Comparative analyses of the bacterial community of hydrothermal deposits and seafloor sediments across Okinawa Trough

NASA Astrophysics Data System (ADS)

Wang, Long; Yu, Min; Liu, Yan; Liu, Jiwen; Wu, Yonghua; Li, Li; Liu, Jihua; Wang, Min; Zhang, Xiao-Hua

2018-04-01

As an ideal place to study back-arc basins and hydrothermal eco-system, Okinawa Trough has attracted the interests of scientists for decades. However, there are still no in-depth studies targeting the bacterial community of the seafloor sediments and hydrothermal deposits in Okinawa Trough. In the present study, we reported the bacterial community of the surface deposits of a newly found hydrothermal field in the southern Okinawa Trough, and the horizontal and vertical variation of bacterial communities in the sediments of the northern Okinawa Trough. The hydrothermal deposits had a relatively high 16S rRNA gene abundance but low bacterial richness and diversity. Epsilonproteobacteria and Bacteroidetes were predominant in hydrothermal deposits whereas Deltaproteobacteria, Gammaproteobacteria and Chloroflexi were abundant across all samples. The bacterial distribution in the seafloor of Okinawa Trough was significantly correlated to the content of total nitrogen, and had consistent relationship with total carbon. Gradual changes of sulfur-oxidizing bacteria were found with the distance away from hydrothermal fields, while the hydrothermal activity did not influence the distribution of the major clades of sulfate-reducing bacteria. Higher abundance of the sulfur cycle related genes (aprA and dsrB), and lower abundance of the bacterial ammonia-oxidizing related gene (amoA) were quantified in hydrothermal deposits. In addition, the present study also compared the inter-field variation of Epsilonproteobacteria among multi-types of hydrothermal vents, revealing that the proportion and diversity of this clade were quite various.

Infectious Risk Assessment of Unsafe Handling Practices and Management of Clinical Solid Waste

PubMed Central

Hossain, Md. Sohrab; Rahman, Nik Norulaini Nik Ab; Balakrishnan, Venugopal; Puvanesuaran, Vignesh R.; Sarker, Md. Zaidul Islam; Kadir, Mohd Omar Ab

2013-01-01

The present study was undertaken to determine the bacterial agents present in various clinical solid wastes, general waste and clinical sharp waste. The waste was collected from different wards/units in a healthcare facility in Penang Island, Malaysia. The presence of bacterial agents in clinical and general waste was determined using the conventional bacteria identification methods. Several pathogenic bacteria including opportunistic bacterial agent such as Pseudomonas aeruginosa, Salmonella spp., Klebsiella pneumoniae, Serratia marcescens, Acinetobacter baumannii, Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Streptococcus pyogenes were detected in clinical solid wastes. The presence of specific pathogenic bacterial strains in clinical sharp waste was determined using 16s rDNA analysis. In this study, several nosocomial pathogenic bacteria strains of Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Lysinibacillus sphaericus, Serratia marcescens, and Staphylococcus aureus were detected in clinical sharp waste. The present study suggests that waste generated from healthcare facilities should be sterilized at the point of generation in order to eliminate nosocomial infections from the general waste or either of the clinical wastes. PMID:23435587

Bacterial Meningitis in Patients using Immunosuppressive Medication: a Population-based Prospective Nationwide Study.

PubMed

van Veen, Kiril E B; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

2017-06-01

We studied occurrence, presentation, disease course, effect of adjunctive dexamethasone, and prognosis of bacterial meningitis in patients using immunosuppressive medication. Patients were selected from our nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 1, 2006 through October 31, 2014. Eighty-seven of 1447 episodes (6 %) of bacterial meningitis occurred in patients using immunosuppressive medication, and consisted of corticosteroids in 82 %. Patients with bacterial meningitis using immunosuppressive medication were less likely to present with headache (P = 0.02) or neck stiffness (P = 0.005), as compared those not on immunosuppressive medication. In 46 % of episodes CSF leukocyte count was below 1000/mm 3 . CSF cultures revealed S. pneumoniae in 41 % and L. monocytogenes in 40 % of episodes. Outcome was unfavorable in 39 of 87 episodes (45 %) and death occurred in 22 of 87 episodes (25 %). Adjunctive dexamethasone was administered in 52 of 87 (60 %) episodes, and mortality tended to be lower in those on adjunctive dexamethasone therapy as compared to those without dexamethasone therapy (10 of 52 [19 %] vs 12 of 35 [34 %], P = 0.14). We conclude that bacterial meningitis in patients using immunosuppressive medication is likely to present with atypical clinical and laboratory features, and is often caused by atypical bacteria, mainly L. monocytogenes. Adjunctive dexamethasone is widely prescribed in these patients and was not associated with harm in this study.

Evaluation of posttraumatic recurrent bacterial meningitis in adults.

PubMed

Deveci, Özcan; Uysal, Cem; Varol, Sefer; Tekin, Recep; Bozkurt, Fatma; Bekçibaşı, Muhammed; Hoşoğlu, Salih

2015-07-01

Acute bacterial meningitis may develop as a complication after head trauma. The aim of this study was to present the demographic, clinical, microbiological and radiological characteristics of adult patients who presented with recurrent bacterial meningitis attacks after trauma. Using a retrospective approach, the medical records of patients with acute recurrent bacterial meningitis (RBM) were reviewed, and those who had a history of trauma were included into the study. RBM was diagnosed based on clinical, bacteriologic and laboratory results. Demographic characteristics, clinical course, laboratory test results including cerebrospinal fluid analysis (CSF), radiological images, and the applied treatments were evaluated. A total of two hundred and twelve patients with acute bacterial meningitis were included into the study. RBM was diagnosed in twenty-five patients (11.8%), and in 18 of these patients (8.5%), the attacks had occurred subsequent to a trauma. In the CSF cultures of four patients, S. pneumoniae growth was observed. CT cisternography indicated CSF leaks in eleven patients. Moreover, bone fractures were observed in the CT images of ten patients. Ceftriaxone therapy was prescribed to 83% of the patients. Eight patients had a history of a fall in childhood, and five were involved in traffic accidents before acute bacterial meningitis. Four of the patients developed epilepsy and one developed deafness as sequelae. Since RBM attacks are frequently observed following trauma, in patients with a history of trauma who present with meningitis, the risk of recurrence should be considered.

Intracerebral Hemorrhages in Adults with Community Associated Bacterial Meningitis in Adults: Should We Reconsider Anticoagulant Therapy?

