microbes, such as Aurantiochytrium, have been found and are studied to produce fuels of new age instead of fossil fuels. Biomass production by microbes is promising, where scale-up, collection of the products and competition against other microbes are the most important challenges. Here, we propose to use hydrogel microtubes to encapsulate, culture, and protect microbes. The tubes can be micro- and mass-fabricated. They allow oxygen and nutrition to go through while they prevent competitive microbes from intruding inside. The microbes and byproducts can be collected together with the tubes. In this paper, we demonstrate the proof-of-concepts experiments: we fabricated hydrogel micro tubes and cultured Coryne glutamicum which produce lactic acid inside the tubes. The microbes were increased inside the tubes and protected even when competitive microbes existed in the culture media. Furthermore, we demonstrated how to collect microbes inside the tubes.

Clinical and subclinical effects of power brushing following experimental induction of biofilm overgrowth in subjects representing a spectrum of periodontal disease.

PubMed

Aspiras, Marcelo B; Barros, Silvana P; Moss, Kevin L; Barrow, David A; Phillips, Sherrill T; Mendoza, Luis; de Jager, Marko; Ward, Marilyn; Offenbacher, Steven

2013-12-01

Investigate short-term effects of power brushing following experimental induction of biofilm overgrowth in periodontal disease states. Overall, 175 subjects representing each of five biofilm-gingival interface (BGI) periodontal groups were enrolled in a single-blind, randomized study. After stent-induced biofilm overgrowth for 21 days subjects received either a manual or a power toothbrush to use during a 4 weeks resolution phase. At baseline and during induction and resolution, standard clinical parameters were measured. Subclinical parameters included multikine analysis of 13 salivary biomarkers and 16s Human Oral Microbe Identification Microarray (HOMIM) probe analysis of subgingival plaque samples. All groups exhibited significantly greater reductions in bleeding on probing (BOP) (p = 0.002), gingival index (GI) (p = 0.0007), pocket depth (PD) (p = 0.04) and plaque index (p = 0.001) with power brushing compared to manual. When BGI groups were combined to form a shallow PD (PD ≤ 3 mm) and a deep PD group (PD > 4 mm) power brushing reduced BOP and GI in subjects with both pocket depths. Power brushing significantly reduced IL-1β levels at resolution while changes in bacterial levels showed non-significant trends between both brushing modalities. Short-term changes in select clinical parameters and subclinical salivary biomarkers may be useful in assessing efficacy of power brushing interventions in a spectrum of periodontal disease states. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Identification of a probiotic bacteria-derived activator of the aryl hydrocarbon receptor that inhibits colitis.

PubMed

Fukumoto, Suguru; Toshimitsu, Takayuki; Matsuoka, Shuji; Maruyama, Atsushi; Oh-Oka, Kyoko; Takamura, Takeyuki; Nakamura, Yuki; Ishimaru, Kayoko; Fujii-Kuriyama, Yoshiaki; Ikegami, Shuji; Itou, Hiroyuki; Nakao, Atsuhito

2014-01-01

The aryl hydrocarbon receptor (AhR) recognizes environmental xenobiotics and is originally thought to be involved in the metabolism (detoxification) of the substances. Recently, AhR is highlighted as an important regulator of inflammation. Notably, accumulating evidence suggests that activation of the AhR suppresses inflammatory bowel diseases (IBDs). Therefore, non-toxic AhR activators become attractive drug candidates for IBD. This study identified 1,4-dihydroxy-2-naphthoic acid (DHNA), a precursor of menaquinone (vitamin K2) abundantly produced by Propionibacterium freudenreichii ET-3 isolated from Swiss-type cheese, as an AhR activator. DHNA activated the AhR pathway in human intestinal epithelial cell line Caco2 cells and in the mouse intestine. Oral treatment of mice with DHNA induced anti-microbial proteins RegIIIβ and γ in the intestine, altered intestinal microbial flora and inhibited dextran sodium sulfate (DSS)-induced colitis, which recapitulated the phenotypes of AhR activation in the gut. As DHNA is commercially available in Japan as a prebiotic supplement without severe adverse effects, DHNA or its derivatives might become a promising drug candidate for IBD via AhR activation. The results also implicate that intestinal AhR might act not only as a sensor for xenobiotics in diet and water but also for commensal bacterial activity because DHNA is a precursor of vitamin K2 produced by vitamin K2-synthesizing commensal bacteria as well as propionic bacteria. Hence, DHNA might be a key bacterial metabolite in the host-microbe interaction to maintain intestinal microbial ecosystem.

Identification of Veillonella Species in the Tongue Biofilm by Using a Novel One-Step Polymerase Chain Reaction Method

PubMed Central

Mashima, Izumi; Theodorea, Citra Fragrantia; Thaweboon, Boonyanit; Thaweboon, Sroisiri; Nakazawa, Futoshi

2016-01-01

Six Veillonella species have been frequently isolated from human oral cavities including infectious sites. Recently, it was reported that diet, smoking, and possibly socioeconomic status can influence the bacterial profile in oral cavities. In addition, oral hygiene habits may also influence oral microbiota in terms of both numbers and diversity of microorganisms. In this study, the identification of Veillonella species in tongue biofilms of Thai children, divided into three groups dependent on their status of oral hygiene. For this, we used a novel one-step PCR method with species-specific primer sets based on sequences of the rpoB gene. As shown in the results, the number of isolates of Veillonella species was 101 strains from only 10 of 89 subjects. However, the total number of bacteria was high for all subjects. Since it was reported in previous studies that Veillonella species were easy to isolate in human tongue biofilms at high numbers, the results obtained in this study may suggest country- or age-specific differences. Moreover, Veillonella species were detected predominantly in subjects who had poor oral hygiene compared to those with good or moderate oral hygiene. From these results, there is a possibility that Veillonella species may be an index of oral hygiene status. Furthermore, V. rogosae was a predominant species in tongue biofilms of Thai children, whereas V. parvula and V. denticariosi were not isolated at all. These characteristics of the distribution and frequency of Veillonella species are similar to those reported in previous studies. Although further studies are needed in other countries, in this study, a successful novel one-step PCR method was established to detect Veillonella species in human oral cavities easily and effectively. Furthermore, this is the first report investigating the distribution and frequency of Veillonella species in tongue biofilms of Thai children. PMID:27326455

An Examination of the Sagan-Coleman formula for application to planetary protection for Europa

NASA Astrophysics Data System (ADS)

Barengoltz, Jack

2016-07-01

The Sagan-Coleman formulafootnote{ Sagan, C.; Coleman, S. (1965). "Spacecraft sterilization standards and contamination of Mars". Journal of Astronautics and Aeronautics 3 (5): 22-27.} was originally published as a method to estimate the probability of contamination of Mars by a spacecraft. This estimate was required to satisfy the NASA planetary protection requirements for Mars, which were at the time specified in terms of a maximum allowed value for the probability of contamination. The form of the formula is: P{}_{c} = N{}_{0}{}_{ }P{}_{1}*P{}_{2}*....P{}_{n}*P{}_{g} Here P{}_{c}, the probability of contamination is the probability that one or more of N{}_{0} microbes on the spacecraft will survive to a release on the surface of Mars and reproduce. P{}_{g} is the probability of growth (reproduction, per microbe). Before the identification of the necessary parameters for a flight mission to Europa, it is worthwhile to clarify the mathematical origin of the formula. In fact, the phrase ``one or more'' of the N{}_{0}{}_{ }microbes provides{}_{ }a clue. The exact mathematical form is: [P_c=1-{(1-p)}^{N_0}] Here p is the probability per microbe that it will survive and grow, 1-p is the probability that it won't, {(1-p)}^{N_0} is the probability that all N{}_{0} microbes fail to survive and grow. Thus the last value subtracted from unity is the probability of ``one or more'' surviving and growing. For the case that N{}_{0} p << 1 , the quantity in parentheses may be approximated by the first two terms of a Taylor expansion as 1 - N{}_{0}{}_{ }p, so that P{}_{c} = N{}_{0}{}_{ }p of course. For planetary protection purposes, the approximation is typically adequate. Nevertheless, an upper limit for the error (the residual from the truncation of the series) is provided. More importantly, the parameters are shown to be in three categories, at least one of which violates the derivation. That category is comprised of parameters that are independent of N{}_{0}, for example, the probability that the spacecraft impacts Europa (or Mars) P{}_{I}. This factor (and possibly others) may not be used to demonstrate N{}_{0} p << 1. The formula is now: [P_c=P_I [1-{(1-p)}^{N_0}

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.

Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms.

PubMed

Klein, Marlise I; Hwang, Geelsu; Santos, Paulo H S; Campanella, Osvaldo H; Koo, Hyun

2015-01-01

Biofilms are highly structured microbial communities that are enmeshed in a self-produced extracellular matrix. Within the complex oral microbiome, Streptococcus mutans is a major producer of extracellular polymeric substances including exopolysaccharides (EPS), eDNA, and lipoteichoic acid (LTA). EPS produced by S. mutans-derived exoenzymes promote local accumulation of microbes on the teeth, while forming a spatially heterogeneous and diffusion-limiting matrix that protects embedded bacteria. The EPS-rich matrix provides mechanical stability/cohesiveness and facilitates the creation of highly acidic microenvironments, which are critical for the pathogenesis of dental caries. In parallel, S. mutans also releases eDNA and LTA, which can contribute with matrix development. eDNA enhances EPS (glucan) synthesis locally, increasing the adhesion of S. mutans to saliva-coated apatitic surfaces and the assembly of highly cohesive biofilms. eDNA and other extracellular substances, acting in concert with EPS, may impact the functional properties of the matrix and the virulence of cariogenic biofilms. Enhanced understanding about the assembly principles of the matrix may lead to efficacious approaches to control biofilm-related diseases.

Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms

PubMed Central

Klein, Marlise I.; Hwang, Geelsu; Santos, Paulo H. S.; Campanella, Osvaldo H.; Koo, Hyun

2015-01-01

Biofilms are highly structured microbial communities that are enmeshed in a self-produced extracellular matrix. Within the complex oral microbiome, Streptococcus mutans is a major producer of extracellular polymeric substances including exopolysaccharides (EPS), eDNA, and lipoteichoic acid (LTA). EPS produced by S. mutans-derived exoenzymes promote local accumulation of microbes on the teeth, while forming a spatially heterogeneous and diffusion-limiting matrix that protects embedded bacteria. The EPS-rich matrix provides mechanical stability/cohesiveness and facilitates the creation of highly acidic microenvironments, which are critical for the pathogenesis of dental caries. In parallel, S. mutans also releases eDNA and LTA, which can contribute with matrix development. eDNA enhances EPS (glucan) synthesis locally, increasing the adhesion of S. mutans to saliva-coated apatitic surfaces and the assembly of highly cohesive biofilms. eDNA and other extracellular substances, acting in concert with EPS, may impact the functional properties of the matrix and the virulence of cariogenic biofilms. Enhanced understanding about the assembly principles of the matrix may lead to efficacious approaches to control biofilm-related diseases. PMID:25763359

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

PubMed

Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

2015-05-17

Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm. NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds. The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.

Pink-pigmented non-fermentative gram-negative rods associated with human infections: a clinical and diagnostic challenge.

PubMed

Hogue, R; Graves, M; Moler, S; Janda, J M

2007-06-01

Over the past several decades, the appearance of pink-pigmented bacteria in clinical specimens has gone from being a microbiologic curiosity in the clinical laboratory to the recognition of these aerobic microorganisms as etiologic agents of human disease, most notably bloodstream infections. Advances in the fields of molecular taxonomy and phylogenetics indicate that at least four distinct genera and eight different species are associated with clinical infections in susceptible patient populations. However, these bacteria are slow growing and present multiple diagnostic challenges to the microbiology laboratory including culture, isolation, and identification to species rank. This article provides a current review of these unusual non-fermentative chromogenic bacteria including their disease spectrum, taxonomy, and laboratory identification. The review also highlights the pitfalls or shortcomings we currently have in our knowledge of these microbes and their disease-producing capabilities.

Identification and discrimination of oral asaccharolytic Eubacterium spp. by pyrolysis mass spectrometry and artificial neural networks.

PubMed

Goodacre, R; Hiom, S J; Cheeseman, S L; Murdoch, D; Weightman, A J; Wade, W G

1996-02-01

Curie-point pyrolysis mass spectra were obtained from 29 oral asaccharolytic Eubacterium strains and 6 abscess isolates previously identified as Peptostreptococcus heliotrinreducens. Pyrolysis mass spectrometry (PyMS) with cluster analysis was able to clarify the taxonomic position of this group of organisms. Artificial neural networks (ANNS) were then trained by supervised learning (with the back-propagation algorithm) to recognize the strains from their pyrolysis mass spectra; all Eubacterium strains were correctly identified, and the abscess isolates were identified as un-named Eubacterium taxon C2 and were distinct from the type strain of P. heliotrinreducens. These results demonstrate that the combination of PyMS and ANNs provides a rapid and accurate identification technique.

Metabolite identification in fecal microbiota transplantation mouse livers and combined proteomics with chronic unpredictive mild stress mouse livers.

PubMed

Li, Bo; Guo, Kenan; Zeng, Li; Zeng, Benhua; Huo, Ran; Luo, Yuanyuan; Wang, Haiyang; Dong, Meixue; Zheng, Peng; Zhou, Chanjuan; Chen, Jianjun; Liu, Yiyun; Liu, Zhao; Fang, Liang; Wei, Hong; Xie, Peng

2018-01-31

Major depressive disorder (MDD) is a common mood disorder. Gut microbiota may be involved in the pathogenesis of depression via the microbe-gut-brain axis. Liver is vulnerable to exposure of bacterial products translocated from the gut via the portal vein and may be involved in the axis. In this study, germ-free mice underwent fecal microbiota transplantation from MDD patients and healthy controls. Behavioral tests verified the depression model. Metabolomics using gas chromatography-mass spectrometry, nuclear magnetic resonance, and liquid chromatography-mass spectrometry determined the influence of microbes on liver metabolism. With multivariate statistical analysis, 191 metabolites were distinguishable in MDD mice from control (CON) mice. Compared with CON mice, MDD mice showed lower levels for 106 metabolites and higher levels for 85 metabolites. These metabolites are associated with lipid and energy metabolism and oxidative stress. Combined analyses of significantly changed proteins in livers from another depression model induced by chronic unpredictive mild stress returned a high score for the Lipid Metabolism, Free Radical Scavenging, and Molecule Transports network, and canonical pathways were involved in energy metabolism and tryptophan degradation. The two mouse models of depression suggest that changes in liver metabolism might be involved in the pathogenesis of MDD. Conjoint analyses of fecal, serum, liver, and hippocampal metabolites from fecal microbiota transplantation mice suggested that aminoacyl-tRNA biosynthesis significantly changed and fecal metabolites showed a close relationship with the liver. These findings may help determine the biological mechanisms of depression and provide evidence about "depression microbes" impacting on liver metabolism.

Tracking heavy water (D 2O) incorporation for identifying and sorting active microbial cells

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

Berry, David; Mader, Esther; Lee, Tae Kwon

Here, microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. Here in this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D 2O) combined with Raman microspectroscopy. Incorporation of D 2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labelingmore » pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D 2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D 2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.« less

Tracking heavy water (D 2O) incorporation for identifying and sorting active microbial cells

DOE PAGES

Berry, David; Mader, Esther; Lee, Tae Kwon; ...

2014-12-30

Here, microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. Here in this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D 2O) combined with Raman microspectroscopy. Incorporation of D 2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labelingmore » pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D 2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D 2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.« less

The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems

PubMed Central

Gougoulias, Christos; Clark, Joanna M; Shaw, Liz J

2014-01-01

It is well known that atmospheric concentrations of carbon dioxide (CO2) (and other greenhouse gases) have increased markedly as a result of human activity since the industrial revolution. It is perhaps less appreciated that natural and managed soils are an important source and sink for atmospheric CO2 and that, primarily as a result of the activities of soil microorganisms, there is a soil-derived respiratory flux of CO2 to the atmosphere that overshadows by tenfold the annual CO2 flux from fossil fuel emissions. Therefore small changes in the soil carbon cycle could have large impacts on atmospheric CO2 concentrations. Here we discuss the role of soil microbes in the global carbon cycle and review the main methods that have been used to identify the microorganisms responsible for the processing of plant photosynthetic carbon inputs to soil. We discuss whether application of these techniques can provide the information required to underpin the management of agro-ecosystems for carbon sequestration and increased agricultural sustainability. We conclude that, although crucial in enabling the identification of plant-derived carbon-utilising microbes, current technologies lack the high-throughput ability to quantitatively apportion carbon use by phylogentic groups and its use efficiency and destination within the microbial metabolome. It is this information that is required to inform rational manipulation of the plant–soil system to favour organisms or physiologies most important for promoting soil carbon storage in agricultural soil. PMID:24425529

Teleosts as Model Organisms To Understand Host-Microbe Interactions.

PubMed

Lescak, Emily A; Milligan-Myhre, Kathryn C

2017-08-01

Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. Copyright © 2017 Lescak and Milligan-Myhre.

Teleosts as Model Organisms To Understand Host-Microbe Interactions

PubMed Central

2017-01-01

ABSTRACT Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. PMID:28439034

TTCs for oral exposure: Identification of outliers in Cramer class I, II and III using the combined database of RepDose (FhG), Toxbase (TNO), Munro and ToxRefDB (USEPA)

EPA Science Inventory

The Thresholds of Toxicological Concern (TTC) are generic human exposure threshold for structural groups of chemicals below which no risk to human health is assumed and therefore no further testing is needed. Different thresholds have been developed for oral exposure e.g. for gen...

Identification of Small Molecule Inhibitors of microRNA Involved in Chemoresistance and Cancer Stem Cells for Ovarian Cancer Intervention

DTIC Science & Technology

2013-09-01

reversion-inducing-cysteine- rich protein with kazal motifs (RECK) in oral cancer . J Biol Chem. 287:29261-72. 2012 3. Lin FC, Liu YP, Lai CH, Shan YS...Annual Meeting, 2012. 8. Jung HM, Patel RS, Cohen DM, Jakymiw A, Kong WM, Cheng JQ, Chan EKL. Subclassification of oral cancers using a miRNA-based

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.

Signaling through IL-17C/IL-17RE Is Dispensable for Immunity to Systemic, Oral and Cutaneous Candidiasis

PubMed Central

Conti, Heather R.; Whibley, Natasha; Coleman, Bianca M.; Garg, Abhishek V.; Jaycox, Jillian R.; Gaffen, Sarah L.

2015-01-01

Candida albicans is a commensal fungal microbe of the human orogastrointestinal tract and skin. C. albicans causes multiple forms of disease in immunocompromised patients, including oral, vaginal, dermal and disseminated candidiasis. The cytokine IL-17 (IL-17A) and its receptor subunits, IL-17RA and IL-17RC, are required for protection to most forms of candidiasis. The importance of the IL-17R pathway has been observed not only in knockout mouse models, but also in humans with rare genetic mutations that impact generation of Th17 cells or the IL-17 signaling pathway, including Hyper-IgE Syndrome (STAT3 or TYK2 mutations) or IL17RA or ACT1 gene deficiency. The IL-17 family of cytokines is a distinct subclass of cytokines with unique structural and signaling properties. IL-17A is the best-characterized member of the IL-17 family to date, but far less is known about other IL-17-related cytokines. In this study, we sought to determine the role of a related IL-17 cytokine, IL-17C, in protection against oral, dermal and disseminated forms of C. albicans infection. IL-17C signals through a heterodimeric receptor composed of the IL-17RA and IL-17RE subunits. We observed that IL-17C mRNA was induced following oral C. albicans infection. However, mice lacking IL-17C or IL-17RE cleared C. albicans infections in the oral mucosa, skin and bloodstream at rates similar to WT littermate controls. Moreover, these mice demonstrated similar gene transcription profiles and recovery kinetics as WT animals. These findings indicate that IL-17C and IL-17RE are dispensable for immunity to the forms of candidiasis evaluated, and illustrate a surprisingly limited specificity of the IL-17 family of cytokines with respect to systemic, oral and cutaneous Candida infections. PMID:25849644

Signaling through IL-17C/IL-17RE is dispensable for immunity to systemic, oral and cutaneous candidiasis.

PubMed

Conti, Heather R; Whibley, Natasha; Coleman, Bianca M; Garg, Abhishek V; Jaycox, Jillian R; Gaffen, Sarah L

2015-01-01

Candida albicans is a commensal fungal microbe of the human orogastrointestinal tract and skin. C. albicans causes multiple forms of disease in immunocompromised patients, including oral, vaginal, dermal and disseminated candidiasis. The cytokine IL-17 (IL-17A) and its receptor subunits, IL-17RA and IL-17RC, are required for protection to most forms of candidiasis. The importance of the IL-17R pathway has been observed not only in knockout mouse models, but also in humans with rare genetic mutations that impact generation of Th17 cells or the IL-17 signaling pathway, including Hyper-IgE Syndrome (STAT3 or TYK2 mutations) or IL17RA or ACT1 gene deficiency. The IL-17 family of cytokines is a distinct subclass of cytokines with unique structural and signaling properties. IL-17A is the best-characterized member of the IL-17 family to date, but far less is known about other IL-17-related cytokines. In this study, we sought to determine the role of a related IL-17 cytokine, IL-17C, in protection against oral, dermal and disseminated forms of C. albicans infection. IL-17C signals through a heterodimeric receptor composed of the IL-17RA and IL-17RE subunits. We observed that IL-17C mRNA was induced following oral C. albicans infection. However, mice lacking IL-17C or IL-17RE cleared C. albicans infections in the oral mucosa, skin and bloodstream at rates similar to WT littermate controls. Moreover, these mice demonstrated similar gene transcription profiles and recovery kinetics as WT animals. These findings indicate that IL-17C and IL-17RE are dispensable for immunity to the forms of candidiasis evaluated, and illustrate a surprisingly limited specificity of the IL-17 family of cytokines with respect to systemic, oral and cutaneous Candida infections.

Identification of Human Intestinal Bacteria that Promote or Inhibit Inflammation

DTIC Science & Technology

2012-11-01

Lactobacillus "acidophilus" Lactobacillus " plantarum " ProvidenCa"sp." Enterobacter"aerogenes" Lactobacillus "paraalimentarius" Salmonella"typhi...8217 indica3ve’of’the’poten3al’of’these’microbes’to’induce’intes3nal’inflamma3on.’ 0" 5" 10" 15" 20" 25" 30" 35" 40" 45" 50" no"bacteria" Lactobacillus "brevis" Escherichea"coli"(DH5a)" Klebsiella"pneumonia" Salmonella...only

Evaluation of Fluoretec-M for detection of oral strains of Bacteroides asaccharolyticus and Bacteroides melaninogenicus.

PubMed Central

Mouton, C; Hammond, P; Slots, J; Genco, R J

1980-01-01

Fluoretec-M is a polyvalent conjugate used in direct fluorescent-antibody staining for identification of the Bacteroides asaccharolyticus-Bacteroides melaninogenicus group. The Fluoretec-M reagent detected all oral and nonoral test strains of B. melaninogaenicus subsp. intermedius, all test strains of B. melaninogenicus subsp. melaninogenicus, and the nonoral strains of B. asaccharolyticus. However, the Fluoretec-M polyvalent reagent and the monovalent conjugates which constitute Fluoretec-M did not detect the oral strains B. asaccharolyticus. The use of Fluoretec-M can therefore generate false-negative results in studies of specimens from oral cavity and from nonoral sites in which an infection with B. asacacharolyticus of oral origin may have taken place. It is suggested that antibodies reactive with the oral antigenic type of B. asaccharolyticus be included in the preparative procedure of the Fluoretec-M reagent. PMID:6107305

Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques.

PubMed

McLean, Jeffrey S; Fansler, Sarah J; Majors, Paul D; McAteer, Kathleen; Allen, Lisa Z; Shirtliff, Mark E; Lux, Renate; Shi, Wenyuan

2012-01-01

Many human microbial infectious diseases including dental caries are polymicrobial in nature. 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 bacteria have been characterized in vitro, their physiology within the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these species remain uncultivated to date with little known besides their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated species will remain enigmatic despite their apparent disease correlation. To start addressing these knowledge gaps, we applied a combination of Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for in vitro temporal monitoring of metabolites and identification of metabolically active and inactive bacterial species. Supragingival plaque samples from caries-free children incubated with (13)C-substrates under imposed healthy (buffered, pH 7) and diseased states (pH 5.5 and pH 4.5) produced lactate as the dominant organic acid from glucose metabolism. Rapid lactate utilization upon glucose depletion was observed under pH 7 conditions. SIP analyses revealed a number of genera containing cultured and uncultivated taxa with metabolic capabilities at pH 5.5. The diversity of active species decreased significantly at pH 4.5 and was dominated by Lactobacillus and Propionibacterium species, both of which have been previously found within carious lesions from children. Our approach allowed for identification of species that metabolize carbohydrates under different pH conditions and supports the importance of Lactobacilli and Propionibacterium in the development of childhood caries. Identification of species within healthy subjects that are active at low pH can lead to a better understanding of oral caries onset and generate appropriate targets for preventative measures in the early stages.

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

PubMed Central

Willner, Dana; Furlan, Mike; Schmieder, Robert; Grasis, Juris A.; Pride, David T.; Relman, David A.; Angly, Florent E.; McDole, Tracey; Mariella, Ray P.; Rohwer, Forest; Haynes, Matthew

2011-01-01

The human oropharynx is a reservoir for many potential pathogens, including streptococcal species that cause endocarditis. Although oropharyngeal microbes have been well described, viral communities are essentially uncharacterized. We conducted a metagenomic study to determine the composition of oropharyngeal DNA viral communities (both phage and eukaryotic viruses) in healthy individuals and to evaluate oropharyngeal swabs as a rapid method for viral detection. Viral DNA was extracted from 19 pooled oropharyngeal swabs and sequenced. Viral communities consisted almost exclusively of phage, and complete genomes of several phage were recovered, including Escherichia coli phage T3, Propionibacterium acnes phage PA6, and Streptococcus mitis phage SM1. Phage relative abundances changed dramatically depending on whether samples were chloroform treated or filtered to remove microbial contamination. pblA and pblB genes of phage SM1 were detected in the metagenomes. pblA and pblB mediate the attachment of S. mitis to platelets and play a significant role in S. mitis virulence in the endocardium, but have never previously been detected in the oral cavity. These genes were also identified in salivary metagenomes from three individuals at three time points and in individual saliva samples by PCR. Additionally, we demonstrate that phage SM1 can be induced by commonly ingested substances. Our results indicate that the oral cavity is a reservoir for pblA and pblB genes and for phage SM1 itself. Further studies will determine the association between pblA and pblB genes in the oral cavity and the risk of endocarditis. PMID:20547834

Hydrogen Peroxide Contributes to the Epithelial Cell Death Induced by the Oral Mitis Group of Streptococci

PubMed Central

Okahashi, Nobuo; Sumitomo, Tomoko; Nakata, Masanobu; Sakurai, Atsuo; Kuwata, Hirotaka; Kawabata, Shigetada

2014-01-01

Members of the mitis group of streptococci are normal inhabitants of the commensal flora of the oral cavity and upper respiratory tract of humans. Some mitis group species, such as Streptococcus oralis and Streptococcus sanguinis, are primary colonizers of the human oral cavity. Recently, we found that hydrogen peroxide (H2O2) produced by S. oralis is cytotoxic to human macrophages, suggesting that streptococcus-derived H2O2 may act as a cytotoxin. Since epithelial cells provide a physical barrier against pathogenic microbes, we investigated their susceptibility to infection by H2O2-producing streptococci in this study. Infection by S. oralis and S. sanguinis was found to stimulate cell death of Detroit 562, Calu-3 and HeLa epithelial cell lines at a multiplicity of infection greater than 100. Catalase, an enzyme that catalyzes the decomposition of H2O2, inhibited S. oralis cytotoxicity, and H2O2 alone was capable of eliciting epithelial cell death. Moreover, S. oralis mutants lacking the spxB gene encoding pyruvate oxidase, which are deficient in H2O2 production, exhibited reduced cytotoxicity toward Detroit 562 epithelial cells. In addition, enzyme-linked immunosorbent assays revealed that both S. oralis and H2O2 induced interleukin-6 production in Detroit 562 epithelial cells. These results suggest that streptococcal H2O2 is cytotoxic to epithelial cells, and promotes bacterial evasion of the host defense systems in the oral cavity and upper respiratory tracts. PMID:24498253

Polyphyllin G exhibits antimicrobial activity and exerts anticancer effects on human oral cancer OECM-1 cells by triggering G2/M cell cycle arrest by inactivating cdc25C-cdc2.