PubMed Central

Mook-Kanamori, Barry B.; Fritz, Daan; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

2012-01-01

Objective To study the incidence, clinical presentation and outcome of intracranial hemorrhagic complications in adult patients with community associated bacterial meningitis. Methods Nationwide prospective cohort study from all hospitals in the Netherlands, from 1 March 2006, through 31 December 2010. Results Of the 860 episodes of bacterial meningitis that were included, 24 were diagnosed with intracranial hemorrhagic complications: 8 upon presentation and 16 during clinical course. Clinical presentation between patients with or without intracranial hemorrhage was similar. Causative bacteria were Streptococcus pneumoniae in 16 patients (67%), Staphylococcus aureus in 5 (21%), Pseudomonas aeruginosa and Listeria monocytogenes both in 1 patient (4%). Occurrence of intracranial hemorrhage was associated with death (63% vs. 15%, P<0.001) and unfavorable outcome (94% vs. 34%, P<0.001). The use of anticoagulants on admission was associated with a higher incidence of intracranial hemorrhages (odds ratio 5.84, 95% confidence interval 2.17–15.76). Conclusion Intracranial hemorrhage is a rare but devastating complication in patients with community-associated bacterial meningitis. Since anticoagulant therapy use is associated with increased risk for intracranial hemorrhage, physicians may consider reversing or temporarily discontinuing anticoagulation in patients with bacterial meningitis. PMID:23028898

Bacterial selection by mycospheres of Atlantic Rainforest mushrooms.

PubMed

Halsey, Joshua Andrew; de Cássia Pereira E Silva, Michele; Andreote, Fernando Dini

2016-10-01

This study focuses on the selection exerted on bacterial communities in the mycospheres of mushrooms collected in the Brazilian Atlantic Rainforest. A total of 24 paired samples (bulk soil vs. mycosphere) were assessed to investigate potential interactions between fungi and bacteria present in fungal mycospheres. Prevalent fungal families were identified as Marasmiaceae and Lepiotaceae (both Basidiomycota) based on ITS partial sequencing. We used culture-independent techniques to analyze bacterial DNA from soil and mycosphere samples. Bacterial communities in the samples were distinguished based on overall bacterial, alphaproteobacterial, and betaproteobacterial PCR-DGGE patterns, which were different in fungi belonging to different taxa. These results were confirmed by pyrosequencing the V4 region of the 16S rRNA gene (based on five bulk soil vs. mycosphere pairs), which revealed the most responsive bacterial families in the different conditions generated beneath the mushrooms, identified as Bradyrhizobiaceae, Burkholderiaceae, and Pseudomonadaceae. The bacterial families Acetobacteraceae, Chrhoniobacteraceae, Planctomycetaceae, Conexibacteraceae, and Burkholderiaceae were found in all mycosphere samples, composing the core mycosphere microbiome. Similarly, some bacterial groups identified as Koribacteriaceae, Acidobacteria (Solibacteriaceae) and an unclassified group of Acidobacteria were preferentially present in the bulk soil samples (found in all of them). In this study we depict the mycosphere effect exerted by mushrooms inhabiting the Brazilian Atlantic Rainforest, and identify the bacteria with highest response to such a specific niche, possibly indicating the role bacteria play in mushroom development and dissemination within this yet-unexplored environment.

Note: An automated image analysis method for high-throughput classification of surface-bound bacterial cell motions.

PubMed

Shen, Simon; Syal, Karan; Tao, Nongjian; Wang, Shaopeng

2015-12-01

We present a Single-Cell Motion Characterization System (SiCMoCS) to automatically extract bacterial cell morphological features from microscope images and use those features to automatically classify cell motion for rod shaped motile bacterial cells. In some imaging based studies, bacteria cells need to be attached to the surface for time-lapse observation of cellular processes such as cell membrane-protein interactions and membrane elasticity. These studies often generate large volumes of images. Extracting accurate bacterial cell morphology features from these images is critical for quantitative assessment. Using SiCMoCS, we demonstrated simultaneous and automated motion tracking and classification of hundreds of individual cells in an image sequence of several hundred frames. This is a significant improvement from traditional manual and semi-automated approaches to segmenting bacterial cells based on empirical thresholds, and a first attempt to automatically classify bacterial motion types for motile rod shaped bacterial cells, which enables rapid and quantitative analysis of various types of bacterial motion.

Mechanistic study on antibacterial action of zinc oxide nanoparticles synthesized using green route.

PubMed

Happy Agarwal; Soumya Menon; Venkat Kumar, S; Rajeshkumar, S

2018-04-25

A large array of diseases caused by bacterial pathogens and origination of multidrug resistance in their gene provokes the need of developing new vectors or novel drug molecules for effective drug delivery and thus, better treatment of disease. The nanoparticle has emerged as a novel drug molecule in last decade and has been used in various industrial fields like cosmetics, healthcare, agricultural, pharmaceuticals due to their high optical, electronic, medicinal properties. Use of nanoparticles as an antibacterial agent remain in current studies with metal nanoparticles like silver, gold, copper, iron and metal oxide nanoparticles like zinc oxide, copper oxide, titanium oxide and iron oxide nanoparticles. The high anti-bacterial activity of nanoparticles is due to their large surface area to volume ratio which allows binding of a large number of ligands on nanoparticle surface and hence, its complexation with receptors present on the bacterial surface. Green synthesis of Zinc Oxide Nanoparticle (ZnO NP) and its anti-bacterial application has been particularly discussed in the review literature. The present study highlights differential nanoparticle attachment to gram + and gram - bacterial surface and different mechanism adopted by nanoparticle for bacterial control. Pharmacokinetics and applications of ZnO NP are also discussed briefly. Copyright © 2018 Elsevier B.V. All rights reserved.

Plumage bacterial assemblages in a breeding wild passerine: relationships with ecological factors and body condition.

PubMed

Saag, Pauli; Tilgar, Vallo; Mänd, Raivo; Kilgas, Priit; Mägi, Marko

2011-05-01

Microorganisms have been shown to play an important role in shaping the life histories of animals, and it has recently been suggested that feather-degrading bacteria influence the trade-off between parental effort and self-preening behavior in birds. We studied a wild breeding population of great tits (Parus major) to explore habitat-, seasonal-, and sex-related variation in feather-degrading and free-living bacteria inhabiting the birds' yellow ventral feathers and to investigate associations with body condition. The density and species richness of bacterial assemblages was studied using flow cytometry and ribosomal intergenic spacer analysis. The density of studied bacteria declined between the nest-building period and the first brood. The number of bacterial phylotypes per bird was higher in coniferous habitat, while bacterial densities were higher in deciduous habitat. Free-living bacterial density was positively correlated with female mass; conversely, there was a negative correlation between attached bacterial density and female mass during the period of peak reproductive effort. Bacterial species richness was sex dependent, with more diverse bacterial assemblages present on males than females. Thus, this study revealed that bacterial assemblages on the feathers of breeding birds are affected both by life history and ecological factors and are related to body condition.

Acute bacterial meningitis in Iran: Systematic review and meta-analysis

PubMed Central

Riahi, Seyed Mohammad; Nasiri, Mohammad Javad; Fallah, Fatemeh; Dabiri, Hossein; Pouriran, Ramin

2017-01-01

Introduction Bacterial meningitis persists in being a substantial cause of high mortality and severe neurological morbidity, despite the advances in antimicrobial therapy. Accurate data has not been available regarding the epidemiology of bacterial meningitis particularly in developing countries, yet. Indeed, the present systematic review provides a comprehensive data analysis on the prevalence and epidemiology of bacterial meningitis in Iran. Methods We systematically reviewed articles from 1994 to 2015. The reports which contained the prevalence and etiology of acute bacterial meningitis by valid clinical and laboratory diagnosis were comprised in the present study. Results Our analysis indicated that Streptococcus pneumoniae (30% [I2 = 56% p < 0.01]), Haemophilus influenza type b (15% [I2 = 82.75% p < 0.001]), coagulase negative staphylococci (CoNS) (14% [I2 = 60.5% p < 0.06]), and Neisseria meningitidis (13% [I2 = 74.16% p < 0.001]) were the most common cause of acute bacterial meningitis among meningitis cases in Iran. Notably, high frequency rates of nosocomial meningitis pathogens were detected in the present analysis. Conclusions It was magnificently attained that the majority of cases for bacterial meningitis in Iran could be avertable by public immunization schemes and by preventive care to inhibit the broadening of hospital acquired pathogens. PMID:28170400

Ericoid Roots and Mycospheres Govern Plant-Specific Bacterial Communities in Boreal Forest Humus.

PubMed

Timonen, Sari; Sinkko, Hanna; Sun, Hui; Sietiö, Outi-Maaria; Rinta-Kanto, Johanna M; Kiheri, Heikki; Heinonsalo, Jussi

2017-05-01

In this study, the bacterial populations of roots and mycospheres of the boreal pine forest ericoid plants, heather (Calluna vulgaris), bilberry (Vaccinium myrtillus), and lingonberry (Vaccinium vitis-idaea), were studied by qPCR and next-generation sequencing (NGS). All bacterial communities of mycosphere soils differed from soils uncolonized by mycorrhizal mycelia. Colonization by mycorrhizal hyphae increased the total number of bacterial 16S ribosomal DNA (rDNA) gene copies in the humus but decreased the number of different bacterial operational taxonomic units (OTUs). Nevertheless, ericoid roots and mycospheres supported numerous OTUs not present in uncolonized humus. Bacterial communities in bilberry mycospheres were surprisingly similar to those in pine mycospheres but not to bacterial communities in heather and lingonberry mycospheres. In contrast, bacterial communities of ericoid roots were more similar to each other than to those of pine roots. In all sample types, the relative abundances of bacterial sequences belonging to Alphaproteobacteria and Acidobacteria were higher than the sequences belonging to other classes. Soil samples contained more Actinobacteria, Deltaproteobacteria, Opitutae, and Planctomycetia, whereas Armatimonadia, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia were more common to roots. All mycosphere soils and roots harbored bacteria unique to that particular habitat. Our study suggests that the habitation by ericoid plants increases the overall bacterial diversity of boreal forest soils.

Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms.

PubMed

Silva-Bedoya, Lina Marcela; Sánchez-Pinzón, María Solange; Cadavid-Restrepo, Gloria Ester; Moreno-Herrera, Claudia Ximena

2016-11-01

The operation of wastewater treatment technologies depends on a combination of physical, chemical and biological factors. Microorganisms present in wastewater treatment plants play essential roles in the degradation and removal of organic waste and xenobiotic pollutants. Several microorganisms have been used in complementary treatments to process effluents rich in fats and oils. Microbial lipases have received significant industrial attention because of their stability, broad substrate specificity, high yields, and regular supply, as well as the fact that the microorganisms producing them grow rapidly on inexpensive media. In Colombia, bacterial community studies have focused on populations of cultivable nitrifying, heterotrophic and nitrogen-fixing bacteria present in constructed wetlands. In this study, culture-dependent methods, culture-independent methods (TTGE, RISA) and enzymatic methods were used to estimate bacterial diversity, to monitor temporal and spatial changes in bacterial communities, and to screen microorganisms that presented lipolytic activity. The dominant microorganisms in the Wastewater Treatment Plant (WWTP) examined in this study belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. The enzymatic studies performed indicated that five bacterial isolates and three fungal isolates possessed the ability to degrade lipids; additionally, the Serratia, Kosakonia and Mucor genera presented lipase-mediated transesterification activity. The implications of these findings in regard to possible applications are discussed later in this paper. Our results indicate that there is a wide diversity of aerobic Gram-negative bacteria inhabiting the different sections of the WWTP, which could indicate its ecological condition, functioning and general efficiency. Copyright © 2016 Elsevier GmbH. All rights reserved.

Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China

NASA Astrophysics Data System (ADS)

Ren, Chengjie; Sun, Pingsheng; Kang, Di; Zhao, Fazhu; Feng, Yongzhong; Ren, Guangxin; Han, Xinhui; Yang, Gaihe

2016-06-01

In the present paper, we investigated the effects of afforestation on nitrogen fractions and microbial communities. A total of 24 soil samples were collected from farmland (FL) and three afforested lands, namely Robinia pseudoacacia L (RP), Caragana korshinskii Kom (CK), and abandoned land (AL), which have been arable for the past 40 years. Quantitative PCR and Illumina sequencing of 16S rRNA genes were used to analyze soil bacterial abundance, diversity, and composition. Additionally, soil nitrogen (N) stocks and fractions were estimated. The results showed that soil N stock, N fractions, and bacterial abundance and diversity increased following afforestation. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla of soil bacterial compositions. Overall, soil bacterial compositions generally changed from Actinobacteria (Acidobacteria)-dominant to Proteobacteria-dominant following afforestation. Soil N fractions, especially for dissolved organic nitrogen (DON), were significantly correlated with most bacterial groups and bacterial diversity, while potential competitive interactions between Proteobacteria (order Rhizobiales) and Cyanobacteria were suggested. In contrast, nitrate nitrogen (NO3--N) influenced soil bacterial compositions less than other N fractions. Therefore, the present study demonstrated that bacterial diversity and specific species respond to farmland-to-forest conversion and hence have the potential to affect N dynamic processes in the Loess Plateau.