PubMed

Cai, Xiaoqing; Guo, Lele; Pei, Fei; Chang, Xiaoyun; Zhang, Rui

2018-04-15

Plant natural products have long been considered to be important sources of bioactive molecules. A large number of antimicrobial and anticancer agents have been isolated form plants. In the present study we evaluated the antimicrobial and anticancer activity of a plant derived secondery metabolite, Polyphyllin G. The results of antibacterial assays showed that Polyphyllin G prevented the growth of both Gram-positive and Gram-negative bacteria with minimum inhibitory concentrations (MICs) ranging from 13.1 to 78 μg/ml. Antifungal activity measured as inhibition of mycelium growth ranged between 38.32 and 56.50%. Further Polyphyllin G was also evaluated against a panel of cancer cell lines. The IC 50 of Polyphyllin G ranged from 10 to 65 μM. However the IC 50 of Polyphyllin G was found to be comparatively high (120 μM) against the normal FR2 cancer cell line. The lowest IC 50 of 10 μM was found against the oral cancer cell line OECM-1. Therefore further studies were carried out on this cell line only. Our results indicated that Polyphyllin G induced cell arrest in oral cancer OECM-1 cells by inactivation of cdc25C-cdc22 via ATM-Chk 1/2 stimulation. Therefore, we propose that Polyphyllin G might prove a lead molecule in the management of oral cancers and at the same time may prevent the growth of opportunistic microbes. Copyright © 2018 Elsevier Inc. All rights reserved.

Purification of Cu/Zn superoxide dismutase from Piper betle leaf and its characterization in the oral cavity.

PubMed

Liu, Yu-Ching; Lee, Miau-Rong; Chen, Chao-Jung; Lin, Yung-Chang; Ho, Heng-Chien

2015-03-04

The aim of this study was to purify protein(s) from Piper betle leaf for identification and further characterization. A functionally unknown protein was purified to apparent homogeneity with a molecular mass of 15.7 kDa and identified as Cu/Zn superoxide dismutase (SOD). The purified SOD appeared to be monomeric and converted to its dimeric form with increased enzymatic activity in betel nut oral extract. This irreversible conversion was mainly induced by slaked lime, resulting from the increase in pH of the oral cavity. Oral extract from chewing areca nut alone also induced SOD dimerization due to the presence of arginine. The enhanced activity of the SOD dimer was responsible for the continuous production of hydrogen peroxide in the oral cavity. Thus, SOD may contribute to oral carcinogenesis through the continuous formation of hydrogen peroxide in the oral cavity, in spite of its protective role against cancer in vivo.

Oral Candida colonization and candidiasis in patients with psoriasis.

PubMed

Bedair, Ahmad A; Darwazeh, Azmi M G; Al-Aboosi, Mustafa M

2012-11-01

The objective of this study was to investigate oral Candida colonization and candidosis in a group of patients with psoriasis and controls. A total of 100 patients with psoriasis and matched controls underwent the concentrated oral rinse test for Candida isolation. Candida species were identified by the VITEK 2 Identification System. Categorical variables were evaluated using the χ(2) test. The median Candida count was compared using the Mann-Whitney U test. Oral candidiasis was diagnosed in 3% of the patients with psoriasis. The Candida count and prevalence were significantly higher in the patients with psoriasis compared with controls (69% vs 44%, P < .001), but with no relationship to the severity or treatment of psoriasis. Oral Candida was significantly higher in late-onset (at age ≥30 years) compared with early-onset psoriasis (at age <30 years). Patients with psoriasis have increased oral Candida colonization and candidiasis. Further studies are needed to clarify the predisposing factor(s) for oral Candida in patients with psoriasis. Copyright © 2012 Elsevier Inc. All rights reserved.

Interleukin-17-induced protein lipocalin 2 is dispensable for immunity to oral candidiasis.

PubMed

Ferreira, Maria Carolina; Whibley, Natasha; Mamo, Anna J; Siebenlist, Ulrich; Chan, Yvonne R; Gaffen, Sarah L

2014-03-01

Oropharyngeal candidiasis (OPC; thrush) is an opportunistic fungal infection caused by the commensal microbe Candida albicans. Immunity to OPC is strongly dependent on CD4+ T cells, particularly those of the Th17 subset. Interleukin-17 (IL-17) deficiency in mice or humans leads to chronic mucocutaneous candidiasis, but the specific downstream mechanisms of IL-17-mediated host defense remain unclear. Lipocalin 2 (Lcn2; 24p3; neutrophil gelatinase-associated lipocalin [NGAL]) is an antimicrobial host defense factor produced in response to inflammatory cytokines, particularly IL-17. Lcn2 plays a key role in preventing iron acquisition by bacteria that use catecholate-type siderophores, and lipocalin 2(-/-) mice are highly susceptible to infection by Escherichia coli and Klebsiella pneumoniae. The role of Lcn2 in mediating immunity to fungi is poorly defined. Accordingly, in this study, we evaluated the role of Lcn2 in immunity to oral infection with C. albicans. Lcn2 is strongly upregulated following oral infection with C. albicans, and its expression is almost entirely abrogated in mice with defective IL-17 signaling (IL-17RA(-/-) or Act1(-/-) mice). However, Lcn2(-/-) mice were completely resistant to OPC, comparably to wild-type (WT) mice. Moreover, Lcn2 deficiency mediated protection from OPC induced by steroid immunosuppression. Therefore, despite its potent regulation during C. albicans infection, Lcn2 is not required for immunity to mucosal candidiasis.

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

Quantitative analysis of periodontal pathogens by ELISA and real-time polymerase chain reaction.

PubMed

Hamlet, Stephen M

2010-01-01

The development of analytical methods enabling the accurate identification and enumeration of bacterial species colonizing the oral cavity has led to the identification of a small number of bacterial pathogens that are major factors in the etiology of periodontal disease. Further, these methods also underpin more recent epidemiological analyses of the impact of periodontal disease on general health. Given the complex milieu of over 700 species of microorganisms known to exist within the complex biofilms found in the oral cavity, the identification and enumeration of oral periodontopathogens has not been an easy task. In recent years however, some of the intrinsic limitations of the more traditional microbiological analyses previously used have been overcome with the advent of immunological and molecular analytical methods. Of the plethora of methodologies reported in the literature, the enzyme-linked immunosorbent assay (ELISA), which combines the specificity of antibody with the sensitivity of simple enzyme assays and the polymerase chain reaction (PCR), has been widely utilized in both laboratory and clinical applications. Although conventional PCR does not allow quantitation of the target organism, real-time PCR (rtPCR) has the ability to detect amplicons as they accumulate in "real time" allowing subsequent quantitation. These methods enable the accurate quantitation of as few as 10(2) (using rtPCR) to 10(4) (using ELISA) periodontopathogens in dental plaque samples.

Identification of genes potentially responsible for extra-oral digestion and overcoming plant defense from salivary glands of the tarnished plant bug (Lygus lineolaris) using cDNA sequencing

USDA-ARS?s Scientific Manuscript database

Saliva is known to play a crucial role in tarnished plant bug (TPB, Lygus lineolaris) feeding. TPBs secrete saliva during feeding to facilitate the piercing into plant tissues. More importantly, the enzyme-rich saliva may be used for extra-oral digestion and for overcoming plant defense before the p...

A Brief Report of the Diagnostic Accuracy of Oral Reading Fluency and Reading Inventory Levels for Reading Failure Risk among Second- and Third-Grade Students

ERIC Educational Resources Information Center

Parker, David C.; Zaslofsky, Anne F.; Burns, Matthew K.; Kanive, Rebecca; Hodgson, Jennifer; Scholin, Sarah E.; Klingbeil, David A.

2015-01-01

The availability of psychometrically sound and usable universal screeners is a key component to successful early identification within a response-to-intervention model. The purpose of this study was to compare the diagnostic accuracy of oral reading fluency (ORF) and an informal reading inventory for identifying students considered at risk for…

Biological Water Processor and Forward Osmosis Secondary Treatment

NASA Technical Reports Server (NTRS)

Shull, Sarah; Meyer, Caitlin

2014-01-01

The goal of the Biological Water Processor (BWP) is to remove 90% organic carbon and 75% ammonium from an exploration-based wastewater stream for four crew members. The innovative design saves on space, power and consumables as compared to the ISS Urine Processor Assembly (UPA) by utilizing microbes in a biofilm. The attached-growth system utilizes simultaneous nitrification and denitrification to mineralize organic carbon and ammonium to carbon dioxide and nitrogen gas, which can be scrubbed in a cabin air revitalization system. The BWP uses a four-crew wastewater comprised of urine and humidity condensate, as on the ISS, but also includes hygiene (shower, shave, hand washing and oral hygiene) and laundry. The BWP team donates 58L per day of this wastewater processed in Building 7.

Adaptation of Candida albicans to commensalism in the gut.

PubMed

Prieto, Daniel; Correia, Inês; Pla, Jesús; Román, Elvira

2016-01-01

Candida albicans is a common resident of the oral cavity, GI tract and vagina in healthy humans where it establishes a commensal relationship with the host. Colonization of the gut, which is an important niche for the microbe, may lead to systemic dissemination and disease upon alteration of host defences. Understanding the mechanisms responsible for the adaptation of C. albicans to the gut is therefore important for the design of new ways of combating fungal diseases. In this review we discuss the available models to study commensalism of this yeast, the main mechanisms controlling the establishment of the fungus, such as microbiota, mucus layer and antimicrobial peptides, and the gene regulatory circuits that ensure its survival in this niche.

Meet the Microbes through the Microbe World Activities with Microbe the Magnificent and Mighty Microbe.

ERIC Educational Resources Information Center

Frame, Kathy, Ed.; Ryan, Karen, Ed.

The activities presented in this book are the product of the Community Outreach Initiative of the Microbial Literacy Collaborative (MLC). This activity book presents a balanced view of microbes, their benefits, and the diseases they cause. Each activity starts with an interesting introductory statement and includes goals, activity time, time to…

Evaluating the effectiveness of PrepSTART for promoting oral language and emergent literacy skills in disadvantaged preparatory students.

PubMed

Lennox, Maria; Westerveld, Marleen F; Trembath, David

2018-04-01

This study examined the effectiveness of a classroom-based intervention programme aimed at improving the oral language and emergent literacy skills of students from low socio-economic, culturally diverse backgrounds within their first formal year of schooling ("prep"). Data from 137 students were available for analysis. Participants were from three primary schools located in Queensland, Australia. Eight classes were allocated to intervention and two classes acted as a business as usual control. All students received literacy instruction as per the Australian Curriculum. However, the intervention group received 24 weeks of scripted, classroom-based, book-based intervention targeting code- and meaning-related emergent literacy skills. All students were assessed individually pre- and post-intervention on code-related measures (i.e. letter identification and phonological awareness) and meaning-related measures (i.e. vocabulary, oral narrative comprehension and retell). All students made significant improvement over time for all measures. Students in the intervention group showed significantly more progress than the business as usual group on all measures, except for letter identification and oral narrative comprehension. This classroom-based book-based intervention can improve the code- and meaning-related emergent literacy skills of prep students from low socio-economic backgrounds and provide these students with the building blocks for successful literacy acquisition.

Mobile Microbiome

PubMed Central

Han, Y.W.; Wang, X.

2013-01-01

The link between oral infections and adverse systemic conditions has attracted much attention in the research community. Several mechanisms have been proposed, including spread of the oral infection due to transient bacteremia resulting in bacterial colonization in extra-oral sites, systemic injury by free toxins of oral pathogens, and systemic inflammation caused by soluble antigens of oral pathogens. Mounting evidence supports a major role of the systemic spread of oral commensals and pathogens to distant body sites causing extra-oral infections and inflammation. We review here the most recent findings on systemic infections and inflammation complicated by oral bacteria, including cardiovascular disease, adverse pregnancy outcomes, rheumatoid arthritis, inflammatory bowel disease and colorectal cancer, respiratory tract infections, and organ inflammations and abscesses. The recently identified virulence mechanisms of oral species Fusobacterium nucleatum, Porphyromonas gingivalis, Streptococcus mutans, and Campylobacter rectus are also reviewed. A pattern emerges indicating that only select subtype(s) of a given species, e.g., F. nucleatum subspecies animalis and polymorphum and S. mutans non-c serotypes, are prone to extra-oral translocation. These findings advocate the importance of identification and quantification of potential pathogens at the subtype levels for accurate prediction of disease potential. PMID:23625375

Close association between oral Candida species and oral mucosal disorders in patients with xerostomia.

PubMed

Shinozaki, S; Moriyama, M; Hayashida, J-N; Tanaka, A; Maehara, T; Ieda, S; Nakamura, S

2012-10-01

Heightened interest in oral health has lead to an increase in patients complaining of xerostomia, which is associated with various oral mucosal disorders. In this study, we investigated the relationship between Candida species and oral mucosal disorders in patients with xerostomia. We evaluated whole salivary flow rate and presence of oral mucosal disorders in 48 patients with xerostomia and 15 healthy controls. The number of Candida species was measured as colony-forming units after propagation on selective medium. Identification of Candida at the species level was carried out by polymerase chain reaction and restriction fragment length polymorphism analysis. We then examined the relationship between Candida species and oral mucosal symptoms. Compared with controls, patients with xerostomia exhibited significantly decreased whole salivary flow rate, increased rate of oral mucosal symptoms, and higher numbers of Candida. Salivary flow rate negatively correlated with the number Candida. Among patients with oral candidiasis, Candida albicans was isolated from the tongue mucosa and Candida glabrata was isolated from the angle of the mouth. These results suggest that particular Candida species are involved in the pathogenesis of oral mucosal disorders in patients with xerostomia. © 2012 John Wiley & Sons A/S.

Oral-facial-digital syndrome type 1 with hypothalamic hamartoma and Dandy-Walker malformation.

PubMed

Azukizawa, Takayuki; Yamamoto, Masahito; Narumiya, Seirou; Takano, Tomoyuki

2013-04-01

We report a 1-year-old girl with oral-facial-digital syndrome type 1 with multiple malformations of the oral cavity, face, digits, and central nervous system, including agenesis of the corpus callosum, the presence of intracerebral cysts, and agenesis of the cerebellar vermis, which is associated with the subarachnoid space separating the medial sides of the cerebellar hemispheres. This child also had a hypothalamic hamartoma and a Dandy-Walker malformation, which have not been reported previously. The clinical features, including cerebral malformations, in several types of oral-facial-digital syndrome, overlap with each other. Further accumulation of new case reports and identification of new genetic mutations in oral-facial-digital syndrome may provide novel and important insights into the genetic mechanisms of this syndrome. Copyright © 2013 Elsevier Inc. All rights reserved.

Progress in oral personalized medicine: contribution of ‘omics’

PubMed Central

Glurich, Ingrid; Acharya, Amit; Brilliant, Murray H.; Shukla, Sanjay K.

2015-01-01

Background Precision medicine (PM), representing clinically applicable personalized medicine, proactively integrates and interprets multidimensional personal health data, including clinical, ‘omics’, and environmental profiles, into clinical practice. Realization of PM remains in progress. Objective The focus of this review is to provide a descriptive narrative overview of: 1) the current status of oral personalized medicine; and 2) recent advances in genomics and related ‘omic’ and emerging research domains contributing to advancing oral-systemic PM, with special emphasis on current understanding of oral microbiomes. Design A scan of peer-reviewed literature describing oral PM or ‘omic’-based research conducted on humans/data published in English within the last 5 years in journals indexed in the PubMed database was conducted using mesh search terms. An evidence-based approach was used to report on recent advances with potential to advance PM in the context of historical critical and systematic reviews to delineate current state-of-the-art technologies. Special focus was placed on oral microbiome research associated with health and disease states, emerging research domains, and technological advances, which are positioning realization of PM. Results This review summarizes: 1) evolving conceptualization of personalized medicine; 2) emerging insight into roles of oral infectious and inflammatory processes as contributors to both oral and systemic diseases; 3) community shifts in microbiota that may contribute to disease; 4) evidence pointing to new uncharacterized potential oral pathogens; 5) advances in technological approaches to ‘omics’ research that will accelerate PM; 6) emerging research domains that expand insights into host–microbe interaction including inter-kingdom communication, systems and network analysis, and salivaomics; and 7) advances in informatics and big data analysis capabilities to facilitate interpretation of host and microbiome-associated datasets. Furthermore, progress in clinically applicable screening assays and biomarker definition to inform clinical care are briefly explored. Conclusion Advancement of oral PM currently remains in research and discovery phases. Although substantive progress has been made in advancing the understanding of the role of microbiome dynamics in health and disease and is being leveraged to advance early efforts at clinical translation, further research is required to discern interpretable constituency patterns in the complex interactions of these microbial communities in health and disease. Advances in biotechnology and bioinformatics facilitating novel approaches to rapid analysis and interpretation of large datasets are providing new insights into oral health and disease, potentiating clinical application and advancing realization of PM within the next decade. PMID:26344171

Pathogenomics: an updated European Research Agenda.

PubMed

Demuth, Andreas; Aharonowitz, Yair; Bachmann, Till T; Blum-Oehler, Gabriele; Buchrieser, Carmen; Covacci, Antonello; Dobrindt, Ulrich; Emödy, Levente; van der Ende, Arie; Ewbank, Jonathan; Fernández, Luis Angel; Frosch, Matthias; García-Del Portillo, Francisco; Gilmore, Michael S; Glaser, Philippe; Goebel, Werner; Hasnain, Seyed E; Heesemann, Jürgen; Islam, Khalid; Korhonen, Timo; Maiden, Martin; Meyer, Thomas F; Montecucco, Cesare; Oswald, Eric; Parkhill, Julian; Pucciarelli, M Graciela; Ron, Eliora; Svanborg, Catharina; Uhlin, Bernt Eric; Wai, Sun Nyunt; Wehland, Jürgen; Hacker, Jörg

2008-05-01

The emerging genomic technologies and bioinformatics provide novel opportunities for studying life-threatening human pathogens and to develop new applications for the improvement of human and animal health and the prevention, treatment, and diagnosis of infections. Based on the ecology and population biology of pathogens and related organisms and their connection to epidemiology, more accurate typing technologies and approaches will lead to better means of disease control. The analysis of the genome plasticity and gene pools of pathogenic bacteria including antigenic diversity and antigenic variation results in more effective vaccines and vaccine implementation programs. The study of newly identified and uncultivated microorganisms enables the identification of new threats. The scrutiny of the metabolism of the pathogen in the host allows the identification of new targets for anti-infectives and therapeutic approaches. The development of modulators of host responses and mediators of host damage will be facilitated by the research on interactions of microbes and hosts, including mechanisms of host damage, acute and chronic relationships as well as commensalisms. The study of multiple pathogenic and non-pathogenic microbes interacting in the host will improve the management of multiple infections and will allow probiotic and prebiotic interventions. Needless to iterate, the application of the results of improved prevention and treatment of infections into clinical tests will have a positive impact on the management of human and animal disease. The Pathogenomics Research Agenda draws on discussions with experts of the Network of Excellence "EuroPathoGenomics" at the management board meeting of the project held during 18-21 April 2007, in the Villa Vigoni, Menaggio, Italy. Based on a proposed European Research Agenda in the field of pathogenomics by the ERA-NET PathoGenoMics the meeting's participants updated the established list of topics as the research agenda for the future.

Identification of infectious microbiota from oral cavity environment of various population group patients as a preventive approach to human health risk factors.

PubMed

Zawadzki, Paweł J; Perkowski, Konrad; Starościak, Bohdan; Baltaza, Wanda; Padzik, Marcin; Pionkowski, Krzysztof; Chomicz, Lidia

2016-12-23

This study presents the results of comparative investigations aimed to determine microbiota that can occur in the oral environment in different human populations. The objective of the research was to identify pathogenic oral microbiota, the potential cause of health complications in patients of different population groups. The study included 95 patients requiring dental or surgical treatment; their oral cavity environment microbiota as risk factors of local and general infections were assessed. In clinical assessment, differences occurred in oral cavity conditions between patients with malformations of the masticatory system, kidney allograft recipients and individuals without indications for surgical procedures. The presence of various pathogenic and opportunistic bacterial strains in oral cavities were revealed by direct microscopic and in vitro culture techniques. Colonization of oral cavities of patients requiring surgical treatment by the potentially pathogenic bacteria constitutes the threat of their spread, and development of general infections. Assessment of oral cavity infectious microbiota should be performed as a preventive measure against peri-surgical complications.

Surface, Water and Air Biocharacterization - A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft Environment

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Cruz, Patricia; Buttner, Mark P.

2009-01-01

A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft (SWAB) will use advanced molecular techniques to comprehensively evaluate microbes on board the space station, including pathogens (organisms that may cause disease). It also will track changes in the microbial community as spacecraft visit the station and new station modules are added. This study will allow an assessment of the risk of microbes to the crew and the spacecraft. Research Summary: Previous microbial analysis of spacecraft only identify microorganisms that will grow in culture, omitting greater than 90% of all microorganisms including pathogens such as Legionella (the bacterium which causes Legionnaires' disease) and Cryptosporidium (a parasite common in contaminated water) The incidence of potent allergens, such as dust mites, has never been systematically studied in spacecraft environments and microbial toxins have not been previously monitored. This study will use modern molecular techniques to identify microorganisms and allergens. Direct sampling of the ISS allows identification of the microbial communities present, and determination of whether these change or mutate over time. SWAB complements the nominal ISS environmental monitoring by providing a comparison of analyses from current media-based and advanced molecular-based technologies.

Microbial Impact on Success of Human Exploration Missions

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Groves, T. O.; Paloski, W. H. (Technical Monitor)

2000-01-01

The purpose of this study is to identify microbiological risks associated with space exploration and identify potential countermeasures available. Identification of microbial risks associated with space habitation requires knowledge of the sources and expected types of microbial agents. Crew data along with environmental data from water, surfaces, air, and free condensate are utilized in risk examination. Data from terrestrial models are also used. Microbial risks to crew health include bacteria, fungi, protozoa, and viruses. Adverse effects of microbes include: infections, allergic reactions, toxin production, release of volatiles, food spoilage, plant disease, material degradation, and environmental contamination. Risk is difficult to assess because of unknown potential changes in microbes (e.g., mutation) and the human host (e.g., immune changes). Prevention of adverse microbial impacts is preferred over remediation. Preventative measures include engineering measures (e.g., air filtration), crew microbial screening, acceptability standards, and active verification by onboard monitoring. Microbiological agents are important risks to human health and performance during space flight and risks increase with mission duration. Acceptable risk level must be defined. Prevention must be given high priority. Careful screening of crewmembers and payloads is an important element of any risk mitigation plan. Improved quantitation of microbiological risks is a high priority.

Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards

PubMed Central

2016-01-01

The literature of environmental microbiology broadly discusses issues associated with microbial hazards in archives, but these publications are mainly devoted to paper documents. There are few articles on historical parchment documents, which used to be very important for the development of literature and the art of writing. These studies present a broad spectrum of methods for the assessment of biodeterioration hazards of the parchment document in question. They are based on both conventional microbiological methods and advanced techniques of molecular biology. Here, a qualitative analysis was conducted, based on genetic identification of bacteria and fungi present on the document as well as denaturing gradient gel electrophoresis profiling and examining the destructive potential of isolated microbes. Moreover, the study involved a quantitative and qualitative microbiological assessment of the indoor air in the room where the parchment was kept. The microbes with the highest destructive potential that were isolated from the investigated item were Bacillus cereus and Acinetobacter lwoffii bacteria and Penicillium chrysogenum, Chaetomium globosum, and Trichoderma longibrachiatum fungi. The presence of the B. cereus strain was particularly interesting since, under appropriate conditions, it leads to complete parchment degradation within several days. PMID:26896133

42 CFR 493.643 - Fee for determination of program compliance.

Code of Federal Regulations, 2011 CFR

2011-10-01

... antibody identification. (vi) The specialty of Pathology, which includes the following subspecialties: (A) Cytology. (B) Histopathology. (C) Oral pathology. (vii) The specialty of Radiobioassay. (viii) The...

Detection of right-to-left shunts: comparison between the International Consensus and Spencer Logarithmic Scale criteria.

PubMed

Lao, Annabelle Y; Sharma, Vijay K; Tsivgoulis, Georgios; Frey, James L; Malkoff, Marc D; Navarro, Jose C; Alexandrov, Andrei V

2008-10-01

International Consensus Criteria (ICC) consider right-to-left shunt (RLS) present when Transcranial Doppler (TCD) detects even one microbubble (microB). Spencer Logarithmic Scale (SLS) offers more grades of RLS with detection of >30 microB corresponding to a large shunt. We compared the yield of ICC and SLS in detection and quantification of a large RLS. We prospectively evaluated paradoxical embolism in consecutive patients with ischemic strokes or transient ischemic attack (TIA) using injections of 9 cc saline agitated with 1 cc of air. Results were classified according to ICC [negative (no microB), grade I (1-20 microB), grade II (>20 microB or "shower" appearance of microB), and grade III ("curtain" appearance of microB)] and SLS criteria [negative (no microB), grade I (1-10 microB), grade II (11-30 microB), grade III (31100 microB), grade IV (101300 microB), grade V (>300 microB)]. The RLS size was defined as large (>4 mm) using diameter measurement of the septal defects on transesophageal echocardiography (TEE). TCD comparison to TEE showed 24 true positive, 48 true negative, 4 false positive, and 2 false negative cases (sensitivity 92.3%, specificity 92.3%, positive predictive value (PPV) 85.7%, negative predictive value (NPV) 96%, and accuracy 92.3%) for any RLS presence. Both ICC and SLS were 100% sensitive for detection of large RLS. ICC and SLS criteria yielded a false positive rate of 24.4% and 7.7%, respectively when compared to TEE. Although both grading scales provide agreement as to any shunt presence, using the Spencer Scale grade III or higher can decrease by one-half the number of false positive TCD diagnoses to predict large RLS on TEE.

The ``Adopt A Microbe'' project: Web-based interactive education connected with scientific ocean drilling

NASA Astrophysics Data System (ADS)

Orcutt, B. N.; Bowman, D.; Turner, A.; Inderbitzen, K. E.; Fisher, A. T.; Peart, L. W.; Iodp Expedition 327 Shipboard Party

2010-12-01

We launched the "Adopt a Microbe" project as part of Integrated Ocean Drilling Program (IODP) Expedition 327 in Summer 2010. This eight-week-long education and outreach effort was run by shipboard scientists and educators from the research vessel JOIDES Resolution, using a web site (https://sites.google.com/site/adoptamicrobe) to engage students of all ages in an exploration of the deep biosphere inhabiting the upper ocean crust. Participants were initially introduced to a cast of microbes (residing within an ‘Adoption Center’ on the project website) that live in the dark ocean and asked to select and virtually ‘adopt’ a microbe. A new educational activity was offered each week to encourage learning about microbiology, using the adopted microbe as a focal point. Activities included reading information and asking questions about the adopted microbes (with subsequent responses from shipboard scientists), writing haiku about the adopted microbes, making balloon and fabric models of the adopted microbes, answering math questions related to the study of microbes in the ocean, growing cultures of microbes, and examining the gases produced by microbes. In addition, the website featured regular text, photo and video updates about the science of the expedition using a toy microbe as narrator, as well as stories written by shipboard scientists from the perspective of deep ocean microbes accompanied by watercolor illustrations prepared by a shipboard artist. Assessment methods for evaluating the effectiveness of the Adopt a Microbe project included participant feedback via email and online surveys, website traffic monitoring, and online video viewing rates. Quantitative metrics suggest that the “Adope A Microbe” project was successful in reaching target audiences and helping to encourage and maintain interest in topics related to IODP Expedition 327. The “Adopt A Microbe” project mdel can be adapted for future oceanographic expeditions to help connect the public at large to cutting-edge, exploratory research and for engaging students in active learning.