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach

PubMed Central

Zapién-Campos, Román; Olmedo-Álvarez, Gabriela; Santillán, Moisés

2015-01-01

Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities. In a previous study, the binary antagonistic interactions of 78 bacterial strains, isolated from Churince, were experimentally determined. We employ these data to develop a computer algorithm to simulate growth experiments in a cellular grid representing the pond. Remarkably, in our model, the dynamics of all the simulated bacterial populations is determined solely by antagonistic interactions. Our results indicate that all bacterial strains (even those that are antagonized by many other bacteria) survive in the long term, and that the underlying mechanism is the formation of bacterial community patches. Patches corresponding to less antagonistic and highly susceptible strains are consistently isolated from the highly-antagonistic bacterial colonies by patches of neutral strains. These results concur with the observed features of the bacterial community structure previously reported. Finally, we study how our findings depend on factors like initial population size, differential population growth rates, homogeneous population death rates, and enhanced bacterial diffusion. PMID:26052318

PGE2 suppresses intestinal T cell function in thermal injury: a cause of enhanced bacterial translocation.

PubMed

Choudhry, M A; Fazal, N; Namak, S Y; Haque, F; Ravindranath, T; Sayeed, M M

2001-09-01

Increased gut bacterial translocation in burn and trauma patients has been demonstrated in a number of previous studies, however, the mechanism for such an increased gut bacterial translocation in injured patients remains poorly understood. Utilizing a rat model of burn injury, in the present study we examined the role of intestinal immune defense by analyzing the T cell functions. We investigated if intestinal T cells dysfunction contributes to bacterial translocation after burn injury. Also our study determined if burn-mediated alterations in intestinal T cell functions are related to enhanced release of PGE2. Finally, we examined whether or not burn-related alterations in intestinal T cell function are due to inappropriate activation of signaling molecule P59fyn, which is required for T cell activation and proliferation. The results presented here showed an increase in gut bacterial accumulation in mesenteric lymph nodes after thermal injury. This was accompanied by a decrease in the intestinal T cell proliferative responses. Furthermore, the treatments of burn-injured animals with PGE2 synthesis blocker (indomethacin or NS398) prevented both the decrease in intestinal T cell proliferation and enhanced bacterial translocation. Finally, our data suggested that the inhibition of intestinal T cell proliferation could result via PGE2-mediated down-regulation of the T cell activation-signaling molecule P59fyn. These findings support a role of T cell-mediated immune defense against bacterial translocation in burn injury.

The clinical presentation of acute bacterial meningitis varies with age, sex and duration of illness.

PubMed

Johansson Kostenniemi, Urban; Norman, David; Borgström, Malin; Silfverdal, Sven Arne

2015-11-01

This Swedish study reviewed differences in clinical presentation and laboratory findings of acute bacterial meningitis in children aged one month to 17 years in Västerbotten County, Sweden. A register-based study was performed for the period 1986 to 2013 using the Västerbotten County Council's patient registration and laboratory records at the Department of Laboratory Medicine at Umeå University Hospital. The medical records were reviewed to extract data and confirm the diagnosis. We found 103 cases of acute bacterial meningitis, and Haemophilus influenzae was the most common pathogen, causing 40.8% of all cases, followed by Streptococcus pneumoniae at 30.1% and Neisseria meningitidis at 9.7%. Significant differences in clinical presentation and laboratory findings were found. Younger children were more unwell than older ones and had more diffuse symptoms on admission. In addition, important sex-related differences were found that might explain the higher case fatality rates for boys than girls. For example, boys tended to have a higher disturbance in the blood-brain barrier, which is known to be a negative prognostic factor. This study showed that clinical presentation for acute bacterial meningitis varied with age and sex and, to a lesser extent, on the duration of the illness. ©2015 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

[Association of the pH change of vaginal environment in bacterial vaginosis with presence of Enterococcus faecalis in vagina].

PubMed

Jahić, Mahira; Nurkić, Mahmud; Fatusić, Zlatan

2006-01-01

Normal pH value of vagina from 3.8 to 4.2 has regulatory and protectors mechanisms of vaginal environment. The change in the pH value indicates to presence of disbalance in the ecosystem of vaginal environment. The value of pH above 4.0 is indicator of the decreased number of lactobacillus bacteria and the increased number of other microorganisms in the vaginal environment. This situation is present in the case of developing of bacterial vaginosis. One of the bacteria which is often isolated from vaginal swabs is Enterococcus faecalis. Aims of this study are to examine presence o f Enterococcus faecalis in vagina in healthy women and womenwith signs of bacterial vaginosis, the most often present signs in patients with bacterial vaginosis and isolated Enterococcus faecalis from vaginal swabs, and to determine whether the change of the pH value of vaginal environment could be indicator for bacterial vaginosis associated with Enterococcus faecalis. In this study there were included 90 patients. To all patients there were done: gynecological survey, determined pH of vaginal environment and color of vaginal secret, amino odor test, and taken vaginal swabs for microbiological examination. Enterococcus faecalis was found in the patients with pH 4.0 in 24.05 % cases, but in the patients with signs of bacterial vaginosis it was found in 52.78 %. Positive findings of Enterococcus faecalis was the most often associated with presence of all tree signs of bacterial vaginosis (pH>4.0, changed color of vaginal secret and positive amino odor test) it is in 60.78 6% cases. With two signs of bacterial vaginosis (pH>4.0, changed color of vaginal secret) Enterococcus faecalis was present in 60 % cases. The only presence of change in the pH>4.0 was associated with Enterococcus faecalis in 52.78 %. This study showed that pH change of vaginal environment was associated with Enterococcus faecalis in bacterial vaginosis in high percentage but it can not be used as the sure sign of presence of Enterococcus faecalis in vaginal discharge. Therefore it is necessary to make microbiology examination vaginal discharge.

Bacterial communities in ancient permafrost profiles of Svalbard, Arctic.

PubMed

Singh, Purnima; Singh, Shiv M; Singh, Ram N; Naik, Simantini; Roy, Utpal; Srivastava, Alok; Bölter, Manfred

2017-12-01

Permafrost soils are unique habitats in polar environment and are of great ecological relevance. The present study focuses on the characterization of bacterial communities from permafrost profiles of Svalbard, Arctic. Counts of culturable bacteria range from 1.50 × 10 3 to 2.22 × 10 5 CFU g -1 , total bacterial numbers range from 1.14 × 10 5 to 5.52 × 10 5 cells g -1 soil. Bacterial isolates are identified through 16S rRNA gene sequencing. Arthrobacter and Pseudomonas are the most dominant genera, and A. sulfonivorans, A. bergeri, P. mandelii, and P. jessenii as the dominant species. Other species belong to genera Acinetobacter, Bacillus, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Rhodococcus, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus. To the best of our knowledge, genera Acinetobacter, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus are the first northernmost records from Arctic permafrost. The present study fills the knowledge gap of culturable bacterial communities and their chronological characterization from permafrost soils of Ny-Ålesund (79°N), Arctic. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China

PubMed Central

Hu, Yinhong; Dou, Xiaolin; Li, Juanyong; Li, Feng

2018-01-01

The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (Sophora japonica Linn.) in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC), and soil moisture content (SMC). The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and diversity across areas with different types of land cover, and soil properties play a more important role than heavy metals. PMID:29545776

The effect of deuteration on the structure of bacterial cellulose

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

Bali, Garima; Foston, Marcus; O'Neill, Hugh Michael

2013-01-01

ABSTRACT In vivo generated deuterated bacterial cellulose, cultivated from 100% deuterated glycerol in D2O medium, was analyzed for deuterium incorporation by ionic liquid dissolution and 2H and 1H nuclear magnetic resonance (NMR). A solution NMR method of the dissolved cellulose was used to determine that this bacterial cellulose had 85 % deuterium incorporation. Acetylation and 1H and 2H NMR of deuterated bacterial cellulose indicated near equal deuteration at all sites of the glucopyranosyl ring except C-6 which was partly deuterated. Despite the high level of deuterium incorporation there were no significant differences in the molecular and morphological properties were observedmore » for the deuterated and protio bacterial cellulose samples. The highly deuterated bacterial cellulose presented here can be used as a model substrate for studying cellulose biopolymer properties via future small angle neutron scattering (SANS) studies.« less

Role of Clinical Presentations and Routine CSF Analysis in the Rapid Diagnosis of Acute Bacterial Meningitis in Cases of Negative Gram Stained Smears

PubMed Central

Fouad, Rabab; El-Kholy, Badawy; Yosry, Ayman

2014-01-01

Background and Aim. Bacterial meningitis is a lethal, disabling endemic disease needing prompt antibiotic management. Gram stained smears is rapid accurate method for diagnosis of bacterial meningitis. In cases of negative gram stained smears diagnosis is delayed till culture results. We aim to assess the role of clinical presentations and routine CSF analysis in the cost-effective rapid diagnosis of negative gram stained smears bacterial meningitis. Methods. Cross sectional study including 623 acute meningitis patients divided into two groups: bacterial meningitis and nonbacterial meningitis groups. The clinical presentations, systemic inflammatory parameters, and CSF analysis were evaluated and compared in both groups. Results. Altered conscious level, localizing neurological signs, Kernig's and Brudzinski's signs together with peripheral leucocytosis (>10.000/mm3), high CRP (>6) together with high CSF protein (>50 gl/dL), CSF neutrophilic count (≥50% of total CSF leucocytic count), and low CSF glucose level (<45 gm/dL) and CSF/serum glucose ≤0.6 were significantly diagnostic in bacterial meningitis patients. From the significant CSF analysis variables CSF protein carried the higher accuracy of diagnosis 78% with sensitivity 88% and specificity 72%. Conclusions. High CSF protein (>50 mg/dL) together with plasma inflammatory markers and CSF cytochemical parameters can diagnose bacterial meningitis in gram stain negative smear till culture results. PMID:24803939

Anti-Halitosis Effect of Toothpaste Supplemented with Alkaline Extract of the Leaves of Sasa senanensis Rehder.

PubMed

Sakagami, Hiroshi; Sheng, Hong; Ono, Koki; Komine, Yusuke; Miyadai, Tomoharu; Terada, Yuji; Nakada, Daisuke; Tanaka, Shoji; Matsumoto, Masaru; Yasui, Toshikazu; Watanabe, Koichi; Junye, Jia; Natori, Takenori; Suguro-Kitajima, Madoka; Oizumi, Hiroshi; Oizumi, Takaaki

2016-01-01

Previous studies have shown activity against viruses, bacteria, inflammation and oral lichenoid dysplasia of alkaline extract of the leaves of Sasa senanensis Rehder (SE), suggesting its possible application to oral diseases. In the present study, we performed a small-scale clinical test to investigate whether SE is effective against halitosis and in oral bacterial reduction. A total of 12 volunteers participated in this study. They brushed their teeth immediately after meals three times each day with SE-containing toothpaste (SETP) or placebo toothpaste. Halitosis in the breath and bacterial number on the tongue were measured by commercially available portable apparatuses at a specified time in the morning. Some relationship was observed between halitosis and bacterial number from each individual, especially when those with severe halitosis were included. Repeated experiments demonstrated that SETP significantly reduced halitosis but not the bacterial number on the tongue. The present study provides for the first time the basis for anti-halitosis activity of SE. Copyright © 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Biomimicry of quorum sensing using bacterial lifecycle model.

PubMed

Niu, Ben; Wang, Hong; Duan, Qiqi; Li, Li

2013-01-01

Recent microbiologic studies have shown that quorum sensing mechanisms, which serve as one of the fundamental requirements for bacterial survival, exist widely in bacterial intra- and inter-species cell-cell communication. Many simulation models, inspired by the social behavior of natural organisms, are presented to provide new approaches for solving realistic optimization problems. Most of these simulation models follow population-based modelling approaches, where all the individuals are updated according to the same rules. Therefore, it is difficult to maintain the diversity of the population. In this paper, we present a computational model termed LCM-QS, which simulates the bacterial quorum-sensing (QS) mechanism using an individual-based modelling approach under the framework of Agent-Environment-Rule (AER) scheme, i.e. bacterial lifecycle model (LCM). LCM-QS model can be classified into three main sub-models: chemotaxis with QS sub-model, reproduction and elimination sub-model and migration sub-model. The proposed model is used to not only imitate the bacterial evolution process at the single-cell level, but also concentrate on the study of bacterial macroscopic behaviour. Comparative experiments under four different scenarios have been conducted in an artificial 3-D environment with nutrients and noxious distribution. Detailed study on bacterial chemotatic processes with quorum sensing and without quorum sensing are compared. By using quorum sensing mechanisms, artificial bacteria working together can find the nutrient concentration (or global optimum) quickly in the artificial environment. Biomimicry of quorum sensing mechanisms using the lifecycle model allows the artificial bacteria endowed with the communication abilities, which are essential to obtain more valuable information to guide their search cooperatively towards the preferred nutrient concentrations. It can also provide an inspiration for designing new swarm intelligence optimization algorithms, which can be used for solving the real-world problems.