Development and Preliminary Evaluation of an Adaptation of Word Identification Fluency for Beginning Readers in New Zealand

ERIC Educational Resources Information Center

Schaughency, Elizabeth; McLennan, Kathryn M.; McDowall, Philippa S.

2015-01-01

A New Zealand (NZ) version of Word Identification Fluency (NZWIF) was administered to 120 children in their second school year at the beginning, middle, and end of the year, along with a curriculum-based measure of oral passage reading fluency at mid- and end-year. Outcome measures included standardized and high-stakes school-used indicators of…

A perspective on inter-kingdom signaling in plant-beneficial microbe interactions.

PubMed

Rosier, Amanda; Bishnoi, Usha; Lakshmanan, Venkatachalam; Sherrier, D Janine; Bais, Harsh P

2016-04-01

Recent work has shown that the rhizospheric and phyllospheric microbiomes of plants are composed of highly diverse microbial species. Though the information pertaining to the diversity of the aboveground and belowground microbes associated with plants is known, an understanding of the mechanisms by which these diverse microbes function is still in its infancy. Plants are sessile organisms, that depend upon chemical signals to interact with the microbiota. Of late, the studies related to the impact of microbes on plants have gained much traction in the research literature, supporting diverse functional roles of microbes on plant health. However, how these microbes interact as a community to confer beneficial traits to plants is still poorly understood. Recent advances in the use of "biologicals" as bio-fertilizers and biocontrol agents for sustainable agricultural practices is promising, and a fundamental understanding of how microbes in community work on plants could help this approach be more successful. This review attempts to highlight the importance of different signaling events that mediate a beneficial plant microbe interaction. Fundamental research is needed to understand how plants react to different benign microbes and how these microbes are interacting with each other. This review highlights the importance of chemical signaling, and biochemical and genetic events which determine the efficacy of benign microbes to promote the development of beneficial traits in plants.

Coercion in the Evolution of Plant-Microbe Communication: A Perspective.

PubMed

Rowe, S L; Norman, J S; Friesen, M L

2018-06-06

Plants and microbes are dependent on chemical signals as a means of interkingdom communication. There are two predicted paths for the evolution of these signals. Ritualization is the oft-assumed pathway for the evolution of plant-microbe communication systems. In this process, chemical signals, which benefit both receiver and sender, evolve from chemical cues, which benefit only the receiver. However, plant-microbe signaling may evolve from coercive interactions as well, a process known as sensory manipulation. Here, we aim to highlight the prevalence of coercive interactions and discuss sensory manipulation in the context of plant-microbe interactions. We present two examples of stabilized coercion: microbial coercion of plants via the release of phytohormones and plant coercion of microbes via manipulation of quorum-sensing compounds. Furthermore, we provide an evolutionary framework for the emergence of signaling from coercive plant-microbe interactions through the process of sensory manipulation. We hope that researchers will recognize the relevance of coercive interactions in plant-microbe systems and consider sensory manipulation as a plausible evolutionary trajectory for the emergence of plant-microbe signaling.

Characterization of Volume F Trash from Four Recent STS Missions: Microbial Occurrence, Numbers, and Identifications

NASA Technical Reports Server (NTRS)

Strayer, Richard F.; Hummerick, Mary E.; Richards, Jeffrey T.; McCoy, LaShelle E.; Roberts, Michael S.; Wheeler, Raymond M.

2011-01-01

The fate of space-generated solid wastes, including trash, for future missions is under consideration by NASA. Several potential treatment options are under active technology development. Potential fates for space-generated solid wastes: Storage without treatment; storage after treatment(s) including volume reduction, water recovery, sterilization, and recovery plus recycling of waste materials. For this study, a microbial characterization was made on trash returned from four recent STS missions. The material analyzed were 'Volume F' trash and other bags of accompanying trash. This is the second of two submitted papers on these wastes. This first one covered trash content, weight and water content. Upon receipt, usually within 2 days of landing, trash contents were catalogued and placed into categories: drink containers, food waste, personal hygiene items, and packaging materials, i.e., plastic film and duct tape. Microbial counts were obtained with cultivatable counts on agar media and direct counts using Acridine Orange fluorescent stain (AODC). Trash bag surfaces, 25 square cm , were also sampled. Direct counts were approximately 1 x 10(exp 6) microbes/square cm and cultivatable counts ranged from 1 x 10 to 1 X 10(exp 4) microbes/ square cm-2. Aerobic microbes, aerobic sporeformers, and yeasts plus molds were common for all four missions. Waste items from each category were placed into sterile ziplock bags and 1.5 L sterile DI water added. These were then dispersed by hand shaking for 2 min. prior to inoculation of count media or determining AODC. In general, cultivatable microbes were found in drinks, food wastes, and personal hygiene items. Direct counts were usually higher than cultivatable counts. Some pathogens were found: Staphylococcus auerus, Escherichia coli (fecal wastes). Count ranges: drink pouches - AODC 2 x 10(exp 6) to 1 X 10(exp 8) g(sub fw) (exp -1); cultivatable counts variable between missions; food wastes: Direct counts were close to aerobic plate counts. Counts ranged from 10(exp 6) to 10(exp 9) per g(sub fw). Identities of isolates from cultivation media were obtained using a Biolog Microbial ID System or microSEQ molecular ID methodology using an ABI3130 gene analyzer.

Diagnostic profiling of salivary exosomal microRNAs in oral lichen planus patients.

PubMed

Byun, J-S; Hong, S-H; Choi, J-K; Jung, J-K; Lee, H-J

2015-11-01

Oral lichen planus is a chronic inflammatory oral mucosal disease whose exact cause is unclear and which requires efficient diagnostic and therapeutic strategies. Identification of disease-specific biomarkers in saliva is an easy, quick, and non-invasive approach for molecular diagnosis. This study was designed to examine salivary exosomal microRNAs (miRNAs) that could be candidates for diagnosing and elucidating the pathogenesis of oral lichen planus. We compared miRNA profiles of salivary exosomes of patients with oral lichen planus with those of healthy controls. Saliva samples from 16 patients with oral lichen planus and eight healthy controls were divided into two sets and examined using miRNA microarray analysis and TaqMan quantitative PCR. The three miRNAs identified (miR-4484, miR-1246, and miR-1290) were further validated. Of these, miR-4484 was significantly upregulated in the salivary exosomes of patients with oral lichen planus. This study thus identifies a potential miRNA biomarker for oral lichen planus and provides insight into the functions of miRNAs in the pathogenesis of oral inflammatory diseases. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Spirocyclic ureas: orally bioavailable 11 beta-HSD1 inhibitors identified by computer-aided drug design.

PubMed

Tice, Colin M; Zhao, Wei; Xu, Zhenrong; Cacatian, Salvacion T; Simpson, Robert D; Ye, Yuan-Jie; Singh, Suresh B; McKeever, Brian M; Lindblom, Peter; Guo, Joan; Krosky, Paula M; Kruk, Barbara A; Berbaum, Jennifer; Harrison, Richard K; Johnson, Judith J; Bukhtiyarov, Yuri; Panemangalore, Reshma; Scott, Boyd B; Zhao, Yi; Bruno, Joseph G; Zhuang, Linghang; McGeehan, Gerard M; He, Wei; Claremon, David A

2010-02-01

Structure-guided drug design led to the identification of a class of spirocyclic ureas which potently inhibit human 11beta-HSD1 in vitro. Lead compound 10j was shown to be orally bioavailable in three species, distributed into adipose tissue in the mouse, and its (R) isomer 10j2 was efficacious in a primate pharmacodynamic model. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

The Relations among Oral and Silent Reading Fluency and Comprehension in Middle School: Implications for Identification and Instruction of Students with Reading Difficulties

ERIC Educational Resources Information Center

Denton, Carolyn A.; Barth, Amy E.; Fletcher, Jack M.; Wexler, Jade; Vaughn, Sharon; Cirino, Paul T.; Romain, Melissa; Francis, David J.

2011-01-01

The purpose of this study was to investigate the relations among oral and silent reading fluency and reading comprehension for students in Grades 6 to 8 (n = 1,421) and the use of fluency scores to identify middle school students who are at risk for failure on a high-stakes reading test. Results indicated moderate positive relations between…

Identification and functional characterization of an uncharacterized antimicrobial peptide from a ciliate Paramecium caudatum.

PubMed

Cui, Pengfei; Dong, Yuan; Li, Zhijian; Zhang, Yubo; Zhang, Shicui

2016-07-01

The global ever-growing concerns about multi-drug resistant (MDR) microbes leads to urgent demands for exploration of new antibiotics including antimicrobial peptides (AMPs). Here we demonstrated that a cDNA from Ciliata Paramecium caudatum, designated Pcamp1, coded for a protein with features characteristic of AMPs, which is not homologous to any AMPs currently known. Both the C-terminal 91 amino acid residues of PcAMP1, cPcAMP1, expressed in Escherichia coli and the C-terminal 26 amino acid residues (predicted mature AMP), cPcAMP1/26, synthesized, underwent a coil-to-helix transition in the presence of TFE, SDS or DPC. Functional assays revealed that cPcAMP1 and cPcAMP1/26 were both able to kill Aeromonas hydrophila and Staphylococcus aureus. ELISA showed that cPcAMP1 and cPcAMP1/26 were able to bind to microbe-associated molecular pattern molecules LPS and LTA, which was further corroborated by the observations that cPcAMP1 could deposit onto the bacterial membranes. Importantly, both cPcAMP1 and cPcAMP1/26 were able to induce bacterial membrane permeabilization and depolarization, and to increase intracellular ROS levels. Additionally, cPcAMP1 and cPcAMP1/26 were not cytotoxic to mammalian cells. Taken together, our results show that PcAMP1 is a potential AMP with a membrane selectivity towards bacterial cells, which renders it a promising template for the design of novel peptide antibiotics against MDR microbes. It also shows that use of signal conserved sequence of AMPs can be an effective tool to identify potential AMPs across different animal classes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbiological Contamination of Spacecraft

NASA Technical Reports Server (NTRS)

Pierson, D. L.; Bruce, R. J.; Groves, T. O.; Novikova, N. D.; Viktorov, A. N.

2000-01-01

The International Space Station (ISS) Phase1 Program resulted in seven US astronauts residing aboard the Russian Space Station Mir between March 1995 and May 1998. Collaboration between U.S. and Russian scientists consisted of collection and analyses of samples from the crewmembers and the Mir and Shuttle environments before, during, and after missions that lasted from 75 to 209 days in duration. The effects of long-duration space flight on the microbial characteristics of closed life support systems and the interactions of microbes with the spacecraft environment and crewmembers were investigated. Air samples were collected using a Russian or U.S.-supplied sampler (SAS, RCS, or Burkard,) while surface samples were collected using contact slides (Hycon) or swabs. Mir recycled condensate and stored potable water sources were analyzed using the U.S.-supplied Water Experiment Kit. In-flight analysis consisted of enumeration of levels of bacteria and fungi. Amounts of microorganisms seen in the air and on surfaces were mostly within acceptability lin1its; observed temporal fluctuations in levels of microbes probably reflect changes in environmental conditions (e.g., humidity). All Mir galley hot water samples were within the standards set for Mir and the ISS. Microbial isolates were returned to Earth for identification of bacterial and fungal isolates. Crew samples (nose, throat, skin, urine, and feces) were analyzed using methods approved for the medical evaluations of Shuttle flight crews. No significant changes in crew microbiota were found during space flight or upon return relative to preflight results. Dissemination of microbes between the crew and environment was demonstrated by D A fingerprinting. Some biodegradation of spacecraft materials was observed. Accumulation of condensate allowed for the recovery of a wide range of bacteria and fungi as well as some protozoa and dust mites.

Significance of Plant Root Microorganisms in Reclaiming Water in CELSS

NASA Technical Reports Server (NTRS)

Bubenheim, David L.; Greene, Catherine; Wignarajah, Kanapathipillai; Kliss, Mark H. (Technical Monitor)

1996-01-01

Since many microorganisms demonstrate the ability to quickly break down complex mixtures of waste and environmental contaminants, examining their potential use for water recycling in a closed environment is appealing. Water contributes approximately 90 percent of the life sustaining provisions in a human space habitat. Nearly half of the daily water requirements will be used for personal hygiene and dish washing. The primary contaminants of the used "gray" water will be the cleansing agents or soaps used to carry out these functions. Reclaiming water from the gray water waste streams is one goal of the NASA program, Controlled Ecological Life Support Systems (CELSS). The microorganisms of plane roots are well documented to be of a beneficial effect to promote plant growth. Most plants exhibit a range of bacteria and fungi which can be highly plant-specific. In our investigations with lettuce grown in hydroponic culture, we identified a microflora of normal rhizosphere. When the roots were exposed to an anionic surfactant, the species diversity changed, based on morphological characteristics, with the numbers of species being reduced from 7 to 2 after 48 hours of exposure. In addition, the species that became dominant in the presence of the anionic surfactant also demonstrated a dramatic increase in population density which corresponded to the degradation of the surfactant in the root zone. The potential for using these or other rhizosphere bacteria as a primary or secondary waste processor is promising, but a number of issues still warrant investigation; these include but are not limited to: (1) the full identification of the microbes, (2) the classes of surfactants the microbes will degrade, (3) the environmental conditions required for optimal processing efficiency and (4) the ability of transferring the microbes to a non-living solid matrix such as a bioreactor.

A novel method for rapidly isolating microbes that suppress soil-borne phytopathogens

NASA Astrophysics Data System (ADS)

Cooper, Sarah; Agnew, Linda; Pereg, Lily

2016-04-01

Seedling establishment faces a large number of challenges related to soil physical properties as well as to fungal root diseases. It is extremely difficult to eliminate fungal pathogens from soils where their populations are established due to the persistent nature of their spores and since fumigation of resident fungi is very ineffective in clay-containing soils. Therefore it is necessary to find ways to overcome disease in areas where the soils are infected with fungal phytopathogens. The phenomenon of disease suppressive soils, where the pathogen is present but no disease observed, suggests that microbial antagonism in the soil may lead to the suppression of the growth of fungal pathogens. There are also cases in the literature where soil microorganisms were isolated that suppress the growth of phytopathogens. Antibiosis is one of the most important mechanisms responsible for fungal antagonism, with some significant antifungal compounds involved including antibiotics, volatile organic compounds, hydrogen cyanide and lytic enzymes. Isolation of pathogen-suppressive microorganisms from the soil is time consuming and tedious. We established a simple method for direct isolation of soil microbes (bacteria and fungi) that suppress fungal phytopathogens as well as procedures for confirmation of disease suppression. We will discuss such methods, which were so far tested with the cotton fungal pathogens Thielaviopsis basicola, Verticillium dahliae and Fusarium oxysporum and Verticillium fungicola. We have isolated a diversity of T. basicola-suppressive fungi and bacteria from two vastly different soil types. Identification of the antagonistic isolates revealed that they are a diverse lot, some belong to groups known to be suppressive of a wide range of fungal pathogens, endorsing the power of this technique to rapidly and directly isolate soil-borne microbes antagonistic to a wide variety of fungal pathogens.

Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges.

PubMed

Deng, Ping; Swanson, Kelly S

2015-01-01

High-throughput DNA sequencing techniques allow for the identification and characterisation of microbes and their genes (microbiome). Using these new techniques, microbial populations in several niches of the human body, including the oral and nasal cavities, skin, urogenital tract and gastrointestinal tract, have been described recently. Very little data on the microbiome of companion animals exist, and most of the data have been derived from the analysis of the faeces of healthy laboratory animals. High-throughput assays provide opportunities to study the complex and dense populations of the gut microbiota, including bacteria, archaea, fungi, protozoa and viruses. Our laboratory and others have recently described the predominant microbial taxa and genes of healthy dogs and cats and how these respond to dietary interventions. In general, faecal microbial phylogeny (e.g. predominance of Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria) and functional capacity (e.g. major functional groups related to carbohydrate, protein, DNA and vitamin metabolism; virulence factors; and cell wall and capsule) of the canine and feline gut are similar to those of the human gut. Initial sequencing projects have provided a glimpse of the microbial super-organism that exists within the canine and feline gut, but leaves much to be explored and discovered. As DNA provides information only about potential functions, studies that focus on the microbial transcriptome, metabolite profiles, and how microbiome changes affect host physiology and health are clearly required. Future studies must determine how diet composition, antibiotics and other drug therapies, breed and disease affect or are affected by the gut microbiome and how this information may be used to improve diets, identify disease biomarkers and develop targeted disease therapies.

In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

PubMed Central

Hatzenpichler, Roland; Scheller, Silvan; Tavormina, Patricia L; Babin, Brett M; Tirrell, David A; Orphan, Victoria J

2014-01-01

Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non-canonical amino acid tagging (BONCAT), is based on the in vivo incorporation of the non-canonical amino acid L-azidohomoalanine (AHA), a surrogate for l-methionine, followed by fluorescent labelling of AHA-containing cellular proteins by azide-alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)-targeted fluorescence in situ hybridization (FISH), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT-FISH to study microbial physiology in situ. A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano-scale secondary ion mass spectrometry (15NH3 assimilation) for individual cells within a sediment-sourced enrichment culture showed concordance between AHA-positive cells and 15N enrichment. BONCAT-FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single-cell level. PMID:24571640

The weapon potential of a microbe.

PubMed

Casadevall, Arturo; Pirofski, Liise-anne

2004-06-01

The designation of a microbe as a potential biological weapon poses the vexing question of how such a decision is made given the many pathogenic microbes that cause disease. Analysis of the properties of microbes that are currently considered biological weapons against humans revealed no obvious relationship to virulence, except that all are pathogenic for humans. Notably, the weapon potential of a microbe rather than its pathogenic properties or virulence appeared to be the major consideration when categorizing certain agents as biological weapons. In an effort to standardize the assessment of the risk that is posed by microbes as biological warfare agents using the basic principles of microbial communicability (defined here as a parameter of transmission) and virulence, a simple formula is proposed for estimating the weapon potential of a microbe.

Genomic dissection of host-microbe and microbe-microbe interactions for advanced plant breeding.

PubMed

Kroll, Samuel; Agler, Matthew T; Kemen, Eric

2017-04-01

Agriculture faces many emerging challenges to sustainability, including limited nutrient resources, losses from diseases caused by current and emerging pathogens and environmental degradation. Microorganisms have great importance for plant growth and performance, including the potential to increase yields, nutrient uptake and pathogen resistance. An urgent need is therefore to understand and engineer plants and their associated microbial communities. Recent massive genomic sequencing of host plants and associated microbes offers resources to identify novel mechanisms of communal assembly mediated by the host. For example, host-microbe and microbe-microbe interactions are involved in niche formation, thereby contributing to colonization. By leveraging genomic resources, genetic traits underlying those mechanisms will become important resources to design plants selecting and hosting beneficial microbial communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Stress as a Normal Cue in the Symbiotic Environment.

PubMed

Schwartzman, Julia A; Ruby, Edward G

2016-05-01

All multicellular hosts form associations with groups of microorganisms. These microbial communities can be taxonomically diverse and dynamic, and their persistence is due to robust, and sometimes coevolved, host-microbe and microbe-microbe interactions. Chemical and physical sources of stress are prominently situated in this molecular exchange, as cues for cellular responses in symbiotic microbes. Stress in the symbiotic environment may arise from three sources: host tissues, microbe-induced immune responses, or other microbes in the host environment. The responses of microbes to these stresses can be general or highly specialized, and collectively may contribute to the stability of the symbiotic system. In this review, we highlight recent work that emphasizes the role of stress as a cue in the symbiotic environment of plants and animals. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Dormant Microbial Component in the Development of Preeclampsia

PubMed Central

Kell, Douglas B.; Kenny, Louise C.

2016-01-01

Preeclampsia (PE) is a complex, multisystem disorder that remains a leading cause of morbidity and mortality in pregnancy. Four main classes of dysregulation accompany PE and are widely considered to contribute to its severity. These are abnormal trophoblast invasion of the placenta, anti-angiogenic responses, oxidative stress, and inflammation. What is lacking, however, is an explanation of how these themselves are caused. We here develop the unifying idea, and the considerable evidence for it, that the originating cause of PE (and of the four classes of dysregulation) is, in fact, microbial infection, that most such microbes are dormant and hence resist detection by conventional (replication-dependent) microbiology, and that by occasional resuscitation and growth it is they that are responsible for all the observable sequelae, including the continuing, chronic inflammation. In particular, bacterial products such as lipopolysaccharide (LPS), also known as endotoxin, are well known as highly inflammagenic and stimulate an innate (and possibly trained) immune response that exacerbates the inflammation further. The known need of microbes for free iron can explain the iron dysregulation that accompanies PE. We describe the main routes of infection (gut, oral, and urinary tract infection) and the regularly observed presence of microbes in placental and other tissues in PE. Every known proteomic biomarker of “preeclampsia” that we assessed has, in fact, also been shown to be raised in response to infection. An infectious component to PE fulfills the Bradford Hill criteria for ascribing a disease to an environmental cause and suggests a number of treatments, some of which have, in fact, been shown to be successful. PE was classically referred to as endotoxemia or toxemia of pregnancy, and it is ironic that it seems that LPS and other microbial endotoxins really are involved. Overall, the recognition of an infectious component in the etiology of PE mirrors that for ulcers and other diseases that were previously considered to lack one. PMID:27965958

[Agriculture microbiology and microbe interaction with plants].

PubMed

Caballero-Mellado, Jesús

2006-01-01

About the characterization and distribution of novel nitrogen-fixing Burkholderia species associated with maize and other plants and their potential use on the plant growth was presented in this symposium. The symposium included studies directed to the revegetation of eroded areas by using plant growth promoting rhizo-bacteria and mycorrizal fungi associated with desert plants, as well as studies related with the resistance of arbuscular mycorrhizal fungi to heavy metals associated with the environmental pollution. In addition, the identification and characterization of a 31-kb chromosomal fragment from Pseudomonas syringae pv. phaseolicola was presented; such a fragment, involved with the phaseolotoxin synthesis, showed characteristic features of a bacterial pathogenicity island.

Technologically important extremophile 16S rRNA sequence Shannon entropy and fractal property comparison with long term dormant microbes

NASA Astrophysics Data System (ADS)

Holden, Todd; Gadura, N.; Dehipawala, S.; Cheung, E.; Tuffour, M.; Schneider, P.; Tremberger, G., Jr.; Lieberman, D.; Cheung, T.

2011-10-01

Technologically important extremophiles including oil eating microbes, uranium and rocket fuel perchlorate reduction microbes, electron producing microbes and electrode electrons feeding microbes were compared in terms of their 16S rRNA sequences, a standard targeted sequence in comparative phylogeny studies. Microbes that were reported to have survived a prolonged dormant duration were also studied. Examples included the recently discovered microbe that survives after 34,000 years in a salty environment while feeding off organic compounds from other trapped dead microbes. Shannon entropy of the 16S rRNA nucleotide composition and fractal dimension of the nucleotide sequence in terms of its atomic number fluctuation analyses suggest a selected range for these extremophiles as compared to other microbes; consistent with the experience of relatively mild evolutionary pressure. However, most of the microbes that have been reported to survive in prolonged dormant duration carry sequences with fractal dimension between 1.995 and 2.005 (N = 10 out of 13). Similar results are observed for halophiles, red-shifted chlorophyll and radiation resistant microbes. The results suggest that prolonged dormant duration, in analogous to high salty or radiation environment, would select high fractal 16S rRNA sequences. Path analysis in structural equation modeling supports a causal relation between entropy and fractal dimension for the studied 16S rRNA sequences (N = 7). Candidate choices for high fractal 16S rRNA microbes could offer protection for prolonged spaceflights. BioBrick gene network manipulation could include extremophile 16S rRNA sequences in synthetic biology and shed more light on exobiology and future colonization in shielded spaceflights. Whether the high fractal 16S rRNA sequences contain an asteroidlike extra-terrestrial source could be speculative but interesting.

Substituted N-aryl-6-pyrimidinones: A new class of potent, selective, and orally active p38 MAP kinase inhibitors

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

Devadas, Balekudru; Selness, Shaun R.; Xing, Li

2012-02-28

A novel series of highly potent and selective p38 MAP kinase inhibitors was developed originating from a substituted N-aryl-6-pyrimidinone scaffold. SAR studies coupled with in vivo evaluations in rat arthritis model culminated in the identification of 10 with excellent oral efficacy. Compound 10 exhibited a significantly enhanced dissolution rate compared to 1, translating to a high oral bioavailability (>90%) in rat. In animal studies 10 inhibited LPS-stimulated production of tumor necrosis factor-{alpha} in a dose-dependent manner and demonstrated robust efficacy comparable to dexamethasone in a rat streptococcal cell wall-induced arthritis model.

Severe congenital cyclic neutropenia: A case report

PubMed Central

Patil, Vidyavathi H; Hugar, Shivayogi M; Balikai, Girish; Patil, Sudha

2016-01-01

Congenital cyclic neutropenia syndrome is a constitutional genetic disorder which is characterized by very low number of neutrophils (neutropenia). Patients suffering from this disorder clinically present with neutropenia at early age, history of recurrent fever, ulcerations in the oral cavity, gingivitis, and other recurrent infections. This paper describes a case report of a child with recurrent mouth ulcers, fever, and later diagnosed with severe congenital cyclic neutropenia. This also emphasizes the importance of identification of rare causes of immunosuppressive conditions in children presenting with recurrent oral ulcers and poor dental hygiene, to prevent long-term complications of oral cavity and also morbidity and mortality secondary to neutropenic sepsis. PMID:27857902

Monitoring marine recreational water quality using multiple microbial indicators in an urban tropical environment

PubMed Central

Shibata, Tomoyuki; Solo-Gabriele, Helena M.; Fleming, Lora E.; Elmir, Samir

2008-01-01

The microbial water quality at two beaches, Hobie Beach and Crandon Beach, in Miami-Dade County, Florida, USA was measured using multiple microbial indicators for the purpose of evaluating correlations between microbes and for identifying possible sources of contamination. The indicator microbes chosen for this study (enterococci, Escherichia coli, fecal coliform, total coliform and C. perfringens) were evaluated through three different sampling efforts. These efforts included daily measurements at four locations during a wet season month and a dry season month, spatially intensive water sampling during low- and high-tide periods, and a sand sampling effort. Results indicated that concentrations did not vary in a consistent fashion between one indicator microbe and another. Daily water quality frequently exceeded guideline levels at Hobie Beach for all indicator microbes except for fecal coliform, which never exceeded the guideline. Except for total coliform, the concentrations of microbes did not change significantly between seasons in spite of the fact that the physical–chemical parameters (rainfall, temperature, pH, and salinity) changed significantly between the two monitoring periods. Spatially intense water sampling showed that the concentrations of microbes were significantly different with distance from the shoreline. The highest concentrations were observed at shoreline points and decreased at offshore points. Furthermore, the highest concentrations of indicator microbe concentrations were observed at high tide, when the wash zone area of the beach was submerged. Beach sands within the wash zone tested positive for all indicator microbes, thereby suggesting that this zone may serve as the source of indicator microbes. Ultimate sources of indicator microbes to this zone may include humans, animals, and possibly the survival and regrowth of indicator microbes due to the unique environmental conditions found within this zone. Overall, the results of this study indicated that the concentrations of indicator microbes do not necessarily correlate with one another. Exceedence of water quality guidelines, and thus the frequency of beach advisories, depends upon which indicator microbe is chosen. PMID:15261551

Honey Bee Health: The Potential Role of Microbes

USDA-ARS?s Scientific Manuscript database

Microbes, are a diverse group of unicellular organisms that include bacteria, fungi, archaea, protists, and sometimes viruses. Bees carry a diverse assemblage of microbes (mostly bacteria and fungi). Very few are pathogenic; most microbes are likely commensal or even beneficial to the colony. Mic...