Biomimicry of quorum sensing using bacterial lifecycle model

PubMed Central

2013-01-01

Background Recent microbiologic studies have shown that quorum sensing mechanisms, which serve as one of the fundamental requirements for bacterial survival, exist widely in bacterial intra- and inter-species cell-cell communication. Many simulation models, inspired by the social behavior of natural organisms, are presented to provide new approaches for solving realistic optimization problems. Most of these simulation models follow population-based modelling approaches, where all the individuals are updated according to the same rules. Therefore, it is difficult to maintain the diversity of the population. Results In this paper, we present a computational model termed LCM-QS, which simulates the bacterial quorum-sensing (QS) mechanism using an individual-based modelling approach under the framework of Agent-Environment-Rule (AER) scheme, i.e. bacterial lifecycle model (LCM). LCM-QS model can be classified into three main sub-models: chemotaxis with QS sub-model, reproduction and elimination sub-model and migration sub-model. The proposed model is used to not only imitate the bacterial evolution process at the single-cell level, but also concentrate on the study of bacterial macroscopic behaviour. Comparative experiments under four different scenarios have been conducted in an artificial 3-D environment with nutrients and noxious distribution. Detailed study on bacterial chemotatic processes with quorum sensing and without quorum sensing are compared. By using quorum sensing mechanisms, artificial bacteria working together can find the nutrient concentration (or global optimum) quickly in the artificial environment. Conclusions Biomimicry of quorum sensing mechanisms using the lifecycle model allows the artificial bacteria endowed with the communication abilities, which are essential to obtain more valuable information to guide their search cooperatively towards the preferred nutrient concentrations. It can also provide an inspiration for designing new swarm intelligence optimization algorithms, which can be used for solving the real-world problems. PMID:23815296

Characterizing the Bacterial Communities in Retail Stores in the United States

DTIC Science & Technology

2015-01-01

community or the factors that affect it. To our knowledge, only one study to date has investigated the indoor bacterial microbiome of retail stores...type of store affects the microbial community present, the impact of store type on the bacterial community was investigated by comparing the bacteria...genes analysis (Figure 2). Additionally, Leff and Fierer (2013) observed a high relative abundance of Enterobacteriaceae on fruits and vegetables but

Phenotypic Signatures Arising from Unbalanced Bacterial Growth

PubMed Central

Tan, Cheemeng; Smith, Robert Phillip; Tsai, Ming-Chi; Schwartz, Russell; You, Lingchong

2014-01-01

Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify “phenotypic signatures” by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under different growth conditions, and to identify the essential architecture of the gene network underlying the observed growth dynamics. Our method has implications for both basic understanding of bacterial physiology and for the classification of bacterial strains. PMID:25101949

Phenotypic signatures arising from unbalanced bacterial growth.

PubMed

Tan, Cheemeng; Smith, Robert Phillip; Tsai, Ming-Chi; Schwartz, Russell; You, Lingchong

2014-08-01

Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify "phenotypic signatures" by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under different growth conditions, and to identify the essential architecture of the gene network underlying the observed growth dynamics. Our method has implications for both basic understanding of bacterial physiology and for the classification of bacterial strains.

Lack of Accuracy of Body Temperature for Detecting Serious Bacterial Infection in Febrile Episodes.

PubMed

De, Sukanya; Williams, Gabrielle J; Teixeira-Pinto, Armando; Macaskill, Petra; McCaskill, Mary; Isaacs, David; Craig, Jonathan C

2015-09-01

Body temperature is a time-honored marker of serious bacterial infection, but there are few studies of its test performance. The aim of our study was to determine the accuracy of temperature measured on presentation to medical care for detecting serious bacterial infection. Febrile children 0-5 years of age presenting to the emergency department of a tertiary care pediatric hospital were sampled consecutively. The accuracy of the axillary temperature measured at presentation was evaluated using logistic regression models to generate receiver operating characteristic curves. Reference standard tests for serious bacterial infection were standard microbiologic/radiologic tests and clinical follow-up. Age, clinicians' impression of appearance of the child (well versus unwell) and duration of illness were assessed as possible effect modifiers. Of 15,781 illness episodes 1120 (7.1%) had serious bacterial infection. The area under the receiver operating characteristic curve for temperature was 0.60 [95% confidence intervals (CI): 0.58-0.62]. A threshold of ≥ 38°C had a sensitivity of 0.67 (95% CI: 0.64-0.70), specificity of 0.45 (95% CI: 0.44-0.46), positive likelihood ratio of 1.2 (95% CI: 1.2-1.3) and negative likelihood ratio of 0.7 (95% CI: 0.7-0.8). Age and illness duration had a small but significant effect on the accuracy of temperature increasing its "rule-in" potential. Measured temperature at presentation to hospital is not an accurate marker of serious bacterial infection in febrile children. Younger age and longer duration of illness increase the rule-in potential of temperature but without substantial overall change in its test accuracy.

Microbiology: Detection of Bacterial Pathogens and Their Occurrence.

ERIC Educational Resources Information Center

Reasoner, Donald J.

1978-01-01

Presents a literature review of bacterial pathogens that are related to water pollution, covering publications from 1976-77. This review includes: (1) bacterial pathogens in animals; and (2) detection and identification of waterborne bacterial pathogens. A list of 129 references is also presented. (HM)

Study of bacterial meningitis in children below 5 years with comparative evaluation of gram staining, culture and bacterial antigen detection.