Cooperative microbial tolerance behaviors in host-microbiota mutualism

PubMed Central

Ayres, Janelle S.

2016-01-01

Animal defense strategies against microbes are most often thought of as a function of the immune system, the primary function of which is to sense and kill microbes through the execution of resistance mechanisms. However, this antagonistic view creates complications for our understanding of beneficial host-microbe interactions. Pathogenic microbes are described as employing a few common behaviors that promote their fitness at the expense of host health and fitness. Here, a complementary framework is proposed to suggest that in addition to pathogens, beneficial microbes have evolved behaviors to manipulate host processes in order to promote their own fitness and do so through the promotion of host health and fitness. In this Perspective, I explore the idea that patterns or behaviors traditionally ascribed to pathogenic microbes are also employed by beneficial microbes to promote host tolerance defense strategies. Such strategies would promote host health without having a negative impact on microbial fitness and would thereby yield cooperative evolutionary dynamics that are likely required to drive mutualistic co-evolution of hosts and microbes. PMID:27259146

A novel multimodal optical imaging system for early detection of oral cancer

PubMed Central

Malik, Bilal H.; Jabbour, Joey M.; Cheng, Shuna; Cuenca, Rodrigo; Cheng, Yi-Shing Lisa; Wright, John M.; Jo, Javier A.; Maitland, Kristen C.

2015-01-01

Objectives Several imaging techniques have been advocated as clinical adjuncts to improve identification of suspicious oral lesions. However, these have not yet shown superior sensitivity or specificity over conventional oral examination techniques. We developed a multimodal, multi-scale optical imaging system that combines macroscopic biochemical imaging of fluorescence lifetime imaging (FLIM) with subcellular morphologic imaging of reflectance confocal microscopy (RCM) for early detection of oral cancer. We tested our system on excised human oral tissues. Study Design A total of four tissue specimen were imaged. These specimens were diagnosed as one each: clinically normal, oral lichen planus, gingival hyperplasia, and superficially-invasive squamous cell carcinoma (SCC). The optical and fluorescence lifetime properties of each specimen were recorded. Results Both quantitative and qualitative differences between normal, benign and SCC lesions can be resolved with FLIM-RCM imaging. The results demonstrate that an integrated approach based on these two methods can potentially enable rapid screening and evaluation of large areas of oral epithelial tissue. Conclusions Early results from ongoing studies of imaging human oral cavity illustrate the synergistic combination of the two modalities. An adjunct device based on such optical characterization of oral mucosa can potentially be used to detect oral carcinogenesis in early stages. PMID:26725720

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.

Open Mouth, Open Mind: Expanding the Role of Primary Care Nurse Practitioners.

PubMed

Clark, Carol A; Kent, Kathleen A; Jackson, Richard D

2016-01-01

Oral health is essential to overall health at any age, although in children it is particularly important because poor oral health can have a deleterious effect on deciduous and permanent dentition. For decades, oral health providers have urged primary care providers to incorporate oral health assessment, risk factor identification, parent education, and preventive therapy into routine well-child visits. Despite recommendations from various professional associations and governmental organizations, the incidence of dental disease in young children remains relatively unchanged. Although the literature has clearly demonstrated that preventive care treatments, such as the application of fluoride varnish performed in the primary care setting, improve oral health in children, very few primary care providers include oral health services in their well-child visits. The purpose of this article is to reduce the barriers and knowledge gaps identified in recent pediatric oral health research and educate primary care nurse practitioners on the application of fluoride varnish to reduce the risk of the development of dental caries in young children. Copyright © 2015 National Association of Pediatric Nurse Practitioners. Published by Elsevier Inc. All rights reserved.

Characterization of the salivary microbiome in people with obesity

PubMed Central

Zhang, Qian

2018-01-01

Background The interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized with microbes, little is known about the oral microbiome in people with obesity. In the present study, we investigated the salivary microbiome in obese and normal weight healthy participants using metagenomic analysis. The subjects were categorized into two groups, obesity and normal weight, based on their BMIs. Methods We characterized the salivary microbiome of 33 adults with obesity and 29 normal weight controls using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene (Illumina MiSeq). None of the selected participants had systemic, oral mucosal, or periodontal diseases. Results The salivary microbiome of the obesity group was distinct from that of the normal weight group. The salivary microbiome of periodontally healthy people with obesity had both significantly lower bacterial diversity and richness compared with the controls. The genus Prevotella, Granulicatella, Peptostreptococcus, Solobacterium, Catonella, and Mogibacterium were significantly more abundant in the obesity group; meanwhile the genus Haemophilus, Corynebacterium, Capnocytophaga, and Staphylococcus were less abundant in the obesity group. We also performed a functional analysis of the inferred metagenomes, and showed that the salivary community associated with obesity had a stronger signature of immune disease and a decreased functional signature related to environmental adaptation and Xenobiotics biodegradation compared with the normal weight controls. Discussion Our study demonstrates that the microbial diversity and structure of the salivary microbiome in people with obesity are significantly different from those of normal weight controls. These results suggested that changes in the structure and function of salivary microbiome in people with obesity might reflect their susceptibility to oral diseases. PMID:29576948

Bacterial DNA detected on pathologically changed heart valves using 16S rRNA gene amplification.

PubMed

Chalupova, Miroslava; Skalova, Anna; Hajek, Tomas; Geigerova, Lenka; Kralova, Dana; Liska, Pavel; Hecova, Hana; Molacek, Jiri; Hrabak, Jaroslav

2018-05-22

Nowadays, dental diseases are one of the most common illnesses in the world. Some of them can lead to translocation of oral bacteria to the bloodstream causing intermittent bacteraemia. Therefore, a potential association between oral infection and cardiovascular diseases has been discussed in recent years as a result of adhesion of oral microbes to the heart valves. The aim of this study was to detect oral bacteria on pathologically changed heart valves not caused by infective endocarditis. In the study, patients with pathologically changed heart valves were involved. Samples of heart valves removed during heart valve replacement surgery were cut into two parts. One aliquot was cultivated aerobically and anaerobically. Bacterial DNA was extracted using Ultra-Deep Microbiome Prep (Molzym GmbH, Bremen, Germany) followed by a 16S rRNA gene PCR amplification using Mastermix 16S Complete kit (Molzym GmbH, Bremen, Germany). Positive PCR products were sequenced and the sequences were analyzed using BLAST database ( http://www.ncbi.nlm.nih/BLAST ). During the study period, 41 samples were processed. Bacterial DNA of the following bacteria was detected in 21 samples: Cutibacterium acnes (formerly Propionibacterium acnes) (n = 11; 52.38% of patients with positive bacterial DNA detection), Staphylococcus sp. (n = 9; 42.86%), Streptococcus sp. (n = 1; 4.76%), Streptococcus sanguinis (n = 4; 19.05%), Streptococcus oralis (n = 1; 4.76%), Carnobacterium sp. (n = 1; 4.76%), Bacillus sp. (n = 2; 9.52%), and Bergeyella sp. (n = 1; 4.76%). In nine samples, multiple bacteria were found. Our results showed significant appearance of bacteria on pathologically changed heart valves in patients with no symptoms of infective endocarditis.

Oral delivery of bioencapsulated exendin-4 expressed in chloroplasts lowers blood glucose level in mice and stimulates insulin secretion in beta-TC6 cells

PubMed Central

Kwon, Kwang-Chul; Nityanandam, Ramya; New, James Stewart; Daniell, Henry

2012-01-01

Summary Glucagon like peptide (GLP-1) increases insulin secretion but is rapidly degraded (half-life: 2 min in circulation). GLP-1 analog, Exenatide (Byetta) has a longer half life (3.3–4 hrs) with potent insulinotropic effects but requires cold storage, daily abdominal injections with short shelf life. Because diabetic patients take >60,000 injections in their life time, alternative delivery methods are highly desired. Exenatide is ideal for oral delivery because insulinotropism is glucose dependent, with reduced risk of hypoglycemia even at higher doses. Therefore, exendin-4 (EX4) was expressed as a cholera toxin B subunit (CTB)-fusion protein in tobacco chloroplasts to facilitate bioencapsulation within plant cells and transmucosal delivery in the gut via GM1 receptors present in the intestinal epithelium. The transgene integration was confirmed by PCR and Southern blot analysis. Expression level of CTB-EX4 reached up to 14.3% of total leaf protein (TLP). Lyophilization of leaf material increased therapeutic protein concentration by 12–24 fold, extended their shelf life up to 15 months when stored at room temperature and eliminated microbes present in fresh leaves. The pentameric structure, disulfide bonds and functionality of CTB-EX4 were well preserved in lyophilized materials. Chloroplast derived CTB-EX4 showed increased insulin secretion similar to the commercial EX4 in beta-TC6, a mouse pancreatic cell line. Even when 5,000-fold excess dose of CTB-EX4 was orally delivered, it stimulated insulin secretion similar to the intraperitoneal injection of commercial EX4 but didn’t cause hypoglycemia in mice. Oral delivery of the bioencapsulated EX4 should eliminate injections, increase patient compliance/convenience and significantly lower their cost. PMID:23078126

Engineered microbes and methods for microbial oil production

DOEpatents

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

2015-02-10

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

A systematic approach to prioritize drug targets using machine learning, a molecular descriptor-based classification model, and high-throughput screening of plant derived molecules: a case study in oral cancer.

PubMed

Randhawa, Vinay; Kumar Singh, Anil; Acharya, Vishal

2015-12-01

Systems-biology inspired identification of drug targets and machine learning-based screening of small molecules which modulate their activity have the potential to revolutionize modern drug discovery by complementing conventional methods. To utilize the effectiveness of such pipelines, we first analyzed the dysregulated gene pairs between control and tumor samples and then implemented an ensemble-based feature selection approach to prioritize targets in oral squamous cell carcinoma (OSCC) for therapeutic exploration. Based on the structural information of known inhibitors of CXCR4-one of the best targets identified in this study-a feature selection was implemented for the identification of optimal structural features (molecular descriptor) based on which a classification model was generated. Furthermore, the CXCR4-centered descriptor-based classification model was finally utilized to screen a repository of plant derived small-molecules to obtain potential inhibitors. The application of our methodology may assist effective selection of the best targets which may have previously been overlooked, that in turn will lead to the development of new oral cancer medications. The small molecules identified in this study can be ideal candidates for trials as potential novel anti-oral cancer agents. Importantly, distinct steps of this whole study may provide reference for the analysis of other complex human diseases.

Genome composition and phylogeny of microbes predict their co-occurrence in the environment

PubMed Central

2017-01-01

The genomic information of microbes is a major determinant of their phenotypic properties, yet it is largely unknown to what extent ecological associations between different species can be explained by their genome composition. To bridge this gap, this study introduces two new genome-wide pairwise measures of microbe-microbe interaction. The first (genome content similarity index) quantifies similarity in genome composition between two microbes, while the second (microbe-microbe functional association index) summarizes the topology of a protein functional association network built for a given pair of microbes and quantifies the fraction of network edges crossing organismal boundaries. These new indices are then used to predict co-occurrence between reference genomes from two 16S-based ecological datasets, accounting for phylogenetic relatedness of the taxa. Phylogenetic relatedness was found to be a strong predictor of ecological associations between microbes which explains about 10% of variance in co-occurrence data, but genome composition was found to be a strong predictor as well, it explains up to 4% the variance in co-occurrence when all genomic-based indices are used in combination, even after accounting for evolutionary relationships between the species. On their own, the metrics proposed here explain a larger proportion of variance than previously reported more complex methods that rely on metabolic network comparisons. In summary, results of this study indicate that microbial genomes do indeed contain detectable signal of organismal ecology, and the methods described in the paper can be used to improve mechanistic understanding of microbe-microbe interactions. PMID:28152007

Periodontitis, Microbiomes and their Role in Alzheimer’s Disease

PubMed Central

Pritchard, Anna B.; Crean, StJohn; Olsen, Ingar; Singhrao, Sim K.

2017-01-01

As far back as the eighteenth and early nineteenth centuries, microbial infections were responsible for vast numbers of deaths. The trend reversed with the introduction of antibiotics coinciding with longer life. Increased life expectancy however, accompanied the emergence of age related chronic inflammatory states including the sporadic form of Alzheimer’s disease (AD). Taken together, the true challenge of retaining health into later years of life now appears to lie in delaying and/or preventing the progression of chronic inflammatory diseases, through identifying and influencing modifiable risk factors. Diverse pathogens, including periodontal bacteria have been associated with AD brains. Amyloid-beta (Aβ) hallmark protein of AD may be a consequence of infection, called upon due to its antimicrobial properties. Up to this moment in time, a lack of understanding and knowledge of a microbiome associated with AD brain has ensured that the role pathogens may play in this neurodegenerative disease remains unresolved. The oral microbiome embraces a range of diverse bacterial phylotypes, which especially in vulnerable individuals, will excite and perpetuate a range of inflammatory conditions, to a wide range of extra-oral body tissues and organs specific to their developing pathophysiology, including the brain. This offers the tantalizing opportunity that by controlling the oral-specific microbiome; clinicians may treat or prevent a range of chronic inflammatory diseases orally. Evolution has equipped the human host to combat infection/disease by providing an immune system, but Porphyromonas gingivalis and selective spirochetes, have developed immune avoidance strategies threatening the host-microbe homeostasis. It is clear from longitudinal monitoring of patients that chronic periodontitis contributes to declining cognition. The aim here is to discuss the contribution from opportunistic pathogens of the periodontal microbiome, and highlight the challenges, the host faces, when dealing with unresolvable oral infections that may lead to clinical manifestations that are characteristic for AD. PMID:29114218

Bacterial protection of beetle-fungus mutualism

Treesearch

Jarrod J. Scott; Dong-Chan Oh; M. Cetin Yuceer; Kier D. Klepzig; Jon Clardy; Cameron R. Currie

2008-01-01

The pervasiveness of beneficial associations between symbiotic microbes and plants and animals in every ecosystem illustrates how the acquisition of a microbe’s physiological capacity confers substantial fitness benefits to hosts (1). However, dependence on mutualistic microbes becomes a liability if antagonistic microbes attack or outcompete beneficial ones (2)....

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.

Interleukin-17-Induced Protein Lipocalin 2 Is Dispensable for Immunity to Oral Candidiasis

PubMed Central

Ferreira, Maria Carolina; Whibley, Natasha; Mamo, Anna J.; Siebenlist, Ulrich; Chan, Yvonne R.

2014-01-01

Oropharyngeal candidiasis (OPC; thrush) is an opportunistic fungal infection caused by the commensal microbe Candida albicans. Immunity to OPC is strongly dependent on CD4+ T cells, particularly those of the Th17 subset. Interleukin-17 (IL-17) deficiency in mice or humans leads to chronic mucocutaneous candidiasis, but the specific downstream mechanisms of IL-17-mediated host defense remain unclear. Lipocalin 2 (Lcn2; 24p3; neutrophil gelatinase-associated lipocalin [NGAL]) is an antimicrobial host defense factor produced in response to inflammatory cytokines, particularly IL-17. Lcn2 plays a key role in preventing iron acquisition by bacteria that use catecholate-type siderophores, and lipocalin 2−/− mice are highly susceptible to infection by Escherichia coli and Klebsiella pneumoniae. The role of Lcn2 in mediating immunity to fungi is poorly defined. Accordingly, in this study, we evaluated the role of Lcn2 in immunity to oral infection with C. albicans. Lcn2 is strongly upregulated following oral infection with C. albicans, and its expression is almost entirely abrogated in mice with defective IL-17 signaling (IL-17RA−/− or Act1−/− mice). However, Lcn2−/− mice were completely resistant to OPC, comparably to wild-type (WT) mice. Moreover, Lcn2 deficiency mediated protection from OPC induced by steroid immunosuppression. Therefore, despite its potent regulation during C. albicans infection, Lcn2 is not required for immunity to mucosal candidiasis. PMID:24343647

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis

PubMed Central

2018-01-01

ABSTRACT Over half of adults experience gingivitis, a mild yet treatable form of periodontal disease caused by the overgrowth of oral microbes. Left untreated, gingivitis can progress to a more severe and irreversible disease, most commonly chronic periodontitis. While periodontal diseases are associated with a shift in the oral microbiota composition, it remains unclear how this shift impacts microbiota function early in disease progression. Here, we analyzed the transition from health to gingivitis through both 16S v4-v5 rRNA amplicon and metatranscriptome sequencing of subgingival plaque samples from individuals undergoing an experimental gingivitis treatment. Beta-diversity analysis of 16S rRNA reveals that samples cluster based on disease severity and patient but not by oral hygiene status. Significant shifts in the abundance of several genera occurred during disease transition, suggesting a dysbiosis due to development of gingivitis. Comparing taxonomic abundance with transcriptomic activity revealed concordance of bacterial diversity composition between the two quantification assays in samples originating from both healthy and diseased teeth. Metatranscriptome sequencing analysis indicates that during the early stages of transition to gingivitis, a number of virulence-related transcripts were significantly differentially expressed in individual and across pooled patient samples. Upregulated genes include those involved in proteolytic and nucleolytic processes, while expression levels of those involved in surface structure assembly and other general virulence functions leading to colonization or adaptation within the host are more dynamic. These findings help characterize the transition from health to periodontal disease and identify genes associated with early disease. PMID:29666288

Airway Microbiota Is Associated with Up-Regulation of the PI3K Pathway in Lung Cancer.

PubMed

Tsay, Jun-Chieh J; Wu, Benjamin G; Badri, Michelle H; Clemente, Jose C; Shen, Nan; Meyn, Peter; Li, Yonghua; Yie, Ting-An; Lhakhang, Tenzin; Olsen, Evan; Murthy, Vivek; Michaud, Gaetane; Sulaiman, Imran; Tsirigos, Aristotelis; Heguy, Adriana; Pass, Harvey; Weiden, Michael D; Rom, William N; Sterman, Daniel H; Bonneau, Richard; Blaser, Martin J; Segal, Leopoldo N

2018-06-04

In lung cancer, upregulation of the PI3K pathway is an early event that contributes to cell proliferation, survival, and tissue invasion. Upregulation of this pathway was recently described as associated with enrichment of the lower airways with bacteria identified as oral commensals. We hypothesize that host-microbe interactions in the lower airways of subjects with lung cancer affect known cancer pathways. Airway brushes were collected prospectively from subjects with lung nodules at time of diagnostic bronchoscopy, including 39 subjects with final lung cancer diagnoses and 36 subjects with non-cancer diagnosis. Additionally, samples from 10 healthy control subjects were included. 16S rRNA gene amplicon sequencing and paired transcriptome sequencing (RNAseq) were performed on all airway samples. In addition, an in vitro model with airway epithelial cells exposed to bacteria/bacterial products was performed. The composition of the lower airway transcriptome in the cancer patients was significantly different from the controls, which included upregulation of ERK and PI3K signaling pathways. The lower airways of lung cancer patients were enriched for oral taxa (Streptococcus and Veillonella), which was associated with upregulation of the ERK and PI3K signaling pathways. In vitro exposure of airway epithelial cells to Veillonella, Prevotella, and Streptococcus led to upregulation of these same signaling pathways. The data presented here shows that several transcriptomic signatures previously identified as relevant to lung cancer pathogenesis are associated with enrichment of the lower airway microbiota with oral commensals.

Engineered microbes and methods for microbial oil production

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

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis andmore » storage properties.« less

Perceptual context and individual differences in the language proficiency of preschool children.

PubMed

Banai, Karen; Yifat, Rachel

2016-02-01

Although the contribution of perceptual processes to language skills during infancy is well recognized, the role of perception in linguistic processing beyond infancy is not well understood. In the experiments reported here, we asked whether manipulating the perceptual context in which stimuli are presented across trials influences how preschool children perform visual (shape-size identification; Experiment 1) and auditory (syllable identification; Experiment 2) tasks. Another goal was to determine whether the sensitivity to perceptual context can explain part of the variance in oral language skills in typically developing preschool children. Perceptual context was manipulated by changing the relative frequency with which target visual (Experiment 1) and auditory (Experiment 2) stimuli were presented in arrays of fixed size, and identification of the target stimuli was tested. Oral language skills were assessed using vocabulary, word definition, and phonological awareness tasks. Changes in perceptual context influenced the performance of the majority of children on both identification tasks. Sensitivity to perceptual context accounted for 7% to 15% of the variance in language scores. We suggest that context effects are an outcome of a statistical learning process. Therefore, the current findings demonstrate that statistical learning can facilitate both visual and auditory identification processes in preschool children. Furthermore, consistent with previous findings in infants and in older children and adults, individual differences in statistical learning were found to be associated with individual differences in language skills of preschool children. Copyright © 2015 Elsevier Inc. All rights reserved.

Isolation of Aureimonas altamirensis, a Brucella canis-like bacterium, from an edematous canine testicle.

PubMed

Reilly, Thomas J; Calcutt, Michael J; Wennerdahl, Laura A; Williams, Fred; Evans, Tim J; Ganjam, Irene K; Bowman, Jesse W; Fales, William H

2014-11-01

Microbiological and histological analysis of a sample from a swollen testicle of a 2-year-old Border Collie dog revealed a mixed infection of the fungus Blastomyces dermatitidis and the Gram-negative bacterium Aureimonas altamirensis. When subjected to an automated microbial identification system, the latter isolate was provisionally identified as Psychrobacter phenylpyruvicus, but the organism shared several biochemical features with Brucella canis and exhibited agglutination, albeit weakly, with anti-B. canis antiserum. Unequivocal identification of the organism was only achieved by 16S ribosomal RNA gene sequencing, ultimately establishing the identity as A. altamirensis. Since its first description in 2006, this organism has been isolated infrequently from human clinical samples, but, to the authors' knowledge, has not been reported from a veterinary clinical sample. While of unknown clinical significance with respect to the pathology observed for the polymicrobial infection described herein, it highlights the critical importance to unambiguously identify the microbe for diagnostic, epidemiological, infection control, and public health purposes. © 2014 The Author(s).

Bio-mining the forest ecosystem of North East India for identification of antimicrobial metabolites from fungi through submerged fermentation.

PubMed

Devi, Sarangthem Indira; Lotjem, H; Devi, Elangbam Julia; Potshangbam, Momota; Ngashangva, Ng; Bora, Jagat; Sahoo, Dinabandhu; Sharma, Chandradev

2017-10-01

In this study, fungi isolated from less explored forest soil ecosystem of Northeast India were studied for the production of potential antimicrobial metabolites (AMM). Out of the 68 fungi isolated from forest soil of Manipur, 7 of them showed AMA against the test pathogens. Among them, Aspergillus terreus (IBSD-F4) showed the most significant activity against Staphylococcus aureus (ATCC-25923), Bacillus anthracis (IBSD-C370), Pseudomonas fluorescens (ATCC-13525), Salmonella typhimurium (ATCC-14028), Escherichia coli (ATCC-25922) and Candida albicans (ATCC-10231). The active metabolite was harvested from the fermentation broth of Aspergillus terreus and purified by column chromatography and semi preparative-HPLC. The compound was identified as 'Sclerotionigrin A' on the basis of UV-vis spectra, MS and NMR analyses. This compound was reported for the first time from A. terreus. The study highlights, the importance of exploring microbes from forest soil for identification of bioactive metabolites for future drug development. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modeling and parameters identification of 2-keto-L-gulonic acid fed-batch fermentation.

PubMed

Wang, Tao; Sun, Jibin; Yuan, Jingqi

2015-04-01

This article presents a modeling approach for industrial 2-keto-L-gulonic acid (2-KGA) fed-batch fermentation by the mixed culture of Ketogulonicigenium vulgare (K. vulgare) and Bacillus megaterium (B. megaterium). A macrokinetic model of K. vulgare is constructed based on the simplified metabolic pathways. The reaction rates obtained from the macrokinetic model are then coupled into a bioreactor model such that the relationship between substrate feeding rates and the main state variables, e.g., the concentrations of the biomass, substrate and product, is constructed. A differential evolution algorithm using the Lozi map as the random number generator is utilized to perform the model parameters identification, with the industrial data of 2-KGA fed-batch fermentation. Validation results demonstrate that the model simulations of substrate and product concentrations are well in coincidence with the measurements. Furthermore, the model simulations of biomass concentrations reflect principally the growth kinetics of the two microbes in the mixed culture.

Use of UV Sources for Detection and Identification of Explosives

NASA Technical Reports Server (NTRS)

Hug, William; Reid, Ray; Bhartia, Rohit; Lane, Arthur

2009-01-01

Measurement of Raman and native fluorescence emission using ultraviolet (UV) sources (<400 nm) on targeted materials is suitable for both sensitive detection and accurate identification of explosive materials. When the UV emission data are analyzed using a combination of Principal Component Analysis (PCA) and cluster analysis, chemicals and biological samples can be differentiated based on the geometric arrangement of molecules, the number of repeating aromatic rings, associated functional groups (nitrogen, sulfur, hydroxyl, and methyl), microbial life cycles (spores vs. vegetative cells), and the number of conjugated bonds. Explosive materials can be separated from one another as well as from a range of possible background materials, which includes microbes, car doors, motor oil, and fingerprints on car doors, etc. Many explosives are comprised of similar atomic constituents found in potential background samples such as fingerprint oils/skin, motor oil, and soil. This technique is sensitive to chemical bonds between the elements that lead to the discriminating separability between backgrounds and explosive materials.

The GAO History Program: A History.

ERIC Educational Resources Information Center

Trask, Roger R.

1991-01-01

Discusses the planning, formation, and history of the General Accounting Office history program. Addresses functions, staff size, organizational placement, and the role of an advisory committee. Stresses oral history, policy research, and identification of documentary sources. (DK)

Associations between adult attachment and: oral health-related quality of life, oral health behaviour, and self-rated oral health.

PubMed

Meredith, Pamela; Strong, Jenny; Ford, Pauline; Branjerdporn, Grace

2016-02-01

Although adult attachment theory has been revealed as a useful theoretical framework for understanding a range of health parameters, the associations between adult attachment patterns and a range of oral health parameters have not yet been examined. The aim of this study was to examine potential associations between attachment insecurity and: (1) oral health-related quality of life (OHRQoL), (2) oral health behaviours, and (3) self-rated oral health. In association with this aim, sample characteristics were compared with normative data. The sample in this cross-sectional study was comprised of 265 healthy adults, recruited via convenience sampling. Data were collected on attachment patterns (Experiences in Close Relationships Scale-Short Form, ECR-S), OHRQoL (Oral Health Impact Profile-14, OHIP-14), oral health behaviours (modified Dental Neglect Scale, m-DNS), and self-rated oral health (one-item global rating of oral health). Multivariate regression models were performed. Both dimensions of attachment insecurity were associated with lowered use of favourable dental visiting behaviours, as well as decreased OHRQoL for both overall well-being and specific aspects of OHRQoL. Attachment avoidance was linked with diminished self-rated oral health. This study supports the potential value of an adult attachment framework for understanding a range of oral health parameters. The assessment of a client's attachment pattern may assist in the identification of people who are at risk of diminished OHRQoL, less adaptive dental visiting behaviours, or poorer oral health. Further research in this field may inform ways in which attachment approaches can enhance oral health-related interventions.

Effects of prey, pitcher age, and microbes on acid phosphatase activity in fluid from pitchers of Sarracenia purpurea (Sarraceniaceae).

PubMed

Luciano, Carl S; Newell, Sandra J

2017-01-01

Carnivory in pitcher plants generally involves digestion of prey, by the plant itself, by symbionts, or both. While symbionts appear to be important in the digestion of prey in Sarracenia purpurea, the importance of pitcher-derived enzymes is less well documented. Our goal was to reduce microbial numbers in pitcher fluid in order to measure the acid phosphatase activity attributable to the pitchers themselves. Preliminary experiments indicated that various antibiotics were minimally effective at reducing microbial populations and that antibiotic-resistant microbes were easily cultured from pitcher fluid. Consequently, we measured the abundance of culturable microbes in every sample taken for the measurement of acid phosphatase activity. Pitchers fed with one sterilized ant had higher levels of acid phosphatase activity than unfed pitchers. Older pitchers were more responsive to feeding than young pitchers. Pitchers with high levels of microbes (on Day 5) had higher acid phosphatase activity than pitchers with low levels of microbes. However, fed pitchers were not more likely to have higher microbe levels and microbe levels were not related to pitcher age. When fluid samples from inside the pitcher were compared to appropriate controls incubated outside the pitcher, acid phosphatase activity was higher inside the pitcher. Results from the feeding experiments are consistent with a primary role of microbes in the digestion of prey in pitchers of S. purpurea. However, the relationship between pitcher age and enzyme activity is not a function of microbes in the pitcher fluid and may depend on enzymes produced by the plant. Our methods would not detect microbes embedded on the inner surface of the pitcher; and if they survived the alcohol rinse and antibiotics, we cannot rule out microbes as the source of the relationship between pitcher age and acid phosphatase activity.

Prevalence of Dental Caries, Oral Hygiene Knowledge, Status, and Practices among Visually Impaired Individuals in Chennai, Tamil Nadu.

PubMed

John, James Rufus; Daniel, Breena; Paneerselvam, Dakshaini; Rajendran, Ganesh

2017-01-01

Aim . To assess the prevalence of dental caries, oral hygiene knowledge, status, and practices among visually impaired individuals in Chennai, Tamil Nadu. Materials and Methods . A cross-sectional study was conducted among 404 visually impaired individuals in Chennai city, Tamil Nadu. Four schools were randomly selected for conducting the study. The oral hygiene status, prevalence of caries, and knowledge and attitude towards oral care among visually impaired individuals were collected and analysed. Results . In the present study, whilst 42% of individuals had fair oral hygiene status, 33% had good hygiene followed by 25% having poor oral hygiene. The overall mean number of DMFT was estimated to be 4.5 ± 2.7. The mean number of decayed teeth was 3.1 ± 2.2, mean number of missing teeth was 0.8 ± 1.4, and mean number of filled teeth was 0.5 ± 1.3. Conclusion . Whilst oral hygiene status was found to be relatively fair, there was a high rate of dental caries among the sample population. This shows that there is lack of knowledge regarding oral health maintenance. Therefore, early identification of caries coupled with effective oral health promotion programs providing practical knowledge to visually impaired students would prove beneficial.

Potential benefits of chewing gum for the delivery of oral therapeutics and its possible role in oral healthcare.

PubMed

Wessel, Stefan W; van der Mei, Henny C; Maitra, Amarnath; Dodds, Michael W J; Busscher, Henk J

2016-10-01

Over the years, chewing gum has developed from a candy towards an oral health-promoting nutraceutical. This review summarizes evidence for the oral health benefits of chewing gum, emphasizing identification of active ingredients in gum that facilitate prevention and removal of oral biofilm. Chewing of sugar-free gum yields oral health benefits that include clearance of food debris, reduction in oral dryness, increase of biofilm pH and remineralization of enamel. These basic effects of chewing gum are attributed to increased mastication and salivation. Active ingredients incorporated in chewing gums aim to expand these effects to inhibition of extrinsic tooth stain and calculus formation, enhanced enamel remineralization, reduction of the numbers of bacteria in saliva and amount of oral biofilm, neutralization of biofilm pH, and reduction of volatile sulfur compounds. Evidence for oral-health benefits of chewing gum additives is hard to obtain due to their relatively low concentrations and rapid wash-out. Clinical effects of gum additives are overshadowed by effects of increased mastication and salivation due to the chewing of gum and require daily chewing of gum for prolonged periods of time. Future studies on active ingredients should focus on specifically targeting pathogenic bacteria, whilst leaving the healthy microbiome unaffected.

Prevalence of Dental Caries, Oral Hygiene Knowledge, Status, and Practices among Visually Impaired Individuals in Chennai, Tamil Nadu

PubMed Central

Daniel, Breena; Paneerselvam, Dakshaini; Rajendran, Ganesh

2017-01-01

Aim. To assess the prevalence of dental caries, oral hygiene knowledge, status, and practices among visually impaired individuals in Chennai, Tamil Nadu. Materials and Methods. A cross-sectional study was conducted among 404 visually impaired individuals in Chennai city, Tamil Nadu. Four schools were randomly selected for conducting the study. The oral hygiene status, prevalence of caries, and knowledge and attitude towards oral care among visually impaired individuals were collected and analysed. Results. In the present study, whilst 42% of individuals had fair oral hygiene status, 33% had good hygiene followed by 25% having poor oral hygiene. The overall mean number of DMFT was estimated to be 4.5 ± 2.7. The mean number of decayed teeth was 3.1 ± 2.2, mean number of missing teeth was 0.8 ± 1.4, and mean number of filled teeth was 0.5 ± 1.3. Conclusion. Whilst oral hygiene status was found to be relatively fair, there was a high rate of dental caries among the sample population. This shows that there is lack of knowledge regarding oral health maintenance. Therefore, early identification of caries coupled with effective oral health promotion programs providing practical knowledge to visually impaired students would prove beneficial. PMID:28458691

Microbial small molecules - weapons of plant subversion.

PubMed

Stringlis, Ioannis A; Zhang, Hao; Pieterse, Corné M J; Bolton, Melvin D; de Jonge, Ronnie

2018-05-25

Covering: up to 2018 Plants live in close association with a myriad of microbes that are generally harmless. However, the minority of microbes that are pathogens can severely impact crop quality and yield, thereby endangering food security. By contrast, beneficial microbes provide plants with important services, such as enhanced nutrient uptake and protection against pests and diseases. Like pathogens, beneficial microbes can modulate host immunity to efficiently colonize the nutrient-rich niches within and around the roots and aerial tissues of a plant, a phenomenon mirroring the establishment of commensal microbes in the human gut. Numerous ingenious mechanisms have been described by which pathogenic and beneficial microbes in the plant microbiome communicate with their host, including the delivery of immune-suppressive effector proteins and the production of phytohormones, toxins and other bioactive molecules. Plants signal to their associated microbes via exudation of photosynthetically fixed carbon sources, quorum-sensing mimicry molecules and selective secondary metabolites such as strigolactones and flavonoids. Molecular communication thus forms an integral part of the establishment of both beneficial and pathogenic plant-microbe relations. Here, we review the current knowledge on microbe-derived small molecules that can act as signalling compounds to stimulate plant growth and health by beneficial microbes on the one hand, but also as weapons for plant invasion by pathogens on the other. As an exemplary case, we used comparative genomics to assess the small molecule biosynthetic capabilities of the Pseudomonas genus; a genus rich in both plant pathogenic and beneficial microbes. We highlight the biosynthetic potential of individual microbial genomes and the population at large, providing evidence for the hypothesis that the distinction between detrimental and beneficial microbes is increasingly fading. Knowledge on the biosynthesis and molecular activity of microbial small molecules will aid in the development of successful biological agents boosting crop resiliency in a sustainable manner and could also provide scientific routes to pathogen inhibition or eradication.

Antimalarial Pyrido[1,2-a]benzimidazoles: Lead Optimization, Parasite Life Cycle Stage Profile, Mechanistic Evaluation, Killing Kinetics, and in Vivo Oral Efficacy in a Mouse Model.

PubMed

Singh, Kawaljit; Okombo, John; Brunschwig, Christel; Ndubi, Ferdinand; Barnard, Linley; Wilkinson, Chad; Njogu, Peter M; Njoroge, Mathew; Laing, Lizahn; Machado, Marta; Prudêncio, Miguel; Reader, Janette; Botha, Mariette; Nondaba, Sindisiwe; Birkholtz, Lyn-Marie; Lauterbach, Sonja; Churchyard, Alisje; Coetzer, Theresa L; Burrows, Jeremy N; Yeates, Clive; Denti, Paolo; Wiesner, Lubbe; Egan, Timothy J; Wittlin, Sergio; Chibale, Kelly

2017-02-23

Further structure-activity relationship (SAR) studies on the recently identified pyrido[1,2-a]benzimidazole (PBI) antimalarials have led to the identification of potent, metabolically stable compounds with improved in vivo oral efficacy in the P. berghei mouse model and additional activity against parasite liver and gametocyte stages, making them potential candidates for preclinical development. Inhibition of hemozoin formation possibly contributes to the mechanism of action.

Microbes to Biomes at Berkeley Lab

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

None

2015-10-28

Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

The Impact of Oral Health on Taste Ability in Acutely Hospitalized Elderly

PubMed Central

Solemdal, Kirsten; Sandvik, Leiv; Willumsen, Tiril; Mowe, Morten; Hummel, Thomas

2012-01-01

Objective To investigate to what extent various oral health variables are associated with taste ability in acutely hospitalized elderly. Background Impaired taste may contribute to weight loss in elderly. Many frail elderly have poor oral health characterized by caries, poor oral hygiene, and dry mouth. However, the possible influence of such factors on taste ability in acutely hospitalized elderly has not been investigated. Materials and Methods The study was cross-sectional. A total of 174 (55 men) acutely hospitalized elderly, coming from their own homes and with adequate cognitive function, were included. Dental status, decayed teeth, oral bacteria, oral hygiene, dry mouth and tongue changes were recorded. Growth of oral bacteria was assessed with CRT® Bacteria Kit. Taste ability was evaluated with 16 taste strips impregnated with sweet, sour, salty and bitter taste solutions in 4 concentrations each. Correct identification was given score 1, and maximum total taste score was 16. Results Mean age was 84 yrs. (range 70–103 yrs.). Total taste score was significantly and markedly reduced in patients with decayed teeth, poor oral hygiene, high growth of oral bacteria and dry mouth. Sweet and salty taste were particularly impaired in patients with dry mouth. Sour taste was impaired in patients with high growth of oral bacteria. Conclusion This study shows that taste ability was reduced in acutely hospitalized elderly with caries activity, high growth of oral bacteria, poor oral hygiene, and dry mouth. Our findings indicate that good oral health is important for adequate gustatory function. Maintaining proper oral hygiene in hospitalized elderly should therefore get high priority among hospital staff. PMID:22570725

Epidermal growth factor receptor expression in different subtypes of oral lichenoid disease

PubMed Central

Cortés-Ramírez, Dionisio A.; Rodríguez-Tojo, María J.; Coca-Meneses, Juan C.; Marichalar-Mendia, Xabier

2014-01-01

The oral lichenoid disease (OLD) includes different chronic inflammatory processes such as oral lichen planus (OLP) and oral lichenoid lesions (OLL), both entities with controversial diagnosis and malignant potential. Epidermal growth factor receptor (EFGR) is an important oral carcinogenesis biomarker and overexpressed in several oral potentially malignant disorders. Objectives: To analyze the EGFR expression in the OLD to find differences between OLP and OLL, and to correlate it with the main clinical and pathological features. Material and Methods: Forty-four OLD cases were studied and classified according to their clinical (Group C1: only papular lesions / Group C2: papular and other lesions) and histopathological features (Group HT: OLP-typical / Group HC: OLP-compatible) based in previous published criteria. Standard immunohistochemical identification of EGFR protein was performed. Comparative and descriptive statistical analyses were performed. Results: Thirty-five cases (79.5%) showed EGFR overexpression without significant differences between clinical and histopathological groups (p<0.05). Histological groups showed significant differences in the EGFR expression pattern (p=0.016). Conlusions: All OLD samples showed high EGFR expression. The type of clinical lesion was not related with EGFR expression; however, there are differences in the EGFR expression pattern between histological groups that may be related with a different biological profile and malignant risk. Key words:Oral lichenoid disease, oral lichen planus, oral lichenoid lesion, oral carcinogenesis, EGFR. PMID:24880441

Triggers of oral lichen planus flares and the potential role of trigger avoidance in disease management.

PubMed

Chen, Hannah X; Blasiak, Rachel; Kim, Edwin; Padilla, Ricardo; Culton, Donna A

2017-09-01

Many patients with oral lichen planus (OLP) report triggers of flares, some of which overlap with triggers of other oral diseases, including oral allergy syndrome and oral contact dermatitis. The purpose of this study was to evaluate the prevalence of commonly reported triggers of OLP flares, their overlap with triggers of other oral diseases, and the potential role of trigger avoidance as a management strategy. Questionnaire-based survey of 51 patients with biopsy-proven lichen planus with oral involvement seen in an academic dermatology specialty clinic and/or oral pathology clinic between June 2014 and June 2015. Of the participants, 94% identified at least one trigger of their OLP flares. Approximately half of the participants (51%) reported at least one trigger that overlapped with known triggers of oral allergy syndrome, and 63% identified at least one trigger that overlapped with known triggers of oral contact dermatitis. Emotional stress was the most commonly reported trigger (77%). Regarding avoidance, 79% of the study participants reported avoiding their known triggers in daily life. Of those who actively avoided triggers, 89% reported an improvement in symptoms and 70% reported a decrease in the frequency of flares. Trigger identification and avoidance can play a potentially effective role in the management of OLP. Copyright © 2017 Elsevier Inc. All rights reserved.

Substituted 2-Phenyl-Imidazopyridines: A New Class of Drug Leads for Human African Trypanosomiasis

PubMed Central

Tatipaka, Hari Babu; Gillespie, J. Robert; Chatterjee, Arnab K.; Norcross, Neil R.; Hulverson, Matthew A.; Ranade, Ranae M.; Nagendar, Pendem; Creason, Sharon A.; McQueen, Joshua; Duster, Nicole A.; Nagle, Advait; Supek, Frantisek; Molteni, Valentina; Wenzler, Tanja; Brun, Reto; Glynne, Richard; Buckner, Frederick S.; Gelb, Michael H.

2014-01-01

A phenotypic screen of a compound library for antiparasitic activity on Trypanosoma brucei, the causative agent of human African trypanosomiasis, led to the identification of substituted 2-(3-aminophenyl) oxazolopyridines as a starting point for hit-to-lead medicinal chemistry. A total of 110 analogues were prepared, which led to the identification of 64, a substituted 2-(3-aminophenyl) imidazopyridine. This compound showed antiparasitic activity in vitro with an EC50 of 2 nM and displayed reasonable drug-like properties when tested in a number of in vitro assays. The compound was orally bioavailable and displayed good plasma and brain exposure in mice. Compound 64 cured mice infected with Trypanosoma brucei when dosed orally down to 2.5 mg/kg. Given its potent anti-parasitic properties and its ease of synthesis, compound 64 represents a new lead for the development of drugs to treat human African trypanosomiasis. PMID:24354316

Design and Synthesis of Novel and Selective Glycine Transporter-1 (GlyT1) Inhibitors with Memory Enhancing Properties.

PubMed

Santora, Vincent J; Almos, Theresa A; Barido, Richard; Basinger, Jillian; Bellows, Chris L; Bookser, Brett Carder; Breitenbucher, J Guy; Broadbent, Nicola J; Cabebe, Clifford; Chai, Chih-Kun; Chen, Mi; Chow, Stephine; Chung, De Michael; Crickard, Lindsay; Danks, Anne M; Freestone, Graeme; Gitnick, Dany; Gupta, Varsha; Hoffmaster, Christine; Hudson, Andrew R; Kaplan, Alan P; Kennedy, Michael R; Lee, Dong; Limberis, James; Ly, Kiev; Mak, Chi Ching; Masatsugu, Brittany; Morse, Andrew C; Na, Jim; Neul, David; Nikpur, John; Peters, Marco; Petroski, Robert E; Renick, Joel; Sebring, Kristen; Sevidal, Samantha; Tabatabaei, Ali; Wen, Jenny; Yan, Yingzhuo; Yoder, Zachary W; Zook, Douglas

2018-06-11

We report here the identification and optimization of a novel series of potent GlyT1 inhibitors. A ligand design campaign that utilized known GlyT1 inhibitors as starting points led to the identification of a novel series of pyrrolo[3,4-c]pyrazoles amides (21-50) with good in vitro potency. Subsequent optimization of physicochemical and in vitro ADME properties produced several compounds with promising pharmacokinetic profiles. In vivo inhibition of GlyT1 was demonstrated for select compounds within this series by measuring the elevation of glycine in the cerebrospinal fluid (CSF) of rats after a single oral dosing of 10 mg/kg. Ultimately, an optimized lead, compound 46, demonstrated in vivo efficacy in a rat Novel Object Recognition (NOR) assay after oral dosing at 0.1, 1, and 3 mg/kg.

Infectious Disease Management through Point-of-Care Personalized Medicine Molecular Diagnostic Technologies

PubMed Central

Bissonnette, Luc; Bergeron, Michel G.

2012-01-01

Infectious disease management essentially consists in identifying the microbial cause(s) of an infection, initiating if necessary antimicrobial therapy against microbes, and controlling host reactions to infection. In clinical microbiology, the turnaround time of the diagnostic cycle (>24 hours) often leads to unnecessary suffering and deaths; approaches to relieve this burden include rapid diagnostic procedures and more efficient transmission or interpretation of molecular microbiology results. Although rapid nucleic acid-based diagnostic testing has demonstrated that it can impact on the transmission of hospital-acquired infections, we believe that such life-saving procedures should be performed closer to the patient, in dedicated 24/7 laboratories of healthcare institutions, or ideally at point of care. While personalized medicine generally aims at interrogating the genomic information of a patient, drug metabolism polymorphisms, for example, to guide drug choice and dosage, personalized medicine concepts are applicable in infectious diseases for the (rapid) identification of a disease-causing microbe and determination of its antimicrobial resistance profile, to guide an appropriate antimicrobial treatment for the proper management of the patient. The implementation of point-of-care testing for infectious diseases will require acceptance by medical authorities, new technological and communication platforms, as well as reimbursement practices such that time- and life-saving procedures become available to the largest number of patients. PMID:25562799

Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms

PubMed Central

Kameshwar, Ayyappa kumar Sista; Qin, Wensheng

2016-01-01

Lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. Lignocellulose is an abundant renewable biomaterial present on the earth. It has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. Microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. Based on the plant materials they degrade these fungi were classified as white rot, brown rot and soft rot. However, some groups of bacteria belonging to the actinomycetes, α-proteobacteria and β-proteobacteria were also found to be efficient in degrading lignocellulosic biomass but not well understood unlike the fungi. In this review we focus on recent advancements deployed for finding and understanding the lignocellulose degradation by microorganisms. Conventional molecular methods like sequencing 16s rRNA and Inter Transcribed Spacer (ITS) regions were used for identification and classification of microbes. Recent progression in genomics mainly next generation sequencing technologies made the whole genome sequencing of microbes possible in a great ease. The whole genome sequence studies reveals high quality information about genes and canonical pathways involved in the lignin and other cell wall components degradation. PMID:26884714

Identification of a new biocontrol gene in Trichoderma atroviride: the role of an ABC transporter membrane pump in the interaction with different plant-pathogenic fungi.

PubMed

Ruocco, Michelina; Lanzuise, Stefania; Vinale, Francesco; Marra, Roberta; Turrà, David; Woo, Sheridan Lois; Lorito, Matteo

2009-03-01

Successful biocontrol interactions often require that the beneficial microbes involved are resistant or tolerant to a variety of toxicants, including antibiotics produced by themselves or phytopathogens, plant antimicrobial compounds, and synthetic chemicals or contaminants. The ability of Trichoderma spp., the most widely applied biocontrol fungi, to withstand different chemical stresses, including those associated with mycoparasitism, is well known. In this work, we identified an ATP-binding cassette transporter cell membrane pump as an important component of the above indicated resistance mechanisms that appears to be supported by an extensive and powerful cell detoxification system. The encoding gene, named Taabc2, was cloned from a strain of Trichoderma atroviride and characterized. Its expression was found to be upregulated in the presence of pathogen-secreted metabolites, specific mycotoxins and some fungicides, and in conditions that stimulate the production in Trichoderma spp. of antagonism-related factors (toxins and enzymes). The key role of this gene in antagonism and biocontrol was demonstrated by the characterization of the obtained deletion mutants. They suffered an increased susceptibility to inhibitory compounds either secreted by pathogenic fungi or possibly produced by the biocontrol microbe itself and lost, partially or entirely, the ability to protect tomato plants from Pythium ultimum and Rhizoctonia solani attack.

Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards.

PubMed

Lech, Tomasz

2016-05-01

The literature of environmental microbiology broadly discusses issues associated with microbial hazards in archives, but these publications are mainly devoted to paper documents. There are few articles on historical parchment documents, which used to be very important for the development of literature and the art of writing. These studies present a broad spectrum of methods for the assessment of biodeterioration hazards of the parchment document in question. They are based on both conventional microbiological methods and advanced techniques of molecular biology. Here, a qualitative analysis was conducted, based on genetic identification of bacteria and fungi present on the document as well as denaturing gradient gel electrophoresis profiling and examining the destructive potential of isolated microbes. Moreover, the study involved a quantitative and qualitative microbiological assessment of the indoor air in the room where the parchment was kept. The microbes with the highest destructive potential that were isolated from the investigated item were Bacillus cereus and Acinetobacter lwoffii bacteria and Penicillium chrysogenum,Chaetomium globosum, and Trichoderma longibrachiatum fungi. The presence of the B. cereuss train was particularly interesting since, under appropriate conditions, it leads to complete parchment degradation within several days. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Indicator microbes correlate with pathogenic bacteria, yeasts and helminthes in sand at a subtropical recreational beach site.

PubMed

Shah, A H; Abdelzaher, A M; Phillips, M; Hernandez, R; Solo-Gabriele, H M; Kish, J; Scorzetti, G; Fell, J W; Diaz, M R; Scott, T M; Lukasik, J; Harwood, V J; McQuaig, S; Sinigalliano, C D; Gidley, M L; Wanless, D; Ager, A; Lui, J; Stewart, J R; Plano, L R W; Fleming, L E

2011-06-01

Research into the relationship between pathogens, faecal indicator microbes and environmental factors in beach sand has been limited, yet vital to the understanding of the microbial relationship between sand and the water column and to the improvement of criteria for better human health protection at beaches. The objectives of this study were to evaluate the presence and distribution of pathogens in various zones of beach sand (subtidal, intertidal and supratidal) and to assess their relationship with environmental parameters and indicator microbes at a non-point source subtropical marine beach. In this exploratory study in subtropical Miami (Florida, USA), beach sand samples were collected and analysed over the course of 6 days for several pathogens, microbial source tracking markers and indicator microbes. An inverse correlation between moisture content and most indicator microbes was found. Significant associations were identified between some indicator microbes and pathogens (such as nematode larvae and yeasts in the genus Candida), which are from classes of microbes that are rarely evaluated in the context of recreational beach use. Results indicate that indicator microbes may predict the presence of some of the pathogens, in particular helminthes, yeasts and the bacterial pathogen Staphylococcus aureus including methicillin-resistant forms. Indicator microbes may thus be useful for monitoring beach sand and water quality at non-point source beaches. The presence of both indicator microbes and pathogens in beach sand provides one possible explanation for human health effects reported at non-point sources beaches. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

The Microbe Directory: An annotated, searchable inventory of microbes' characteristics.

PubMed

Shaaban, Heba; Westfall, David A; Mohammad, Rawhi; Danko, David; Bezdan, Daniela; Afshinnekoo, Ebrahim; Segata, Nicola; Mason, Christopher E

2018-01-05

The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes' characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY-Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism's taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart ( https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.

Irradiation of Microbes from Spent Nuclear Fuel Storage Pool Environments

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

Breckenridge, C.R.; Watkins, C.S.; Bruhn, D.F.

Microbes have been isolated and identified from spent nuclear fuel storage pools at the Idaho National Engineering and Environmental Laboratory (INEEL). Included among these are Corynebacterium aquaticum, Pseudomonas putida, Comamonas acidovorans, Gluconobacter cerinus, Micrococcus diversus, Rhodococcus rhodochrous, and two strains of sulfate-reducing bacteria (SRB). We examined the sensitivity of these microbes to a variety of total exposures of radiation generated by a 6-MeV linear accelerator (LINAC). The advantage of using a LINAC is that it provides a relatively quick screen of radiation tolerance. In the first set of experiments, we exposed each of the aforementioned microbes along with four additionalmore » microbes, pseudomonas aeruginosa, Micrococcus luteus, Escherchia coli, and Deinococcus radiodurans to exposures of 5 x 10{sup 3} and 6 x 10{sup 4} rad. All microbial specimens withstood the lower exposure with little or no reduction in cell population. Upon exposing the microbes to the larger dose of 6 x 10{sup 4} rad, we observed two distinct groupings: microbes that demonstrate resistance to radiation, and microbes that display intolerance through a dramatic reduction from their initial population. Microbes in the radiation tolerant grouping were exposed to 1.1 x 10{sup 5} rad to examine the extent of their resistance. We observe a correlation between radiation resistance and gram stain. The gram-positive species we examined seem to demonstrate a greater radiation resistance.« less

Longitudinal Stability and Predictors of Poor Oral Comprehenders and Poor Decoders

PubMed Central

Elwér, Åsa; Keenan, Janice M.; Olson, Richard K.; Byrne, Brian; Samuelsson, Stefan

2012-01-01

Two groups of 4th grade children were selected from a population sample (N= 926) to either be Poor Oral Comprehenders (poor oral comprehension but normal word decoding), or Poor Decoders (poor decoding but normal oral comprehension). By examining both groups in the same study with varied cognitive and literacy predictors, and examining them both retrospectively and prospectively, we could assess how distinctive and stable the predictors of each deficit are. Predictors were assessed retrospectively at preschool, at the end of kindergarten, 1st, and 2nd grades. Group effects were significant at all test occasions, including those for preschool vocabulary (worse in poor oral comprehenders) and rapid naming (RAN) (worse in poor decoders). Preschool RAN and Vocabulary prospectively predicted grade 4 group membership (77–79% correct classification) within the selected samples. Reselection in preschool of at-risk poor decoder and poor oral comprehender subgroups based on these variables led to significant but relatively weak prediction of subtype membership at grade 4. Implications of the predictive stability of our results for identification and intervention of these important subgroups are discussed. PMID:23528975

Novel Insights into Insect-Microbe Interactions—Role of Epigenomics and Small RNAs

PubMed Central

Kim, Dohyup; Thairu, Margaret W.; Hansen, Allison K.

2016-01-01

It has become increasingly clear that microbes form close associations with the vast majority of animal species, especially insects. In fact, an array of diverse microbes is known to form shared metabolic pathways with their insect hosts. A growing area of research in insect-microbe interactions, notably for hemipteran insects and their mutualistic symbionts, is to elucidate the regulation of this inter-domain metabolism. This review examines two new emerging mechanisms of gene regulation and their importance in host-microbe interactions. Specifically, we highlight how the incipient areas of research on regulatory “dark matter” such as epigenomics and small RNAs, can play a pivotal role in the evolution of both insect and microbe gene regulation. We then propose specific models of how these dynamic forms of gene regulation can influence insect-symbiont-plant interactions. Future studies in this area of research will give us a systematic understanding of how these symbiotic microbes and animals reciprocally respond to and regulate their shared metabolic processes. PMID:27540386

[Juvenile idiopathic arthritis and oral health].

PubMed

Kobus, Agnieszka; Kierklo, Anna; Sielicka, Danuta; Szajda, Sławomir Dariusz

2016-05-04

Juvenile idiopathic arthritis (JIA) is the most common autoimmune inflammatory disease of connective tissue in children. It is characterized by progressive joint destruction which causes preserved changes in the musculoskeletal system. The literature describes fully clinical symptoms and radiological images in different subtypes of JIA. However, there is still a limited number of studies reporting on the medical condition of the oral cavity of ill children. JIA can affect hard and soft tissues of the oral cavity by: the general condition of the child's health, arthritis of the upper limbs, as the result of the pharmacotherapy, changes in secretion and composition of saliva, inflammation of the temporomandibular joint and facial deformity. The study summarizes the available literature on the condition of the teeth and periodontal and oral hygiene in the course of JIA. The presence of diverse factors that modify the oral cavity, such as facial growth, functioning of salivary glands, or the supervision and care provided by adults, prevents clear identification if JIA leads to severe dental caries and periodontal disease. Despite conflicting results in studies concerning the clinical oral status, individuals with JIA require special attention regarding disease prevention and maintenance of oral health.