PubMed

Yadhav Ml, Kala

2014-04-01

Bacterial meningitis is one of the most serious infections seen in infants and children, which is associated with acute complications and chronic morbidity. Infections of Central Nervous System (CNS) still dominate the scene of childhood neurological disorders in most of the developing tropical countries. To isolate, identify and determine the antibiotic susceptibility patterns of pathogens associated with bacterial meningitis. We also aimed to comparatively evaluate of Gram staining, culture and bacterial antigen detection in cerebrospinal fluid samples. Present comparative study included 100 CSF samples of children below the age of 5 years, who were clinically suspected meningitis cases. The samples were subjected to Gram staining, culture and Latex agglutination test (LAT). The organisms isolated in the study were characterized and antibiotic susceptibility test was done according to standard guidelines. It was done by using Gaussian test. Of the 100 cases, 24 were diagnosed as Acute bacterial meningitis (ABM) cases by. Gram staining, culture and latex agglutination test. 21 (87.5%) cases were culture positive, with 2 cases being positive for polymicrobial isolates. Gram staining was positive in 17 (70.53%) cases and LAT was positive in 18 (33.33%) cases. Streptococcus pneumoniae was the predominant organism which was isolated and it was sensitive to antibiotics. In the present study, male to female ratio was 1.27:1, which showed a male preponderance. With the combination of Gram staining, culture, and LAT, 100% sensitivity and specificity can be achieved (p < 0.001). Gram staining and LAT can detect 85% of cases of ABM. Bacterial meningitis is a medical emergency and making an early diagnosis and providing treatment early are life saving and they reduce chronic morbidity.

Effect of species, breed, and age on bacterial load in bovine and bubaline semen

PubMed Central

Sannat, Chandrahas; Nair, Ajit; Sahu, S. B.; Sahasrabudhe, S. A.; Kumar, Ashish; Gupta, Amit Kumar; Shende, R. K.

2015-01-01

Aim: The present study was conducted to investigate the effect of species, breed and age on bacterial load in fresh and frozen semen of Cattle and Buffalo bull. Materials and Methods: Present study covered 56 cow and 10 buffalo bulls stationed at Central Semen Station Anjora, Durg (Chhattisgarh). Impact of breeds on bacterial load in semen was assessed using six breeds of cattle viz. Sahiwal, Gir, Red Sindhi, Tharparkar, Jersey and Holstein Friesian (HF) cross. Cow bulls were categorized into four different groups based on their age (<4 years, 4-5 years, 5-6 years and > 6 years) to study variation among age groups. Bacterial load was measured in fresh and frozen semen samples from these bulls using the standard plate count (SPC) method and count was expressed as colony forming unit (CFU) per ml of semen. Results: Higher bacterial load was reported in fresh (2.36 × 104 ± 1943 CFU/ml) and frozen (1.00 × 10 ± 90 CFU/ml) semen of cow bulls as compared to buffalo bulls (1.95 × 104 ± 2882 and 7.75 × 102 ± 160 CFU/ml in fresh and frozen semen, respectively). Jersey bull showed significantly higher bacterial count (p < 0.05) both in fresh (4.07 × 104 ± 13927 CFU/ml) and frozen (1.92 × 103 ± 178 CFU/ml) semen followed by HF cross, Sahiwal, Gir, Red Sindhi and Tharparkar bull. Bulls aged < 4 years and more than 6 years yielded increased bacterial load in their semen. Although a minor variation was reported between species and among age groups, no significant differences were measured. Conclusion: Bacterial load in semen did not differ significantly between species and age groups; however significant variation was reported among different breeds. Bulls of Jersey breed showed significantly higher bacterial load in semen as compared to the crossbred and indigenous bull. PMID:27047115

‘Nodophagy’

PubMed Central

Travassos, Leonardo H

2010-01-01

Autophagy is a homeostatic pathway that processes and recycles damaged organelles and other cytoplasmic contents. While studies have implicated autophagy in the immune response to infection, the understanding of how the autophagic machinery specifically targets intracellular pathogens has remained elusive. Two recent studies have uncovered an autophagy-mediated immune response to bacteria through their detection by Nod receptors. In particular, Nod1 and Nod2 recruit the autophagic protein ATG16L1 to the plasma membrane at the bacterial entry site to promote an autophagy-dependent elimination of bacteria. In addition, Nod2 and ATG16L1 synergize to initiate an adaptive immune response to bacterial invasion by enhancing major histocompatibility complex (MHC) class II antigen presentation. These findings link two Crohn disease-associated susceptibility genes and reveal that cells expressing the risk-associated variants of ATG16L1 are defective in autophagy-mediated bacterial handling and antigen presentation. This could lead to bacterial persistence and contribute to the pathogenesis of the disease. PMID:21327039

Metal homeostasis in infectious disease: recent advances in bacterial metallophores and the human metal-withholding response.

PubMed

Neumann, Wilma; Gulati, Anmol; Nolan, Elizabeth M

2017-04-01

A tug-of-war between the mammalian host and bacterial pathogen for nutrients, including first-row transition metals (e.g. Mn, Fe, Zn), occurs during infection. Here we present recent advances about three metal-chelating metabolites that bacterial pathogens deploy when invading the host: staphylopine, staphyloferrin B, and enterobactin. These highlights provide new insights into the mechanisms of bacterial metal acquisition and regulation, as well as the contributions of host-defense proteins during the human innate immune response. The studies also underscore that the chemical composition of the microenvironment at an infection site can influence bacterial pathogenesis and the innate immune system. Copyright © 2016 Elsevier Ltd. All rights reserved.

Preliminary study on biosynthesis and characterization of bacteria cellulose films from coconut water

NASA Astrophysics Data System (ADS)

Indrianingsih, A. W.; Rosyida, V. T.; Jatmiko, T. H.; Prasetyo, D. J.; Poeloengasih, C. D.; Apriyana, W.; Nisa, K.; Nurhayati, S.; Hernawan; Darsih, C.; Pratiwi, D.; Suwanto, A.; Ratih, D.

2017-12-01

Bacterial cellulose produced by Acetobacter xylinum is a unique type of bacterial cellulose. It contains more than 90% of water. A preliminary study had shown that bacterial cellulose films has remarkable mechanical properties. The aim of this study was to investigate the optimum condition such as percentage of carbon source, time of cultivation, and pH to produce bacterial cellulose films from local coconut water, and its characterization on morphology, swelling ability and tensile strength of dried bacterial cellulose. A. xylinum was grown on coconut water culture medium with addition of 3%, 5%, and 7% of sugar, while the cultivation time was vary from 3 days, 5 days and 7 days. pH condition was conducted in pH 3, pH 5 and pH 7. Bacterial cellulose samples were dried using oven with temperature of 100°C until the moisture content reached 4-5%. This study showed that several parameters for optimum condition to produce bacterial cellulose films from local waste of coconut water had been obtained (5% of carbon source; pH 5; and 7 day of incubation period). The electron microscopy also showed that dried bacterial cellulose films had pores covered by fibrils on the surface. Therefore, the present work proposes the optimum formula and condition that can be used based on properties of end product needed.