[Improvement of oral health care in geriatric care by training of nurses and nursing assistants for the elderly].

PubMed

Jordan, R; Sirsch, E; Gesch, D; Zimmer, S; Bartholomeyczik, S

2012-04-01

Because oral health among residents of German nursing homes is inadequate, this intervention study evaluated the effects of dental training for nurses and nursing assistants (RN and RA) in homes for the elderly on their assessment of oral health in residents and, as a consequence, on the status of residents' oral health. 53 residents and the RNs and RAs from three homes for the elderly participated in this study. The nursing staff received training in dental health care. As primary outcome, the competence in performing the Brief Oral Health Examination (BOHSE) was measured at baseline date and four months after training. Additional outcome measures were dental and denture hygiene in residents, functional status of dentures, and treatment needs. Dental training was shown to improve the nursing staff's competences in oral health assessment in tendency. Residents' oral hygiene improved significantly, whereas no relevant effects on hygiene and functional status of dentures were registered. The need for dental treatment turned out to be considerable at both measurements. Modifications in test tools with identification of dental treatment needs seem to be indicated in order to improve cooperation between nursing staff and dentists in homes for the elderly.

Studies on adaptation to complete dentures. Part II: Oral stereognosis and tactile sensibility.

PubMed

Müller, F; Link, I; Fuhr, K; Utz, K H

1995-10-01

High oral perception is thought to contribute to poor adaptation to new dentures. The aim of this study was to evaluate the oral stereognosis and tactile sensibility in edentate subjects and relate these to patient age and capability of adaptation to new prostheses. A total of 67 patients were provided with new complete dentures 2-3 weeks before the experiment. In 54 subjects, the oral stereognosis was evaluated by 12 different test-pieces, which were placed unseen on the tongue and had to be recognized. In 38 patients, the oral tactile sensibility was determined in the premolar area using copper foils. The capability of adaptation was evaluated by a questionnaire. Denture retention was assessed by clinical examination. The number of correctly identified test-pieces and the average identification time were related to the age, but no relation was found to patients' capability of adaptation. The tactile sensibility was found to be impaired with age and diminished capability of adaptation. Both adaptation and oral tactile sensibility were significantly lower in subjects with poor lower-denture retention. In conclusion, the results cannot support a relationship between high oral stereognosis and adaptation problems. However, good denture retention facilitates the adaptation process.

Survey of medical ethnobotanicals for dental and oral medicine conditions and pathologies.

PubMed

Colvard, Michael D; Cordell, Geoffrey A; Villalobos, Rodrigo; Sancho, Gina; Soejarto, Doel D; Pestle, William; Echeverri, Tatiana Lobo; Perkowitz, Kathleen M; Michel, Joanna

2006-08-11

Ethnomedical questionnaires were distributed in Chicago, Costa Rica, and Colombia to identify the most common over-the-counter (OTC) plant or plant-based products advocated for treating oral pain, ulcerative conditions, and cancer within these locations. Over 100 plants or plant-based herbal preparations and commercial products, purchased from local botanical markets and pharmacies, were advocated for the treatment of oral medicine conditions. Locally familiar and common language names were attributed to the plant products at the time of purchase. Plant products or plant-based commercial products containing plant-based essential oils, anesthetic constituents, and or chemical compounds recommended as OTC oral medicine preparations were systematized, tabulated, and correlated with the published phytotherapeutic literature. Though pharmacognostic research is available for some of the species collected, further ethnographic research is needed to correlate common names with the accurate taxonomic identification for each plant species. Furthermore, epidemiological research is needed to verify the use and standardized dosage for OTC ethnomedicine preparations for oral medicine conditions. Pharmacognostic research and clinical trails which can verify taxonomy, dose, safety, active principles, and efficacy of these OTC oral medicine products must be enhanced in order to verify the claimed validity in contemporary, global, oral medicine practice.

Simple device for the direct visualization of oral-cavity tissue fluorescence

NASA Astrophysics Data System (ADS)

Lane, Pierre M.; Gilhuly, Terence; Whitehead, Peter D.; Zeng, Haishan; Poh, Catherine; Ng, Samson; Williams, Michelle; Zhang, Lewei; Rosin, Miriam; MacAulay, Calum E.

2006-03-01

Early identification of high-risk disease could greatly reduce both mortality and morbidity due to oral cancer. We describe a simple handheld device that facilitates the direct visualization of oral-cavity fluorescence for the detection of high-risk precancerous and early cancerous lesions. Blue excitation light (400 to 460 nm) is employed to excite green-red fluorescence from fluorophores in the oral tissues. Tissue fluorescence is viewed directly along an optical axis collinear with the axis of excitation to reduce inter- and intraoperator variability. This robust, field-of-view device enables the direct visualization of fluorescence in the context of surrounding normal tissue. Results from a pilot study of 44 patients are presented. Using histology as the gold standard, the device achieves a sensitivity of 98% and specificity of 100% when discriminating normal mucosa from severe dysplasia/carcinoma in situ (CIS) or invasive carcinoma. We envisage this device as a suitable adjunct for oral cancer screening, biopsy guidance, and margin delineation.

Prospective Evaluation of Multimodal Optical Imaging with Automated Image Analysis to Detect Oral Neoplasia In Vivo.

PubMed

Quang, Timothy; Tran, Emily Q; Schwarz, Richard A; Williams, Michelle D; Vigneswaran, Nadarajah; Gillenwater, Ann M; Richards-Kortum, Rebecca

2017-10-01

The 5-year survival rate for patients with oral cancer remains low, in part because diagnosis often occurs at a late stage. Early and accurate identification of oral high-grade dysplasia and cancer can help improve patient outcomes. Multimodal optical imaging is an adjunctive diagnostic technique in which autofluorescence imaging is used to identify high-risk regions within the oral cavity, followed by high-resolution microendoscopy to confirm or rule out the presence of neoplasia. Multimodal optical images were obtained from 206 sites in 100 patients. Histologic diagnosis, either from a punch biopsy or an excised surgical specimen, was used as the gold standard for all sites. Histopathologic diagnoses of moderate dysplasia or worse were considered neoplastic. Images from 92 sites in the first 30 patients were used as a training set to develop automated image analysis methods for identification of neoplasia. Diagnostic performance was evaluated prospectively using images from 114 sites in the remaining 70 patients as a test set. In the training set, multimodal optical imaging with automated image analysis correctly classified 95% of nonneoplastic sites and 94% of neoplastic sites. Among the 56 sites in the test set that were biopsied, multimodal optical imaging correctly classified 100% of nonneoplastic sites and 85% of neoplastic sites. Among the 58 sites in the test set that corresponded to a surgical specimen, multimodal imaging correctly classified 100% of nonneoplastic sites and 61% of neoplastic sites. These findings support the potential of multimodal optical imaging to aid in the early detection of oral cancer. Cancer Prev Res; 10(10); 563-70. ©2017 AACR . ©2017 American Association for Cancer Research.

Engineering microbes for efficient production of chemicals

DOEpatents

Gong, Wei; Dole, Sudhanshu; Grabar, Tammy; Collard, Andrew Christopher; Pero, Janice G; Yocum, R Rogers

2015-04-28

This present invention relates to production of chemicals from microorganisms that have been genetically engineered and metabolically evolved. Improvements in chemical production have been established, and particular mutations that lead to those improvements have been identified. Specific examples are given in the identification of mutations that occurred during the metabolic evolution of a bacterial strain genetically engineered to produce succinic acid. This present invention also provides a method for evaluating the industrial applicability of mutations that were selected during the metabolic evolution for increased succinic acid production. This present invention further provides microorganisms engineered to have mutations that are selected during metabolic evolution and contribute to improved production of succinic acid, other organic acids and other chemicals of commercial interest.

Microbes to Biomes at Berkeley Lab

ScienceCinema

None

2018-06-21

Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

Knowledge of Future Dental Practitioners towards Oral Cancer: Exploratory Findings from a Public University in Malaysia

PubMed Central

Bhagavathula, Akshaya Srikanth; Bin Zakaria, Nazrin; Jamshed, Shazia Qasim

2015-01-01

Objective. To assess knowledge and awareness of oral cancer in the early identification of risk factors among undergraduate dental students. Methods. A total of 162 undergraduate (third, fourth, and fifth year) dental students at International Islamic University, Malaysia, were approached to participate in the study, and those who agreed were administered. A 9-item pretested questionnaire contains questions on oral examination, oral cancer risk factors, and requests for further information. Descriptive statistics were conducted using chi-square testing. Results. The response rate of the study was 70.3% (114/162), with 26 (22.8%) males and 88 (77.2%) females. All undergraduate dental students were familiar with examining the oral mucosa of their patients and most were likely to advise patients about the risk factors for developing oral cancer (98.2%). Nearly one-third (32.4%) of students reported examining patients with oral lesions as early signs for oral cancer (P < 0.001) and nearly 70% agreed that they did not have sufficient knowledge regarding the prevention and detection of oral cancer (P < 0.001). In addition, more than 95.6% agreed that there is a need for additional information/teaching regarding oral cancer. Further, 61.3% and 14.1% identified tobacco smoking and drinking alcohol as major risk factors for developing oral cancer. Conclusion. This study demonstrated lack of awareness about risk factors among undergraduate dental students regarding oral cancer. Reinforcing awareness and enhancing the benefits of early detection on prevention of oral cancer should be done through training and/or educational intervention. PMID:26839548

Toluidine blue aids in detection of dysplasia and carcinoma in suspicious oral lesions.

PubMed

Chainani-Wu, N; Madden, E; Cox, D; Sroussi, H; Epstein, J; Silverman, S

2015-10-01

Accurate clinical identification of 'higher-risk' oral premalignant lesions or 'higher-risk' areas within lesions is important. Assessment methods that predict their presence have great utility. A cross-sectional, observational study enrolled a consecutive sample of consenting patients diagnosed with oral leukoplakia, erythroleukoplakia, or erythroplakia. Medical history, visual oral examination, ViziLite(®) examination, toluidine blue staining (TBlue(®) ), and finally a biopsy were completed in a single clinic visit. Seventy-seven of 100 examined lesions in 43 patients were biopsied. Sensitivity, specificity, and positive and negative predictive values were computed for visual examination, ViziLite(®) , and TBlue(®) using biopsy results as the gold standard. The sensitivity of TBlue(®) in detecting high-risk lesions (carcinoma in situ or carcinoma) was 94 (71-100, P < 0.0003) and specificity 45 (32-58, P < 0.53), while for carcinoma, sensitivity was 100 (54-100, P < 0.032) and specificity 39 (28-52, P < 0.097). The results of ViziLite(®) testing either by itself or in combination with the information from toluidine blue testing revealed low sensitivity for the detection of high-risk lesions. Clinical examination of leukoplakia, erythroplakia, or erythroleukoplakia lesions combined with toluidine blue staining may aid in the identification of severe dysplasia (carcinoma in situ) or carcinoma. This may help in determining whether, when, and where (the site within a lesion) a biopsy should be taken. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Effects of prey, pitcher age, and microbes on acid phosphatase activity in fluid from pitchers of Sarracenia purpurea (Sarraceniaceae)

PubMed Central

Newell, Sandra J.

2017-01-01

Carnivory in pitcher plants generally involves digestion of prey, by the plant itself, by symbionts, or both. While symbionts appear to be important in the digestion of prey in Sarracenia purpurea, the importance of pitcher-derived enzymes is less well documented. Our goal was to reduce microbial numbers in pitcher fluid in order to measure the acid phosphatase activity attributable to the pitchers themselves. Preliminary experiments indicated that various antibiotics were minimally effective at reducing microbial populations and that antibiotic-resistant microbes were easily cultured from pitcher fluid. Consequently, we measured the abundance of culturable microbes in every sample taken for the measurement of acid phosphatase activity. Pitchers fed with one sterilized ant had higher levels of acid phosphatase activity than unfed pitchers. Older pitchers were more responsive to feeding than young pitchers. Pitchers with high levels of microbes (on Day 5) had higher acid phosphatase activity than pitchers with low levels of microbes. However, fed pitchers were not more likely to have higher microbe levels and microbe levels were not related to pitcher age. When fluid samples from inside the pitcher were compared to appropriate controls incubated outside the pitcher, acid phosphatase activity was higher inside the pitcher. Results from the feeding experiments are consistent with a primary role of microbes in the digestion of prey in pitchers of S. purpurea. However, the relationship between pitcher age and enzyme activity is not a function of microbes in the pitcher fluid and may depend on enzymes produced by the plant. Our methods would not detect microbes embedded on the inner surface of the pitcher; and if they survived the alcohol rinse and antibiotics, we cannot rule out microbes as the source of the relationship between pitcher age and acid phosphatase activity. PMID:28719666

An improved in-house lysis-filtration protocol for bacterial identification from positive blood culture bottles with high identification rates by MALDI-TOF MS.

PubMed

Tsuchida, Sachio; Murata, Syota; Miyabe, Akiko; Satoh, Mamoru; Takiwaki, Masaki; Matsushita, Kazuyuki; Nomura, Fumio

2018-05-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is now a well-established method for identification of microorganisms from positive blood cultures. Pretreatments to effectively remove non-bacterial proteins are a prerequisite for successful identification, and a variety of protocols have been reported. Although commercially available kits, mainly the Sepsityper Kit, are increasingly used, the identification rates reported often are not satisfactory, particularly for Gram-positive isolates. We developed a new, in-house lysis-filtration protocol and prospectively evaluated its performance compared to the Sepsityper kit. The in-house protocol consists of three simple steps: lysis by ammonium chloride, aspiration with a syringe fitted with a 0.45-μm membrane, and centrifugation to collect microbes. The novel protocol requires only 20 min. Performance of the in-house protocol was evaluated using a total of 117 monomicrobial cases of positive blood culture. Medium from blood culture bottles was pretreated by the in-house protocol or the commercial kit, and isolated cells were subjected to direct identification by mass spectrometry fingerprinting in parallel with conventional subculturing for reference identification. The overall MALDI-TOF MS-based identification rates with score > 1.7 and > 2.0 obtained using the in-house protocol were 99.2% and 85.5%, respectively, whereas those obtained using the Sepsityper Kit were 85.4% and 61.5%, respectively. For Gram-positive cases, the in-house protocol yielded scores >1.7 and > 2.0 at 98.5% and 76.1%, respectively, whereas the commercial kit yielded these scores at 76.1% and 43.3%, respectively. Although these are preliminary results, these values suggest that this easy lysis-filtration protocol deserves assessment in a larger-scale test. Copyright © 2018 Elsevier B.V. All rights reserved.

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

DOE PAGES

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei; ...

2015-12-03

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

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

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Toenail infection by Cladophialophora boppii.

PubMed

Brasch, J; Dressel, S; Müller-Wening, K; Hügel, R; von Bremen, D; de Hoog, G S

2011-02-01

Cladophialophora boppii is a black yeast-like fungus that up to now has been only rarely described as a cause of human infection and whose role as a pathogen was not established despite its repeated isolation and genetic identification in these reports. Here we report the first case of a verified toenail infection caused by this fungus in a woman without any systemic disease or evidence of immunodeficiency. Identical dark molds were isolated from the same toenail at three points of time. Species identification was performed by scrutinizing the isolates morphologic, physiologic and genetic characteristics which resulted in their identification as Cladophialophora boppii. Oral treatment with terbinafin plus topical ciclopiroxolamine was effective.

An Alternative Approach to "Identification of Unknowns": Designing a Protocol to Verify the Identities of Nitrogen Fixing Bacteria.

PubMed

Martinez-Vaz, Betsy M; Denny, Roxanne; Young, Nevin D; Sadowsky, Michael J

2015-12-01

Microbiology courses often include a laboratory activity on the identification of unknown microbes. This activity consists of providing students with microbial cultures and running biochemical assays to identify the organisms. This approach lacks molecular techniques such as sequencing of genes encoding 16S rRNA, which is currently the method of choice for identification of unknown bacteria. A laboratory activity was developed to teach students how to identify microorganisms using 16S rRNA polymerase chain reaction (PCR) and validate microbial identities using biochemical techniques. We hypothesized that designing an experimental protocol to confirm the identity of a bacterium would improve students' knowledge of microbial identification techniques and the physiological characteristics of bacterial species. Nitrogen-fixing bacteria were isolated from the root nodules of Medicago truncatula and prepared for 16S rRNA PCR analysis. Once DNA sequencing revealed the identity of the organisms, the students designed experimental protocols to verify the identity of rhizobia. An assessment was conducted by analyzing pre- and posttest scores and by grading students' verification protocols and presentations. Posttest scores were higher than pretest scores at or below p = 0.001. Normalized learning gains (G) showed an improvement of students' knowledge of microbial identification methods (LO4, G = 0.46), biochemical properties of nitrogen-fixing bacteria (LO3, G = 0.45), and the events leading to the establishment of nitrogen-fixing symbioses (LO1&2, G = 0.51, G = 0.37). An evaluation of verification protocols also showed significant improvement with a p value of less than 0.001.

Rapid screening of tannase producing microbes by using natural tannin

PubMed Central

Jana, Arijit; Maity, Chiranjit; Halder, Suman Kumar; Pati, Bikas Ranjan; Mondal, Keshab Chandra; Mohapatra, Pradeep Kumar Das

2012-01-01

Use of natural tannin in the screening of tannase producing microbes is really promising. The present work describes about the possibility and integrity of the newly formulated method over the previously reported methods. Tannin isolated from Terminalia belerica Roxb. (Bahera) was used to differentiate between tanninolytic and nontanninolytic microbes. The method is simple, sensitive and superior for the rapid screening and isolation of tannase-producing microbes. PMID:24031931

Rapid screening of tannase producing microbes by using natural tannin.

PubMed

Jana, Arijit; Maity, Chiranjit; Halder, Suman Kumar; Pati, Bikas Ranjan; Mondal, Keshab Chandra; Mohapatra, Pradeep Kumar Das

2012-07-01

Use of natural tannin in the screening of tannase producing microbes is really promising. The present work describes about the possibility and integrity of the newly formulated method over the previously reported methods. Tannin isolated from Terminalia belerica Roxb. (Bahera) was used to differentiate between tanninolytic and nontanninolytic microbes. The method is simple, sensitive and superior for the rapid screening and isolation of tannase-producing microbes.

IL-17-mediated immunity to the opportunistic fungal pathogen Candida albicans

PubMed Central

Conti, Heather R.; Gaffen, Sarah L.

2015-01-01

IL-17 (IL-17A) has emerged as a key mediator of protection against extracellular microbes, but this cytokine also drives pathology in various autoimmune diseases. Overwhelming data in both humans and mice reveal a clear and surprisingly specific role for IL-17 in protection against the fungus Candida albicans, a commensal of the human oral cavity, gastrointestinal tract and reproductive mucosa. The IL-17 pathway regulates antifungal immunity through upregulation of pro-inflammatory cytokines including IL-6, neutrophil-recruiting chemokines such as CXCL1 and CXCL5 and antimicrobial peptides such as the defensins, which act in concert to limit fungal overgrowth. This review will focus on diseases caused by C. albicans, the role of IL-17-mediated immunity in candidiasis, and the implications for clinical therapies for both autoimmune conditions and fungal infections. PMID:26188072

Parasite-specific immune response in adult Drosophila melanogaster: a genomic study

PubMed Central

Roxström-Lindquist, Katarina; Terenius, Olle; Faye, Ingrid

2004-01-01

Insects of the order Diptera are vectors for parasitic diseases such as malaria, sleeping sickness and leishmania. In the search for genes encoding proteins involved in the antiparasitic response, we have used the protozoan parasite Octosporea muscaedomesticae for oral infections of adult Drosophila melanogaster. To identify parasite-specific response molecules, other flies were exposed to virus, bacteria or fungi in parallel. Analysis of gene expression patterns after 24 h of microbial challenge, using Affymetrix oligonucleotide microarrays, revealed a high degree of microbe specificity. Many serine proteases, key intermediates in the induction of insect immune responses, were uniquely expressed following infection of the different organisms. Several lysozyme genes were induced in response to Octosporea infection, while in other treatments they were not induced or downregulated. This suggests that lysozymes are important in antiparasitic defence. PMID:14749722

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

PubMed Central

2014-01-01

Background The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW, <1,500 g) neonates via conventional broad-spectrum antibiotic treatment. We hypothesize the built environment (BE), specifically room surfaces frequently touched by humans, is a predominant source of colonizing microbes in the gut of premature VLBW infants. Here, we present the first matched fecal-BE time series analysis of two preterm VLBW neonates housed in a neonatal intensive care unit (NICU) over the first month of life. Results Fresh fecal samples were collected every 3 days and metagenomes sequenced on an Illumina HiSeq2000 device. For each fecal sample, approximately 33 swabs were collected from each NICU room from 6 specified areas: sink, feeding and intubation tubing, hands of healthcare providers and parents, general surfaces, and nurse station electronics (keyboard, mouse, and cell phone). Swabs were processed using a recently developed ‘expectation maximization iterative reconstruction of genes from the environment’ (EMIRGE) amplicon pipeline in which full-length 16S rRNA amplicons were sheared and sequenced using an Illumina platform, and short reads reassembled into full-length genes. Over 24,000 full-length 16S rRNA sequences were produced, generating an average of approximately 12,000 operational taxonomic units (OTUs) (clustered at 97% nucleotide identity) per room-infant pair. Dominant gut taxa, including Staphylococcus epidermidis, Klebsiella pneumoniae, Bacteroides fragilis, and Escherichia coli, were widely distributed throughout the room environment with many gut colonizers detected in more than half of samples. Reconstructed genomes from infant gut colonizers revealed a suite of genes that confer resistance to antibiotics (for example, tetracycline, fluoroquinolone, and aminoglycoside) and sterilizing agents, which likely offer a competitive advantage in the NICU environment. Conclusions We have developed a high-throughput culture-independent approach that integrates room surveys based on full-length 16S rRNA gene sequences with metagenomic analysis of fecal samples collected from infants in the room. The approach enabled identification of discrete ICU reservoirs of microbes that also colonized the infant gut and provided evidence for the presence of certain organisms in the room prior to their detection in the gut. PMID:24468033

Method of degrading pollutants in soil

DOEpatents

Hazen, Terry C.; Lopez-De-Victoria, Geralyne

1994-01-01

A method and system for enhancing the motility of microorganisms by placing an effective amount of chlorinated hydrocarbons, preferably chlorinated alkenes, and most preferably trichloroethylene in spaced relation to the microbes so that the surprisingly strong, monomodal, chemotactic response of the chlorinated hydrocarbon on subsurface microbes can draw the microbes away from or towards and into a substance, as desired. In remediation of groundwater pollution, for example, TCE can be injected into the plume to increase the population of microbes at the plume whereby the plume can be more quickly degraded. A TCE-degrading microbe, such as Welchia alkenophilia, can be used to degrade the TCE following the degradation of the original pollutant.

[Development of a microenvironment test chamber for airborne microbe research].

PubMed

Zhan, Ningbo; Chen, Feng; Du, Yaohua; Cheng, Zhi; Li, Chenyu; Wu, Jinlong; Wu, Taihu

2017-10-01

One of the most important environmental cleanliness indicators is airborne microbe. However, the particularity of clean operating environment and controlled experimental environment often leads to the limitation of the airborne microbe research. This paper designed and implemented a microenvironment test chamber for airborne microbe research in normal test conditions. Numerical simulation by Fluent showed that airborne microbes were evenly dispersed in the upper part of test chamber, and had a bottom-up concentration growth distribution. According to the simulation results, the verification experiment was carried out by selecting 5 sampling points in different space positions in the test chamber. Experimental results showed that average particle concentrations of all sampling points reached 10 7 counts/m 3 after 5 minutes' distributing of Staphylococcus aureus , and all sampling points showed the accordant mapping of concentration distribution. The concentration of airborne microbe in the upper chamber was slightly higher than that in the middle chamber, and that was also slightly higher than that in the bottom chamber. It is consistent with the results of numerical simulation, and it proves that the system can be well used for airborne microbe research.

With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology-An Introduction to the Symposium.

PubMed

Kohl, Kevin D; Dearing, M Denise

2017-10-01

The role that host-associated microbes play in animal biology is gaining attention in comparative biology. Numerous research groups study the roles that microbes play in human health and nutrition, or in enhancing the production of agricultural animals. However, inclusion of host-associated microbes into research questions of integrative and comparative biology has lagged behind. We hosted a symposium to bring together top researchers in the field of host-associated microbes who also incorporate aspects of integrative and comparative biology. In this introduction, we highlight recent research demonstrating the profound roles that host-associated microbes play in many aspects of animal biology, such as immune function, endocrinology, and even behavior. It is our hope that integrative and comparative biologists will begin to include aspects of host-associated microbes into their research programs, enhancing both the fields of comparative biology and host-microbe interactions. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Harnessing Insect-Microbe Chemical Communications To Control Insect Pests of Agricultural Systems.

PubMed

Beck, John J; Vannette, Rachel L

2017-01-11

Insect pests cause serious economic, yield, and food safety problems to managed crops worldwide. Compounding these problems, insect pests often vector pathogenic or toxigenic microbes to plants. Previous work has considered plant-insect and plant-microbe interactions separately. Although insects are well-understood to use plant volatiles to locate hosts, microorganisms can produce distinct and abundant volatile compounds that in some cases strongly attract insects. In this paper, we focus on the microbial contribution to plant volatile blends, highlighting the compounds emitted and the potential for variation in microbial emission. We suggest that these aspects of microbial volatile emission may make these compounds ideal for use in agricultural applications, as they may be more specific or enhance methods currently used in insect control or monitoring. Our survey of microbial volatiles in insect-plant interactions suggests that these emissions not only signal host suitability but may indicate a distinctive time frame for optimal conditions for both insect and microbe. Exploitation of these host-specific microbe semiochemicals may provide important microbe- and host-based attractants and a basis for future plant-insect-microbe chemical ecology investigations.

78 FR 14272 - Department of Defense Task Force on the Care, Management, and Transition of Recovering Wounded...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-05

.... EDT each day. ADDRESSES: DoubleTree by Hilton Hotel Washington DC-Crystal City, 300 Army Navy Drive... submitted for an oral presentation by the person making the submission. Identification information must be...

78 FR 59918 - Department of Defense Task Force on the Care, Management, and Transition of Recovering Wounded...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-30

.... EDT. ADDRESSES: DoubleTree by Hilton Hotel Washington DC-Crystal City, 300 Army Navy Drive, Arlington... submitted for an oral presentation by the person making the submission. Identification information must be...

Pyrosequencing for Microbial Identification and Characterization

PubMed Central

Cummings, Patrick J.; Ahmed, Ray; Durocher, Jeffrey A.; Jessen, Adam; Vardi, Tamar; Obom, Kristina M.

2013-01-01

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns. PMID:23995536

Pyrosequencing for microbial identification and characterization.

PubMed

Cummings, Patrick J; Ahmed, Ray; Durocher, Jeffrey A; Jessen, Adam; Vardi, Tamar; Obom, Kristina M

2013-08-22

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.

Wound Healing Finally Enters the Age of Molecular Diagnostic Medicine

PubMed Central

Tatum, Owatha L.; Dowd, Scot E.

2012-01-01

Background Many wounds are difficult to heal because of the large, complex community of microbes present within the wound. The Problem Classical laboratory culture methods do not provide an accurate picture of the microbial interactions or representation of microorganisms within a wound. There is an inherent bias in diagnosis based upon classical culture stemming from the ability of certain organisms to thrive in culture while others are underrepresented or fail to be identified in culture altogether. Chronic wounds also contain polymicrobial infections existing as a cooperative community that is resistant to antibiotic therapy. Basic/Clinical Science Advances New methods in molecular diagnostic medicine allow the identification of nearly all organisms present in a wound irrespective of the ability of these organisms to be grown in culture. Advances in DNA analyses allow absolute identification of microorganisms from very small clinical specimens. These new methods also provide a quantitative representation of all microorganisms contributing to these polymicrobial infections. Clinical Care Relevance Technological advances in laboratory diagnostics can significantly shorten the time required to heal chronic wounds. Identification of the genetic signatures of organisms present within a wound allows clinicians to identify and treat the primary organisms responsible for nonhealing wounds. Conclusion Advanced genetic technologies targeting the specific needs of wound care patients are now accessible to all wound care clinicians. PMID:24527290

Applications of copolymer for rapid identification of bacteria in blood culture broths using matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Ashizawa, Kazuho; Murata, Syota; Terada, Takashi; Ito, Daisuke; Bunya, Masaru; Watanabe, Koji; Teruuchi, Yoko; Tsuchida, Sachio; Satoh, Mamoru; Nishimura, Motoi; Matsushita, Kazuyuki; Sugama, Yuji; Nomura, Fumio

2017-08-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) can be used to identify pathogens in blood culture samples. However, sample pretreatment is needed for direct identification of microbes in blood culture bottles. Conventional protocols are complex and time-consuming. Therefore, in this study, we developed a method for collecting bacteria using polyallylamine-polystyrene copolymer for application in wastewater treatment technology. Using representative bacterial species Escherichia coli and Staphylococcus capitis, we found that polyallylamine-polystyrene can form visible aggregates with bacteria, which can be identified using MALDI-TOF MS. The processing time of our protocol was as short as 15min. Hemoglobin interference in MALDI spectra analysis was significantly decreased in our method compared with the conventional method. In a preliminary experiment, we evaluated the use of our protocol to identify clinical isolates from blood culture bottles. MALDI-TOF MS-based identification of 17 strains from five bacterial species (E. coli, Klebsiella pneumoniae, Enterococcus faecalis, S. aureus, and S. capitis) collected by our protocol was satisfactory. Prospective large-scale studies are needed to further evaluate the clinical application of this novel and simple method of collecting bacteria in blood culture bottles. Copyright © 2017 Elsevier B.V. All rights reserved.

Functional expression of dental plaque microbiota.

PubMed

Peterson, Scott N; Meissner, Tobias; Su, Andrew I; Snesrud, Erik; Ong, Ana C; Schork, Nicholas J; Bretz, Walter A

2014-01-01

Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free) or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota's transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota.

Functional expression of dental plaque microbiota

PubMed Central

Peterson, Scott N.; Meissner, Tobias; Su, Andrew I.; Snesrud, Erik; Ong, Ana C.; Schork, Nicholas J.; Bretz, Walter A.

2014-01-01

Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free) or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota's transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota. PMID:25177549

Oral hygiene and mouth care for older people in acute hospitals: part 1.

PubMed

Steel, Ben J

2017-10-31

The oral health of older people in acute hospitals has rarely been studied. Hospital admission provides a prime opportunity for identification and rectification of problems, and oral health promotion. This two-part article explores oral hygiene and mouth care provision for older adults in acute hospitals. The first article presents the findings of a literature review exploring oral and dental disease in older adults, the importance of good oral health and mouth care, and the current situation. Searches of electronic databases and the websites of relevant professional health service bodies in the UK were undertaken to identify articles and guidelines. The literature shows a high prevalence of oro-dental disease in this population, with many known detrimental effects, combined with suboptimal oral hygiene and mouth care provision in acute hospitals. Several guidelines exist, although the emphasis on oral health is weaker than other aspects of hospital care. Older adults admitted to acute hospitals have a high burden of oro-dental disease and oral and mouth care needs, but care provision tends to be suboptimal. The literature is growing, but this area is still relatively neglected. Great potential exists to develop oral and mouth care in this context. The second part of this article explores clinical recommendations. ©2012 RCN Publishing Company Ltd. All rights reserved. Not to be copied, transmitted or recorded in any way, in whole or part, without prior permission of the publishers.

Ataxia Telangiectasia in Siblings: Oral Motor and Swallowing Characterization.

PubMed

Rondon-Melo, Silmara; de Almeida, Isabel Junqueira; Andrade, Claudia Regina Furquim de; Sassi, Fernanda Chiarion; Molini-Avejonas, Daniela Regina

2017-07-12

BACKGROUND The body of literature on oral motor and swallowing disorders in patients with ataxia telangiectasia (AT) is limited. CASE REPORT The purpose of this study was to characterize oral motor and swallowing disorders in two siblings with AT, based on oral motor and swallowing assessments. Specific procedures were applied for oral motor and swallowing assessments and both patients underwent videofluoroscopy (VFS). Case 1 presented vocal instability, change in postural control during feeding; food retention in oral cavity; slower oral transit time; and multiple swallowing (signs for solid and liquid). Case 2 presented parted lips at rest and reduced muscle strength; reduced strength and mobility of the tongue; vocal weakness and instability; reduced speech precision and intelligibility; decreased intonation pattern; food retention in oral cavity during feeding; slower oral transit time; multiple swallowing (signs for solid and liquid); poor bolus ejection; incoordination and difficulty in controlling the sips of water taken from the cup; altered cervical auscultation after swallowing and respiratory distress (liquid and puree). For both patients VFS results revealed laryngeal penetration for liquid. CONCLUSIONS Although the literature describes the occurrence of dysarthria and swallowing disorders in patients with AT, little attention has been given to describing which oral motor deficits are responsible for these disorders. Early identification of swallowing alterations and rehabilitation could decrease the risk of aspiration pneumonia. Future studies are necessary in order to investigate the deterioration process of swallowing in AT and the influence of rehabilitation in maintaining functional health.

The Pathogenic Potential of a Microbe

PubMed Central

2017-01-01

ABSTRACT Virulence is a microbial property that is realized only in susceptible hosts. There is no absolute measurement for virulence, and consequently it is always measured relative to a standard, usually another microbe or host. This article introduces the concept of pathogenic potential, which provides a new approach to measuring the capacity of microbes for virulence. The pathogenic potential is proportional to the fraction of individuals who become symptomatic after infection with a defined inoculum and can include such attributes as mortality, communicability, and the time from infection to disease. The calculation of the pathogenic potential has significant advantages over the use of the lethal dose that kills 50% of infected individuals (LD50) and allows direct comparisons between individual microbes. An analysis of the pathogenic potential of several microbes for mice reveals a continuum, which in turn supports the view that there is no dividing line between pathogenic and nonpathogenic microbes. PMID:28251180

Thermo-tolerant phosphate-solubilizing microbes for multi-functional biofertilizer preparation.

PubMed

Chang, Cheng-Hsiung; Yang, Shang-Shyng

2009-02-01

In order to prepare the multi-functional biofertilizer, thermo-tolerant phosphate-solubilizing microbes including bacteria, actinomycetes, and fungi were isolated from different compost plants and biofertilizers. Except Streptomycesthermophilus J57 which lacked pectinase, all isolates possessed amylase, CMCase, chitinase, pectinase, protease, lipase, and nitrogenase activities. All isolates could solubilize calcium phosphate and Israel rock phosphate; various isolates could solubilize aluminum phosphate, iron phosphate, and hydroxyapatite. During composting, biofertilizers inoculated with the tested microbes had a significantly higher temperature, ash content, pH, total nitrogen, soluble phosphorus content, and germination rate than non-inoculated biofertilizer; total organic carbon and carbon-to-nitrogen ratio showed the opposite pattern. Adding these microbes can shorten the period of maturity, improve the quality, increase the soluble phosphorus content, and enhance the populations of phosphate-solubilizing and proteolytic microbes in biofertilizers. Therefore, inoculating thermo-tolerant phosphate-solubilizing microbes into agricultural and animal wastes represents a practical strategy for preparing multi-functional biofertilizer.

In vivo soft tissue differentiation by diffuse reflectance spectroscopy: preliminary results

NASA Astrophysics Data System (ADS)

Zam, Azhar; Stelzle, Florian; Tangermann-Gerk, Katja; Adler, Werner; Nkenke, Emeka; Neukam, Friedrich Wilhelm; Schmidt, Michael; Douplik, Alexandre

Remote laser surgery does not provide haptic feedback to operate layer by layer and preserve vulnerable anatomical structures like nerve tissue or blood vessels. The aim of this study is identification of soft tissue in vivo by diffuse reflectance spectroscopy to set the base for a feedback control system to enhance nerve preservation in oral and maxillofacial laser surgery. Various soft tissues can be identified by diffuse reflectance spectroscopy in vivo. The results may set the base for a feedback system to prevent nerve damage during oral and maxillofacial laser surgery.

The Biomolecule Sequencer Project: Nanopore Sequencing as a Dual-Use Tool for Crew Health and Astrobiology Investigations

NASA Technical Reports Server (NTRS)

John, K. K.; Botkin, D. S.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lehman, N.; Lupisella, M. L.; Mason, C. E.; Smith, D. J.;

Gold-FISH: A correlative approach to microscopic imaging of single microbial cells in environmental samples

NASA Astrophysics Data System (ADS)

Schmidt, Hannes; Seki, David; Woebken, Dagmar; Eickhorst, Thilo

2017-04-01

Fluorescence in situ hybridization (FISH) is routinely used for the phylogenetic identification, detection, and quantification of single microbial cells environmental microbiology. Oligonucleotide probes that match the 16S rRNA sequence of target organisms are generally applied and the resulting signals are visualized via fluorescence microscopy. Consequently, the detection of the microbial cells of interest is limited by the resolution and the sensitivity of light microscopy where objects smaller than 0.2 µm can hardly be represented. Visualizing microbial cells at magnifications beyond light microscopy, however, can provide information on the composition and potential complexity of microbial habitats - the actual sites of nutrient cycling in soil and sediments. We present a recently developed technique that combines (1) the phylogenetic identification and detection of individual microorganisms by epifluorescence microscopy, with (2) the in situ localization of gold-labelled target cells on an ultrastructural level by SEM. Based on 16S rRNA targeted in situ hybridization combined with catalyzed reporter deposition, a streptavidin conjugate labeled with a fluorescent dye and nanogold particles is introduced into whole microbial cells. A two-step visualization process including an autometallographic enhancement of nanogold particles then allows for either fluorescence or electron microscopy, or a correlative application thereof. We will present applications of the Gold-FISH protocol to samples of marine sediments, agricultural soils, and plant roots. The detection and enumeration of bacterial cells in soil and sediment samples was comparable to CARD-FISH applications via fluorescence microscopy. Examples of microbe-surface interaction analysis will be presented on the basis of bacteria colonizing the rhizoplane of rice roots. In principle, Gold-FISH can be performed on any material to give a snapshot of microbe-surface interactions and provides a promising tool for the acquisition of correlative information on microorganisms within their respective habitats.

Assessment of Lactobacillus gasseri as a Candidate Oral Vaccine Vector ▿

PubMed Central

Stoeker, Laura; Nordone, Shila; Gunderson, Sara; Zhang, Lin; Kajikawa, Akinobu; LaVoy, Alora; Miller, Michael; Klaenhammer, Todd R.; Dean, Gregg A.

2011-01-01

Lactobacillus species are commensal bacteria that have long been recognized as probiotic microbes and are generally regarded as safe (GRAS) for human consumption. We have investigated the use of L. gasseri as a vaccine vector for oral immunization against mucosal pathogens. Recent research has shown that the immune response to different lactobacilli can vary widely depending on the species or subspecies of Lactobacillus being studied. While some lactobacilli seem to induce oral tolerance, others induce an adaptive immune response. This study characterized the systemic and mucosal immune response to wild-type and genetically modified L. gasseri. L. gasseri primarily activates TLR2/6, with additional activation through the TLR2 homodimer. To expand the Toll-like receptor (TLR) activation profile of L. gasseri and the immunogenicity of the vector, a plasmid containing fliC, the gene encoding bacterial flagellin, was introduced which resulted in the strong activation of TLR5. The treatment of human myeloid dendritic cells with recombinant lactobacilli expressing flagellin triggered phenotypic maturation and the release of proinflammatory cytokines. In contrast, bacterial treatment also resulted in a statistically significant increase in IL-10 production. In vivo studies established that treatment with L. gasseri led to a diversification of B-cell populations in the lamina propria of the murine colon. Furthermore, treatment with genetically modified L. gasseri led to a significant decrease in the percentage of FoxP3+ colonic lymphocytes. Taken together, these data clarify the interaction of L. gasseri with the host immune system and support further investigation of the in vivo immunogenicity of L. gasseri expressing both flagellin and candidate vaccine antigens. PMID:21900526

Assessment of Lactobacillus gasseri as a candidate oral vaccine vector.

PubMed

Stoeker, Laura; Nordone, Shila; Gunderson, Sara; Zhang, Lin; Kajikawa, Akinobu; LaVoy, Alora; Miller, Michael; Klaenhammer, Todd R; Dean, Gregg A

2011-11-01

Lactobacillus species are commensal bacteria that have long been recognized as probiotic microbes and are generally regarded as safe (GRAS) for human consumption. We have investigated the use of L. gasseri as a vaccine vector for oral immunization against mucosal pathogens. Recent research has shown that the immune response to different lactobacilli can vary widely depending on the species or subspecies of Lactobacillus being studied. While some lactobacilli seem to induce oral tolerance, others induce an adaptive immune response. This study characterized the systemic and mucosal immune response to wild-type and genetically modified L. gasseri. L. gasseri primarily activates TLR2/6, with additional activation through the TLR2 homodimer. To expand the Toll-like receptor (TLR) activation profile of L. gasseri and the immunogenicity of the vector, a plasmid containing fliC, the gene encoding bacterial flagellin, was introduced which resulted in the strong activation of TLR5. The treatment of human myeloid dendritic cells with recombinant lactobacilli expressing flagellin triggered phenotypic maturation and the release of proinflammatory cytokines. In contrast, bacterial treatment also resulted in a statistically significant increase in IL-10 production. In vivo studies established that treatment with L. gasseri led to a diversification of B-cell populations in the lamina propria of the murine colon. Furthermore, treatment with genetically modified L. gasseri led to a significant decrease in the percentage of FoxP3(+) colonic lymphocytes. Taken together, these data clarify the interaction of L. gasseri with the host immune system and support further investigation of the in vivo immunogenicity of L. gasseri expressing both flagellin and candidate vaccine antigens.

Phenotypic Identification of Actinomyces and Related Species Isolated from Human Sources

PubMed Central

Sarkonen, Nanna; Könönen, Eija; Summanen, Paula; Könönen, Mauno; Jousimies-Somer, Hannele

2001-01-01

Recent advancements in chemotaxonomic and molecular biology-based identification methods have clarified the taxonomy of the genus Actinomyces and have led to the recognition of several new Actinomyces and related species. Actinomyces-like gram-positive rods have increasingly been isolated from various clinical specimens. Thus, an easily accessible scheme for reliable differentiation at the species level is needed in clinical and oral microbiology laboratories, where bacterial identification is mainly based on conventional biochemical methods. In the present study we designed a two-step protocol that consists of a flowchart that describes rapid, cost-efficient tests for preliminary identification of Actinomyces and closely related species and an updated more comprehensive scheme that also uses fermentation reactions for accurate differentiation of Actinomyces and closely related species. PMID:11682514

Oral health conditions affect functional and social activities of terminally-ill cancer patients

PubMed Central

Fischer, D.J.; Epstein, J.B.; Yao, Y.; Wilkie, D.J.

2013-01-01

Purpose Oral conditions are established complications in terminally-ill cancer patients. Yet despite significant morbidity, the characteristics and impact of oral conditions in these patients are poorly documented. The study objective was to characterize oral conditions in terminally-ill cancer patients to determine the presence, severity, and the functional and social impact of these oral conditions. Methods This was an observational clinical study including terminally-ill cancer patients (2.5–3 week life expectancy). Data were obtained via the Oral Problems Scale (OPS) that measures the presence of subjective xerostomia, orofacial pain, taste change, and the functional/social impact of oral conditions and a demographic questionnaire. A standardized oral examination was used to assess objective salivary hypofunction, fungal infection, mucosal erythema, and ulceration. Regression analysis and t test investigated the associations between measures. Results Of 104 participants, most were ≥50 years of age, female, and high-school educated; 45% were African American, 43% Caucasian, and 37% married. Oral conditions frequencies were: salivary hypofunction (98%), mucosal erythema (50%), ulceration (20%), fungal infection (36%), and other oral problems (46%). Xerostomia, taste change, and orofacial pain all had significant functional impact; p<.001, p=.042 and p<.001, respectively. Orofacial pain also had a significant social impact (p<.001). Patients with oral ulcerations had significantly more orofacial pain with a social impact than patients without ulcers (p=.003). Erythema was significantly associated with fungal infection and with mucosal ulceration (p<.001). Conclusions Oral conditions significantly affect functional and social activities in terminally-ill cancer patients. Identification and management of oral conditions in these patients should therefore be an important clinical consideration. PMID:24232310

Evaluation of "shotgun" proteomics for identification of biological threat agents in complex environmental matrixes: experimental simulations.

PubMed

Verberkmoes, Nathan C; Hervey, W Judson; Shah, Manesh; Land, Miriam; Hauser, Loren; Larimer, Frank W; Van Berkel, Gary J; Goeringer, Douglas E

2005-02-01

There is currently a great need for rapid detection and positive identification of biological threat agents, as well as microbial species in general, directly from complex environmental samples. This need is most urgent in the area of homeland security, but also extends into medical, environmental, and agricultural sciences. Mass-spectrometry-based analysis is one of the leading technologies in the field with a diversity of different methodologies for biothreat detection. Over the past few years, "shotgun"proteomics has become one method of choice for the rapid analysis of complex protein mixtures by mass spectrometry. Recently, it was demonstrated that this methodology is capable of distinguishing a target species against a large database of background species from a single-component sample or dual-component mixtures with relatively the same concentration. Here, we examine the potential of shotgun proteomics to analyze a target species in a background of four contaminant species. We tested the capability of a common commercial mass-spectrometry-based shotgun proteomics platform for the detection of the target species (Escherichia coli) at four different concentrations and four different time points of analysis. We also tested the effect of database size on positive identification of the four microbes used in this study by testing a small (13-species) database and a large (261-species) database. The results clearly indicated that this technology could easily identify the target species at 20% in the background mixture at a 60, 120, 180, or 240 min analysis time with the small database. The results also indicated that the target species could easily be identified at 20% or 6% but could not be identified at 0.6% or 0.06% in either a 240 min analysis or a 30 h analysis with the small database. The effects of the large database were severe on the target species where detection above the background at any concentration used in this study was impossible, though the three other microbes used in this study were clearly identified above the background when analyzed with the large database. This study points to the potential application of this technology for biological threat agent detection but highlights many areas of needed research before the technology will be useful in real world samples.

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.

A target and nontarget strategy for identification or characterization of the chemical ingredients in Chinese herb preparation Shuang-Huang-Lian oral liquid by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry.

PubMed

Zhang, Feng-Xiang; Li, Min; Yao, Zhi-Hong; Li, Chang; Qiao, Li-Rui; Shen, Xiu-Yu; Yu, Kate; Dai, Yi; Yao, Xin-Sheng

2018-03-01

A target and nontarget strategy based on in-house chemical components library was developed for rapid and comprehensive analysis of complicated components from traditional Chinese medicine preparation Shuang-Huang-Lian oral liquid. The sample was analyzed by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry using generic acquisition parameters. Automated detection and data filtering were performed on the UNIFI™ software and the detected peaks were evaluated against an in-house library. As a result, a total of 170 chemical components (110 target compounds and 60 nontarget ones) were identified or tentatively characterized, including 54 flavonoids, 30 phenylethanoid glycosides, 16 iridoid glycosides, 14 lignans, 32 organic acids, 19 triterpenoid saponins and five other types of compounds. Among them, 44 compounds were further confirmed by comparison with reference standards. It was demonstrated that this systematical approach could be successfully applied for rapid identification of multiple compounds in traditional Chinese medicine and its preparations. Furthermore, this work established the foundation for the further investigation on the metabolic fates of multiple ingredients in Shuang-Huang-Lian oral liquid. Copyright © 2017 John Wiley & Sons, Ltd.

Comparison of duplex PCR and phenotypic analysis in differentiating Candida dubliniensis from Candida albicans from oral samples.

PubMed

Sampath, Asanga; Weerasekera, Manjula; Dilhari, Ayomi; Gunasekara, Chinthika; Bulugahapitiya, Uditha; Fernando, Neluka; Samaranayake, Lakshman

2017-12-01

Candida dubliniensis shares a wide range of phenotypic characteristics with Candida albicans including a common trait called germ tube positivity. Hence, laboratory differentiation of these two species is cumbersome. Duplex PCR analyses for C. albicans and C. dubliniensis was performed directly on DNA extracted from a total of 122 germ tube positive isolates derived from 100 concentrated oral rinse samples from a random cohort of diabetics attending a clinic in Sri Lanka. These results were confirmed by DNA sequencing of internal transcribed spacer (ITS) region of rDNA of the yeasts. Performance efficacy of duplex PCR was then compared with phenotypic identification using a standard battery of phenotypic tests. Of the 122 germ tube positive isolates three were identified by duplex PCR as C. dubliniensis and the remainder as C. albicans. On the contrary, when the standard phenotypic tests, sugar assimilation and chlamydospore formation, were used to differentiate the two species 13 germ tube positive isolates were erroneously identified as C. dubliniensis. Duplex PCR was found to be rapid, sensitive and more specific than phenotypic identification methods in discriminating C. dubliniensis from C. albicans. This is also the first report on the oral carriage of C. dubliniensis in a Sri Lankan population.

Cutaneous fungal microbiome: Malassezia yeasts in seborrheic dermatitis scalp in a randomized, comparative and therapeutic trial.

PubMed

Kamamoto, C S L; Nishikaku, A S; Gompertz, O F; Melo, A S; Hassun, K M; Bagatin, E

2017-01-01

Malassezia spp in skin microbiome scalp has been implicated in seborrheic dermatitis pathogenesis. Thus, treatment based in antifungal combined to topical keratolitic agents have been indicated as well as oral isotretinoin as it reduces the sebum production, glandular's size and possesses anti-inflammatory properties. This randomized, comparative and therapeutic trial aimed toper form the genotypic identification of Malassezia species before and after low-dose oral isotretinoin or topical antifungal treatments for moderate to severe seborrhea and/or seborrheic dermatitis on scalp. Scales and sebum of the scalp were seeded in the middle of modified Dixon and incubated at 32°C. For genotypic identification polymerase chain reaction primers for the ITS and D1/D2 ribossomal DNA were used and followed by samples sequencing. The procedure was conducted before and after therapeutic and randomized intervention for moderate to severe seborrhea/seborrheic dermatitis on the scalp, including oral isotretinoin, 10 mg, every other day and anti-seborrheic shampoo (piroctone olamine), over six months. The M. globosa and M. restricta were the most frequent species isolated on the scalp before and after both treatments. Other non- Malassezia species were also identified. The Malassezia spp. were maintained in the scalp after both treatments that were equally effective for the control of seborrhea/seborrheic dermatitis clinical signs.

Diffuse reflectance spectroscopy for optical nerve identification. Preliminary ex vivo results for feedback controlled oral and maxillofacial laser surgery

NASA Astrophysics Data System (ADS)

Stelzle, Florian; Zam, Azhar; Adler, Werner; Douplik, Alexandre; Tangermann-Gerk, Katja; Nkenke, Emeka; Neukam, Friedrich Wilhelm; Schmidt, Michael

Objective: Laser surgery has many advantages. However, due to a lack of haptic feedback it is accompanied by the risk of iatrogenic nerve damage. The aim of this study was to evaluate the possibilities of optical nerve identification by diffuse reflectance spectroscopy to set the base for a feedback control system to enhance nerve preservation in oral and maxillofacial laser surgery. Materials and Methods: Diffuse reflectance spectra of nerve tissue, skin, mucosa, fat tissue, muscle, cartilage and bone (15120 spectra) of ex vivo pig heads were acquired in the wavelength range of 350-650 nm. Tissue differentiation was performed by principal components analysis (PCA) followed by linear discriminant analysis (LDA). Specificity and sensitivity were calculated by receiver operating characteristic (ROC) analysis and the area under curve (AUC). Results: Nerve tissue could correctly be identified and differed from skin, mucosa, fat tissue, muscle, cartilage and bone in more than 90% of the cases (AUC results) with a specificity of over 78% and a sensitivity of more than 86%. Conclusion: Nerve tissue can be identified by diffuse reflectance spectroscopy with high precision and reliability. The results may set the base for a feedback system to prevent iatrogenic nerve damage performing oral and maxillofacial laser surgery.

Method of degrading pollutants in soil

DOEpatents

Hazen, T.C.; Lopez-De-Victoria, G.

1994-07-05

Disclosed are a method and system for enhancing the motility of microorganisms. This is accomplished by placing an effective amount of chlorinated hydrocarbons, preferably chlorinated alkenes, and most preferably trichloroethylene in spaced relation to the microbes so that the surprisingly strong, monomodal, chemotactic response of the chlorinated hydrocarbon on subsurface microbes can draw the microbes away from or towards and into a substance, as desired. In remediation of groundwater pollution, for example, TCE can be injected into the plume to increase the population of microbes at the plume whereby the plume can be more quickly degraded. A TCE-degrading microbe, such as Welchia alkenophilia, can be used to degrade the TCE following the degradation of the original pollutant. 5 figures.

Scoping the potential use of microbial inoculants in cotton production systems

NASA Astrophysics Data System (ADS)

Pereg, Lily

2014-05-01

There is a growing body of research showing that beneficial microbes can enhance soil productivity and yield in cropping systems. To appreciate the potential uses of beneficial microbes for increasing yield, it is necessary to understand how the microbes promote the growth of plants in terms of biofertilization and disease control, what are the mechanisms employed, what are the challenges for the isolation and use of plant growth promoting microbes, as well as what might hinder their successful application. This presentation critically reviews information on microbial inoculants, giving ample of examples of identified plant growth promoting microbes (including commercial products) and how they may benefit the plant, with particular focus on cotton and cotton related systems.

Microbially Induced Calcite Precipitation Employing Environmental Isolates

PubMed Central

Kim, Gunjo; Youn, Heejung

2016-01-01

In this study, five microbes were employed to precipitate calcite in cohesionless soils. Four microbes were selected from calcite-precipitating microbes isolated from calcareous sand and limestone cave soils, with Sporosarcina pasteurii ATCC 11859 (standard strain) used as a control. Urease activities of the four microbes were higher than that of S. pasteurii. The microbes and urea–CaCl2 medium were injected at least four times into cohesionless soils of two different relative densities (60% and 80%), and the amount of calcite precipitation was measured. It was found that the relative density of cohesionless soils significantly affects the amount of calcite precipitation and that there is a weak correlation between urease activity and calcite precipitation. PMID:28773600

Microbially Induced Calcite Precipitation Employing Environmental Isolates.

PubMed

Kim, Gunjo; Youn, Heejung

2016-06-15

In this study, five microbes were employed to precipitate calcite in cohesionless soils. Four microbes were selected from calcite-precipitating microbes isolated from calcareous sand and limestone cave soils, with Sporosarcina pasteurii ATCC 11859 (standard strain) used as a control. Urease activities of the four microbes were higher than that of S. pasteurii . The microbes and urea-CaCl₂ medium were injected at least four times into cohesionless soils of two different relative densities (60% and 80%), and the amount of calcite precipitation was measured. It was found that the relative density of cohesionless soils significantly affects the amount of calcite precipitation and that there is a weak correlation between urease activity and calcite precipitation.

Electron shuttles in biotechnology.

PubMed

Watanabe, Kazuya; Manefield, Mike; Lee, Matthew; Kouzuma, Atsushi

2009-12-01

Electron-shuttling compounds (electron shuttles [ESs], or redox mediators) are essential components in intracellular electron transfer, while microbes also utilize self-produced and naturally present ESs for extracellular electron transfer. These compounds assist in microbial energy metabolism by facilitating electron transfer between microbes, from electron-donating substances to microbes, and/or from microbes to electron-accepting substances. Artificially supplemented ESs can create new routes of electron flow in the microbial energy metabolism, thereby opening up new possibilities for the application of microbes to biotechnology processes. Typical examples of such processes include halogenated-organics bioremediation, azo-dye decolorization, and microbial fuel cells. Herein we suggest that ESs can be applied widely to create new microbial biotechnology processes.

Bacillus Classification Based on Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry-Effects of Culture Conditions.

PubMed

Shu, Lin-Jie; Yang, Yu-Liang

2017-11-14

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a reliable and rapid technique applied widely in the identification and classification of microbes. MALDI-TOF MS has been used to identify many endospore-forming Bacillus species; however, endospores affect the identification accuracy when using MALDI-TOF MS because they change the protein composition of samples. Since culture conditions directly influence endospore formation and Bacillus growth, in this study we clarified how culture conditions influence the classification of Bacillus species by using MALDI-TOF MS. We analyzed members of the Bacillus subtilis group and Bacillus cereus group using different incubation periods, temperatures and media. Incubation period was found to affect mass spectra due to endospores which were observed mixing with vegetative cells after 24 hours. Culture temperature also resulted in different mass spectra profiles depending on the temperature best suited growth and sporulation. Conversely, the four common media for Bacillus incubation, Luria-Bertani agar, nutrient agar, plate count agar and brain-heart infusion agar did not result in any significant differences in mass spectra profiles. Profiles in the range m/z 1000-3000 were found to provide additional data to the standard ribosomal peptide/protein region m/z 3000-15000 profiles to enable easier differentiation of some highly similar species and the identification of new strains under fresh culture conditions. In summary, control of culture conditions is vital for Bacillus identification and classification by MALDI-TOF MS.

Rapid label-free identification of Klebsiella pneumoniae antibiotic resistant strains by the drop-coating deposition surface-enhanced Raman scattering method

NASA Astrophysics Data System (ADS)

Cheong, Youjin; Kim, Young Jin; Kang, Heeyoon; Choi, Samjin; Lee, Hee Joo

2017-08-01

Although many methodologies have been developed to identify unknown bacteria, bacterial identification in clinical microbiology remains a complex and time-consuming procedure. To address this problem, we developed a label-free method for rapidly identifying clinically relevant multilocus sequencing typing-verified quinolone-resistant Klebsiella pneumoniae strains. We also applied the method to identify three strains from colony samples, ATCC70063 (control), ST11 and ST15; these are the prevalent quinolone-resistant K. pneumoniae strains in East Asia. The colonies were identified using a drop-coating deposition surface-enhanced Raman scattering (DCD-SERS) procedure coupled with a multivariate statistical method. Our workflow exhibited an enhancement factor of 11.3 × 106 to Raman intensities, high reproducibility (relative standard deviation of 7.4%), and a sensitive limit of detection (100 pM rhodamine 6G), with a correlation coefficient of 0.98. All quinolone-resistant K. pneumoniae strains showed similar spectral Raman shifts (high correlations) regardless of bacterial type, as well as different Raman vibrational modes compared to Escherichia coli strains. Our proposed DCD-SERS procedure coupled with the multivariate statistics-based identification method achieved excellent performance in discriminating similar microbes from one another and also in subtyping of K. pneumoniae strains. Therefore, our label-free DCD-SERS procedure coupled with the computational decision supporting method is a potentially useful method for the rapid identification of clinically relevant K. pneumoniae strains.

Risk factors associated with deforming oral habits in children aged 5 to 11: a case-control study.

PubMed

Reyes Romagosa, Daniel Enrique; Paneque Gamboa, María Rosa; Almeida Muñiz, Yamilka; Quesada Oliva, Leticia María; Escalona Oliva, Damiana; Torres Naranjo, Sonia

2014-03-31

Dental and maxillofacial anomalies have multiple and complex causes. Most frequent among these are poor oral habits. A large number of children present with oral malocclusions, most of which are caused by deforming oral habits. It is important to learn about risk factors for this condition in order to institute preventive measures, early detection and treatment, and identification of low- and high-risk groups. To identify risk factors associated with deforming oral habits, which, if maintained over time, are responsible for occlusion defects, speech disorders, and can affect physical and emotional child development. A case-control study of children presenting with deforming oral habits in the municipality of Manzanillo in Granma province was conducted between January and August 2013. 540 children aged 5 to 11 were included of which 180 had deforming oral habits and were asked to fill out a survey to identify specific type of habits leading to malocclusion. The case group was composed of children with deforming habits, and the remaining 360 children without poor oral habits were the control group. Each case was randomly matched to two control cases. The children mothers were also surveyed to gather supplemental information. Children with deforming oral habits were mostly female. At age 10, onychophagia was the predominant oral deforming habit. Risk factors detected for these habits were sociobiological maternal and child variables such as low and high birth weight, maternal breastfeeding inexperience, and discord in the family. The study identified likely risk factors associated with deforming oral habits. These are discord in the family, birth weight, and lack of breastfeeding experience.

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile.

PubMed

Kumar, Ranjit; Maynard, Craig L; Eipers, Peter; Goldsmith, Kelly T; Ptacek, Travis; Grubbs, J Aaron; Dixon, Paula; Howard, Donna; Crossman, David K; Crowley, Michael R; Benjamin, William H; Lefkowitz, Elliot J; Weaver, Casey T; Rodriguez, J Martin; Morrow, Casey D

2016-01-13

Fecal microbiota transplants (FMT) are an effective treatment for patients with gut microbe dysbiosis suffering from recurrent C. difficile infections. To further understand how FMT reconstitutes the patient's gut commensal microbiota, we have analyzed the colonization potential of the donor, recipient and recipient post transplant fecal samples using transplantation in gnotobiotic mice. A total of nine samples from three human donors, recipient's pre and post FMT were transplanted into gnotobiotic mice. Microbiome analysis of three donor fecal samples revealed the presence of a high relative abundance of commensal microbes from the family Bacteriodaceae and Lachnospiraceae that were almost absent in the three recipient pre FMT fecal samples (<0.01%). The microbe composition in gnotobiotic mice transplanted with the donor fecal samples was similar to the human samples. The recipient samples contained Enterobacteriaceae, Lactobacillaceae, Enterococcaceae in relative abundance of 43, 11, 8%, respectively. However, gnotobiotic mice transplanted with the recipient fecal samples had an average relative abundance of unclassified Clostridiales of 55%, approximately 7000 times the abundance in the recipient fecal samples prior to transplant. Microbiome analysis of fecal samples from the three patients early (2-4 weeks) after FMT revealed a microbe composition with the relative abundance of both Bacteriodaceae and Lachnospiraceae that was approximately 7% of that of the donor. In contrast, gnotobioitc mice transplanted with the fecal samples obtained from the three at early times post FMT revealed increases in the relative abundance of Bacteriodaceae and Lachnospiraceae microbe compositions to levels similar to the donor fecal samples. Furthermore, the unclassified Clostridiales in the recipient samples post FMT was reduced to an average of 10%. We have used transplantation into gnotobiotic mice to evaluate the colonization potential of microbiota in FMT patients early after transplant. The commensal microbes present at early times post FMT out competed non-commensal microbes (e.g. such as unclassified Clostridiales) for niche space. The selective advantage of these commensal microbes to occupy niches in the gastrointestinal tract helps to explain the success of FMT to reconstitute the gut microbe community of patients with recurrent C. difficile infections.

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.

Quantitative proteomic analysis of microdissected oral epithelium for cancer biomarker discovery.

PubMed

Xiao, Hua; Langerman, Alexander; Zhang, Yan; Khalid, Omar; Hu, Shen; Cao, Cheng-Xi; Lingen, Mark W; Wong, David T W

2015-11-01

Specific biomarkers are urgently needed for the detection and progression of oral cancer. The objective of this study was to discover cancer biomarkers from oral epithelium through utilizing high throughput quantitative proteomics approaches. Morphologically malignant, epithelial dysplasia, and adjacent normal epithelial tissues were laser capture microdissected (LCM) from 19 patients and used for proteomics analysis. Total proteins from each group were extracted, digested and then labelled with corresponding isobaric tags for relative and absolute quantitation (iTRAQ). Labelled peptides from each sample were combined and analyzed by liquid chromatography-mass spectrometry (LC-MS/MS) for protein identification and quantification. In total, 500 proteins were identified and 425 of them were quantified. When compared with adjacent normal oral epithelium, 17 and 15 proteins were consistently up-regulated or down-regulated in malignant and epithelial dysplasia, respectively. Half of these candidate biomarkers were discovered for oral cancer for the first time. Cornulin was initially confirmed in tissue protein extracts and was further validated in tissue microarray. Its presence in the saliva of oral cancer patients was also explored. Myoglobin and S100A8 were pre-validated by tissue microarray. These data demonstrated that the proteomic biomarkers discovered through this strategy are potential targets for oral cancer detection and salivary diagnostics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Medication Safety of Five Oral Chemotherapies: A Proactive Risk Assessment

PubMed Central

Weingart, Saul N.; Spencer, Justin; Buia, Stephanie; Duncombe, Deborah; Singh, Prabhjyot; Gadkari, Mrinalini; Connor, Maureen

2011-01-01

Purpose: Oral chemotherapies represent an emerging risk area in ambulatory oncology practice. To examine the hazards associated with five oral chemotherapies, we performed a proactive risk assessment. Methods: We convened interdisciplinary teams and conducted failure mode and effects analyses (FMEAs) for five oral chemotherapy agents: capecitabine, imatinib, temozolomide, 6-mercaptopurine, and an investigational agent. This involved the creation of process maps for each medication, identification of failure modes, selection of high-risk failure modes, and development of recommendations to mitigate these risks. We analyzed the number of steps and types of failure modes and compared this information across the study drugs. Results: Key vulnerabilities include patient education about drug handling and adverse effects, prescription writing, patient self-administration and medication adherence, and failure to monitor and manage toxicities. Many of these failure modes were common across the five oral chemotherapies, suggesting the presence of common targets for improvement. Streamlining the FMEA itself may promote the dissemination of this method. Conclusion: Each stage of the medication process poses risks to the safe use of oral chemotherapies. FMEAs may identify opportunities to improve medication safety and reduce the risk of patient harm. PMID:21532801

KF-finder: identification of key factors from host-microbial networks in cervical cancer.

PubMed

Hu, Jialu; Gao, Yiqun; Zheng, Yan; Shang, Xuequn

2018-04-24

The human body is colonized by a vast number of microbes. Microbiota can benefit many normal life processes, but can also cause many diseases by interfering the regular metabolism and immune system. Recent studies have demonstrated that the microbial community is closely associated with various types of cell carcinoma. The search for key factors, which also refer to cancer causing agents, can provide an important clue in understanding the regulatory mechanism of microbiota in uterine cervix cancer. In this paper, we investigated microbiota composition and gene expression data for 58 squamous and adenosquamous cell carcinoma. A host-microbial covariance network was constructed based on the 16s rRNA and gene expression data of the samples, which consists of 259 abundant microbes and 738 differentially expressed genes (DEGs). To search for risk factors from host-microbial networks, the method of bi-partite betweenness centrality (BpBC) was used to measure the risk of a given node to a certain biological process in hosts. A web-based tool KF-finder was developed, which can efficiently query and visualize the knowledge of microbiota and differentially expressed genes (DEGs) in the network. Our results suggest that prevotellaceade, tissierellaceae and fusobacteriaceae are the most abundant microbes in cervical carcinoma, and the microbial community in cervical cancer is less diverse than that of any other boy sites in health. A set of key risk factors anaerococcus, hydrogenophilaceae, eubacterium, PSMB10, KCNIP1 and KRT13 have been identified, which are thought to be involved in the regulation of viral response, cell cycle and epithelial cell differentiation in cervical cancer. It can be concluded that permanent changes of microbiota composition could be a major force for chromosomal instability, which subsequently enables the effect of key risk factors in cancer. All our results described in this paper can be freely accessed from our website at http://www.nwpu-bioinformatics.com/KF-finder/ .

A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases.

PubMed

Chen, Xing; Huang, Yu-An; You, Zhu-Hong; Yan, Gui-Ying; Wang, Xue-Song

2017-03-01

Accumulating clinical observations have indicated that microbes living in the human body are closely associated with a wide range of human noninfectious diseases, which provides promising insights into the complex disease mechanism understanding. Predicting microbe-disease associations could not only boost human disease diagnostic and prognostic, but also improve the new drug development. However, little efforts have been attempted to understand and predict human microbe-disease associations on a large scale until now. In this work, we constructed a microbe-human disease association network and further developed a novel computational model of KATZ measure for Human Microbe-Disease Association prediction (KATZHMDA) based on the assumption that functionally similar microbes tend to have similar interaction and non-interaction patterns with noninfectious diseases, and vice versa. To our knowledge, KATZHMDA is the first tool for microbe-disease association prediction. The reliable prediction performance could be attributed to the use of KATZ measurement, and the introduction of Gaussian interaction profile kernel similarity for microbes and diseases. LOOCV and k-fold cross validation were implemented to evaluate the effectiveness of this novel computational model based on known microbe-disease associations obtained from HMDAD database. As a result, KATZHMDA achieved reliable performance with average AUCs of 0.8130 ± 0.0054, 0.8301 ± 0.0033 and 0.8382 in 2-fold and 5-fold cross validation and LOOCV framework, respectively. It is anticipated that KATZHMDA could be used to obtain more novel microbes associated with important noninfectious human diseases and therefore benefit drug discovery and human medical improvement. Matlab codes and dataset explored in this work are available at http://dwz.cn/4oX5mS . xingchen@amss.ac.cn or zhuhongyou@gmail.com or wangxuesongcumt@163.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Prediction of microbe-disease association from the integration of neighbor and graph with collaborative recommendation model.

PubMed

Huang, Yu-An; You, Zhu-Hong; Chen, Xing; Huang, Zhi-An; Zhang, Shanwen; Yan, Gui-Ying

2017-10-16

Accumulating clinical researches have shown that specific microbes with abnormal levels are closely associated with the development of various human diseases. Knowledge of microbe-disease associations can provide valuable insights for complex disease mechanism understanding as well as the prevention, diagnosis and treatment of various diseases. However, little effort has been made to predict microbial candidates for human complex diseases on a large scale. In this work, we developed a new computational model for predicting microbe-disease associations by combining two single recommendation methods. Based on the assumption that functionally similar microbes tend to get involved in the mechanism of similar disease, we adopted neighbor-based collaborative filtering and a graph-based scoring method to compute association possibility of microbe-disease pairs. The promising prediction performance could be attributed to the use of hybrid approach based on two single recommendation methods as well as the introduction of Gaussian kernel-based similarity and symptom-based disease similarity. To evaluate the performance of the proposed model, we implemented leave-one-out and fivefold cross validations on the HMDAD database, which is recently built as the first database collecting experimentally-confirmed microbe-disease associations. As a result, NGRHMDA achieved reliable results with AUCs of 0.9023 ± 0.0031 and 0.9111 in the validation frameworks of fivefold CV and LOOCV. In addition, 78.2% microbe samples and 66.7% disease samples are found to be consistent with the basic assumption of our work that microbes tend to get involved in the similar disease clusters, and vice versa. Compared with other methods, the prediction results yielded by NGRHMDA demonstrate its effective prediction performance for microbe-disease associations. It is anticipated that NGRHMDA can be used as a useful tool to search the most potential microbial candidates for various diseases, and therefore boosts the medical knowledge and drug development. The codes and dataset of our work can be downloaded from https://github.com/yahuang1991/NGRHMDA .

Multimodal Alexia: Neuropsychological Mechanisms and Implications for Treatment

PubMed Central

Kim, Esther S.; Rapcsak, Steven Z.; Andersen, Sarah; Beeson, Pélagie M.

2011-01-01

Letter-by-letter (LBL) reading is the phenomenon whereby individuals with acquired alexia decode words by sequential identification of component letters. In cases where letter recognition or letter naming is impaired, however, a LBL reading approach is obviated, resulting in a nearly complete inability to read, or global alexia. In some such cases, a treatment strategy wherein letter tracing is used to provide tactile and/or kinesthetic input has resulted in improved letter identification. In this study, a kinesthetic treatment approach was implemented with an individual who presented with severe alexia in the context of relatively preserved recognition of orally spelled words, and mildly impaired oral/written spelling. Eight weeks of kinesthetic treatment resulted in improved letter identification accuracy and oral reading of trained words; however, the participant remained unable to successfully decode untrained words. Further testing revealed that, in addition to the visual-verbal disconnection that resulted in impaired word reading and letter naming, her limited ability to derive benefit from the kinesthetic strategy was attributable to a disconnection that prevented access to letter names from kinesthetic input. We propose that this kinesthetic-verbal disconnection resulted from damage to the left parietal lobe and underlying white matter, a neuroanatomical feature that is not typically observed in patients with global alexia or classic LBL reading. This unfortunate combination of visual-verbal and kinesthetic-verbal disconnections demonstrated in this individual resulted in a persistent multimodal alexia syndrome that was resistant to behavioral treatment. To our knowledge, this is the first case in which the nature of this form of multimodal alexia has been fully characterized, and our findings provide guidance regarding the requisite cognitive skills and lesion profiles that are likely to be associated with a positive response to tactile/kinesthetic treatment. PMID:21952194

Multimodal alexia: neuropsychological mechanisms and implications for treatment.

PubMed

Kim, Esther S; Rapcsak, Steven Z; Andersen, Sarah; Beeson, Pélagie M

2011-11-01

Letter-by-letter (LBL) reading is the phenomenon whereby individuals with acquired alexia decode words by sequential identification of component letters. In cases where letter recognition or letter naming is impaired, however, a LBL reading approach is obviated, resulting in a nearly complete inability to read, or global alexia. In some such cases, a treatment strategy wherein letter tracing is used to provide tactile and/or kinesthetic input has resulted in improved letter identification. In this study, a kinesthetic treatment approach was implemented with an individual who presented with severe alexia in the context of relatively preserved recognition of orally spelled words, and mildly impaired oral/written spelling. Eight weeks of kinesthetic treatment resulted in improved letter identification accuracy and oral reading of trained words; however, the participant remained unable to successfully decode untrained words. Further testing revealed that, in addition to the visual-verbal disconnection that resulted in impaired word reading and letter naming, her limited ability to derive benefit from the kinesthetic strategy was attributable to a disconnection that prevented access to letter names from kinesthetic input. We propose that this kinesthetic-verbal disconnection resulted from damage to the left parietal lobe and underlying white matter, a neuroanatomical feature that is not typically observed in patients with global alexia or classic LBL reading. This unfortunate combination of visual-verbal and kinesthetic-verbal disconnections demonstrated in this individual resulted in a persistent multimodal alexia syndrome that was resistant to behavioral treatment. To our knowledge, this is the first case in which the nature of this form of multimodal alexia has been fully characterized, and our findings provide guidance regarding the requisite cognitive skills and lesion profiles that are likely to be associated with a positive response to tactile/kinesthetic treatment. Copyright © 2011 Elsevier Ltd. All rights reserved.

Optimizing Oral Bioavailability in Drug Discovery: An Overview of Design and Testing Strategies and Formulation Options.

PubMed

Aungst, Bruce J

2017-04-01

For discovery teams working toward new, orally administered therapeutic agents, one requirement is to attain adequate systemic exposure after oral dosing, which is best accomplished when oral bioavailability is optimized. This report summarizes the bioavailability challenges currently faced in drug discovery, and the design and testing methods and strategies currently utilized to address the challenges. Profiling of discovery compounds usually includes separate assessments of solubility, permeability, and susceptibility to first-pass metabolism, which are the 3 most likely contributors to incomplete oral bioavailability. An initial assessment of absorption potential may be made computationally, and high throughput in vitro assays are typically performed to prioritize compounds for in vivo studies. The initial pharmacokinetic study is a critical decision point in compound evaluation, and the importance of the effect the dosing vehicle or formulation can have on oral bioavailability, especially for poorly water soluble compounds, is emphasized. Dosing vehicles and bioavailability-enabling formulations that can be used for discovery and preclinical studies are described. Optimizing oral bioavailability within a chemical series or for a lead compound requires identification of the barrier limiting bioavailability, and methods used for this purpose are outlined. Finally, a few key guidelines are offered for consideration when facing the challenges of optimizing oral bioavailability in drug discovery. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Oral health disparities and the workforce: a framework to guide innovation.

PubMed

Hilton, Irene V; Lester, Arlene M

2010-06-01

Oral health disparities currently exist in the United States, and workforce innovations have been proposed as one strategy to address these disparities. A framework is needed to logically assess the possible role of workforce as a contributor to and to analyze workforce strategies addressing the issue of oral health disparities. Using an existing framework, A Strategic Framework for Improving Racial/Ethnic Minority Health and Eliminating Racial/Ethnic Health Disparities, workforce was sequentially applied across individual, environmental/community, and system levels to identify long-term problems, contributing factors, strategies/innovation, measurable outcomes/impacts, and long-term goals. Examples of current workforce innovations were applied to the framework. Contributing factors to oral health disparities included lack of racial/ethnic diversity of the workforce, lack of appropriate training, provider distribution, and a nonuser-centered system. The framework was applied to selected workforce innovation models delineating the potential impact on contributing factors across the individual, environmental/community, and system levels. The framework helps to define expected outcomes from workforce models that would contribute to the goal of reducing oral health disparities and examine impacts across multiple levels. However, the contributing factors to oral health disparities cannot be addressed by workforce innovation alone. The Strategic Framework is a logical approach to guide workforce innovation, solutions, and identification of other aspects of the oral healthcare delivery system that need innovation in order to reduce oral health disparities.

Human trafficking: Role of oral health care providers.

PubMed

Nuzzolese, E

2014-11-30

Trafficking in human beings is a modern form of slavery and is a well-known phenomenon throughout the European Union and beyond. After drug dealing and the weapons industry, human trafficking is the second largest criminal activity in the world today and it is a growing crime. The aim of governmental and non-governmental agencies, which are either directly or indirectly involved in combating trafficking in human beings, is the identification and referral of victims of trafficking and also to encourage self-referrals. Identification is the most important step to provide protection and assistance to victims of trafficking. Victims often have a variety of physical and mental health needs, including psychological trauma, injuries from violence, head and neck trauma, sexually transmitted infections and other gynaecological problems, dental/oral problems and have poor nutrition. The author's experience in the field of community dentistry in presented within. Volunteer dental services are offered to non-European Union patients held in a centre for asylum seekers in Bari (Italy). Dental professionals can, in fact, contribute to the identification, assistance and protection of trafficked persons, as well as offering forensic services to assist the police investigation in order to identify crimes and find the criminal organizations behind them. As for domestic violence and child abuse cases, there are ethical concerns involved in the identification and protection of the trafficked persons, as well as the need for interdisciplinary work and awareness. Adequate training in behavioural science and intercultural learning is paramount in order to avoid misunderstandings and increase sensitivity.

Butyrate-producing bacteria, including mucin degraders, from the swine intestinal tract

USDA-ARS?s Scientific Manuscript database

Butyrate-producing microbes promote gastrointestinal health in the human gut, and similar benefits are likely derived from butyrate-producing microbes in other animal hosts. Consequently, there is considerable potential for butyrate-producing microbes to be utilized in health-promoting application...

Antibiotic Susceptibilities of Bacteria Isolated within the Oral Flora of Florida Blacktip Sharks: Guidance for Empiric Antibiotic Therapy

PubMed Central

Unger, Nathan R.; Ritter, Erich; Borrego, Robert; Goodman, Jay; Osiyemi, Olayemi O.

2014-01-01

Sharks possess a variety of pathogenic bacteria in their oral cavity that may potentially be transferred into humans during a bite. The aim of the presented study focused on the identification of the bacteria present in the mouths of live blacktip sharks, Carcharhinus limbatus, and the extent that these bacteria possess multi-drug resistance. Swabs were taken from the oral cavity of nineteen live blacktip sharks, which were subsequently released. The average fork length was 146 cm (±11), suggesting the blacktip sharks were mature adults at least 8 years old. All swabs underwent standard microbiological work-up with identification of organisms and reporting of antibiotic susceptibilities using an automated microbiology system. The oral samples revealed an average of 2.72 (±1.4) bacterial isolates per shark. Gram-negative bacteria, making up 61% of all bacterial isolates, were significantly (p<0.001) more common than gram-positive bacteria (39%). The most common organisms were Vibrio spp. (28%), various coagulase-negative Staphylococcus spp. (16%), and Pasteurella spp. (12%). The overall resistance rate was 12% for all antibiotics tested with nearly 43% of bacteria resistant to at least one antibiotic. Multi-drug resistance was seen in 4% of bacteria. No association between shark gender or fork length with bacterial density or antibiotic resistance was observed. Antibiotics with the highest overall susceptibility rates included fluoroquinolones, 3rd generation cephalosporins and sulfamethoxazole/trimethoprim. Recommended empiric antimicrobial therapy for adult blacktip shark bites should encompass either a fluoroquinolone or combination of a 3rd generation cephalosporin plus doxycycline. PMID:25110948

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.

Oral Health Care in the Future: Expansion of the Scope of Dental Practice to Improve Health.

PubMed

Lamster, Ira B; Myers-Wright, Noreen

2017-09-01

The health care environment in the U.S. is changing. The population is aging, the prevalence of non-communicable diseases (NCDs) is increasing, edentulism is decreasing, and periodontal infection/inflammation has been identified as a risk factor for NCDs. These trends offer an opportunity for oral health care providers to broaden the scope of traditional dental practice, specifically becoming more involved in the management of the general health of patients. This new practice paradigm will promote a closer integration with the larger health care system. This change is based on the realization that a healthy mouth is essential for a healthy life, including proper mastication, communication, esthetics, and comfort. Two types of primary care are proposed: screenings for medical conditions that are directly affected by oral disease (and may modify the provision of dental care), and a broader emphasis on prevention that focuses on lifestyle behaviors. Included in the former category are screenings for NCDs (e.g., the risk of cardiovascular disease and identification of patients with undiagnosed dysglycemia or poorly managed diabetes mellitus), as well as identification of infectious diseases, such as HIV or hepatitis C. Reducing the risk of disease can be accomplished by an emphasis on smoking cessation and dietary intake and the prevention of obesity. These activities will promote interprofessional health care education and practice. While change is always challenging, this new practice paradigm could improve both oral health and health outcomes of patients seen in the dental office. This article was written as part of the project "Advancing Dental Education in the 21 st Century."

Molecular identification of bacteria associated with canine periodontal disease.

PubMed

Riggio, Marcello P; Lennon, Alan; Taylor, David J; Bennett, David

2011-06-02

Periodontal disease is one of the most common diseases of adult dogs, with up to 80% of animals affected. The aetiology of the disease is poorly studied, although bacteria are known to play a major role. The purpose of this study was to identify the bacteria associated with canine gingivitis and periodontitis and to compare this with the normal oral flora. Swabs were obtained from the gingival margin of three dogs with gingivitis and three orally healthy controls, and subgingival plaque was collected from three dogs with periodontitis. Samples were subjected to routine bacterial culture. The prevalent species identified in the normal, gingivitis and periodontitis groups were uncultured bacterium (12.5% of isolates), Bacteroides heparinolyticus/Pasteurella dagmatis (10.0%) and Actinomyces canis (19.4%), respectively. Bacteria were also identified using culture-independent methods (16S rRNA gene sequencing) and the predominant species identified were Pseudomonas sp. (30.9% of clones analysed), Porphyromonas cangingivalis (16.1%) and Desulfomicrobium orale (12.0%) in the normal, gingivitis and periodontitis groups, respectively. Uncultured species accounted for 13.2%, 2.0% and 10.5%, and potentially novel species for 38.2%, 38.3% and 35.3%, of clones in the normal, gingivitis and periodontitis groups, respectively. This is the first study to use utilise culture-independent methods for the identification of bacteria associated with this disease. It is concluded that the canine oral flora in health and disease is highly diverse and also contains a high proportion of uncultured and, in particular, potentially novel species. Copyright © 2011 Elsevier B.V. All rights reserved.