Molecular comparison of the sampling efficiency of four types of airborne bacterial samplers.

PubMed

Li, Kejun

2011-11-15

In the present study, indoor and outdoor air samples were collected using four types of air samplers often used for airborne bacterial sampling. These air samplers included two solid impactors (BioStage and RCS), one liquid impinger (BioSampler), and one filter sampler with two kinds of filters (a gelatin and a cellulose acetate filter). The collected air samples were further processed to analyze the diversity and abundance of culturable bacteria and total bacteria through standard culture techniques, denaturing gradient gel electrophoresis (DGGE) fingerprinting and quantitative polymerase chain reaction (qPCR) analysis. The DGGE analysis indicated that the air samples collected using the BioStage and RCS samplers have higher culturable bacterial diversity, whereas the samples collected using the BioSampler and the cellulose acetate filter sampler have higher total bacterial diversity. To obtain more information on the sampled bacteria, some gel bands were excised and sequenced. In terms of sampling efficiency, results from the qPCR tests indicated that the collected total bacterial concentration was higher in samples collected using the BioSampler and the cellulose acetate filter sampler. In conclusion, the sampling bias and efficiency of four kinds of air sampling systems were compared in the present study and the two solid impactors were concluded to be comparatively efficient for culturable bacterial sampling, whereas the liquid impactor and the cellulose acetate filter sampler were efficient for total bacterial sampling. Copyright © 2011 Elsevier B.V. All rights reserved.

A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

PubMed

Shang, Shuanghua; Yi, Yanli

2015-12-01

The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

Effects of the Diet on the Microbiota of the Red Palm Weevil (Coleoptera: Dryophthoridae)

PubMed Central

Montagna, Matteo; Chouaia, Bessem; Mazza, Giuseppe; Prosdocimi, Erica Maria; Crotti, Elena; Mereghetti, Valeria; Vacchini, Violetta; Giorgi, Annamaria; De Biase, Alessio; Longo, Santi; Cervo, Rita; Lozzia, Giuseppe Carlo; Alma, Alberto; Bandi, Claudio; Daffonchio, Daniele

2015-01-01

Rhynchophorus ferrugineus, also known as the red palm weevil, is regarded as the major pest of palm trees. Although studies of the microbiota associated with this species have been performed in recent years, little attention has been dedicated to the influence of the diet in shaping the host bacterial community. Here, we investigated the influence of food sources (i.e. palm tissues vs apple based substrate) on the microbial diversity associated with RPW, which was compared with the microbiota associated with wild individuals of the sister species Rhynchophorus vulneratus. The bacterial characterization was performed using a culture independent approach, i.e. the 16S rRNA pyrotag, and a culture dependent approach for a subset of the samples, in order to obtain bacterial isolates from RPW tissues. The bacterial community appeared significantly influenced by diet. Proteobacteria resulted to be the most abundant clade and was present in all the specimens of the three examined weevil groups. Within Proteobacteria, Enterobacteriaceae were identified in all the organs analysed, including hemolymph and reproductive organs. The apple-fed RPWs and the wild R. vulneratus showed a second dominant taxon within Firmicutes that was scarcely present in the microbiota associated with palm-fed RPWs. A comparative analysis on the bacteria associated with the palm tissues highlighted that 12 bacterial genera out of the 13 identified in the plant tissues were also present in weevils, thus indicating that palm tissues may present a source for bacterial acquisition. PMID:25635833

Bacterial community shift during the startup of a full-scale oxidation ditch treating sewage.

PubMed

Chen, Yajun; Ye, Lin; Zhao, Fuzheng; Xiao, Lin; Cheng, Shupei; Zhang, Xu-Xiang

2016-10-06

Oxidation ditch (OD) is one of the most widely used processes for treating municipal wastewater. However, the microbial communities in the OD systems have not been well characterized and little information about the shift of bacterial community during the startup process of the OD systems is available. In this study, we investigated the bacterial community changes during the startup period (over 100 days) of a full-scale OD. The results showed that the bacterial community dramatically changed during the startup period. Similar to the activated sludge samples in other studies, Proteobacteria (accounting for 26.3%~48.4%) was the most dominant bacterial phylum in the OD system but its relative abundance declined nearly 40% during the startup process. It was also found that Planctomycetes proliferated greatly (from 4.79% to 13.5%) and finally replaced Bacteroidetes as the second abundant phylum in the OD system. Specifically, some bacteria affiliated with Flavobacterium genus of exhibited remarkable decreasing trends, while bacterial species belonging to OD1 candidate division and Saprospiraceae family were found to increase during the startup process. Despite of the bacterial community shift, the organic matter, nitrogen and phosphorus in the effluent were always in low concentrations, suggesting the functional redundancy of the bacterial community. Moreover, by comparing with the bacterial community in other municipal wastewater treatment bioreactors, some potentially novel bacterial species were found to be present in the OD system. Collectively, this study improved our understandings of bacterial community structure and the microbial ecology during the startup of full-scale wastewater treatment bioreactor.

Antiviral activity and specific modes of action of bacterial prodigiosin against Bombyx mori nucleopolyhedrovirus in vitro.

PubMed

Zhou, Wei; Zeng, Cheng; Liu, RenHua; Chen, Jie; Li, Ru; Wang, XinYan; Bai, WenWen; Liu, XiaoYuan; Xiang, TingTing; Zhang, Lin; Wan, YongJi

2016-05-01

Prodigiosin, the tripyrrole red pigment, is a bacterial secondary metabolite with multiple bioactivities; however, the antiviral activity has not been reported yet. In the present study, we found the antiviral activity of bacterial prodigiosin on Bombyx mori nucleopolyhedrovirus (BmNPV)-infected cells in vitro, with specific modes of action. Prodigiosin at nontoxic concentrations selectively killed virus-infected cells, inhibited viral gene transcription, especially viral early gene ie-1, and prevented virus-mediated membrane fusion. Under prodigiosin treatment, both progeny virus production and viral DNA replication were significantly inhibited. Fluorescent assays showed that prodigiosin predominantly located in cytoplasm which suggested it might interact with cytoplasm factors to inhibit virus replication. In conclusion, the present study clearly indicates that prodigiosin possesses significant antiviral activity against BmNPV.

STUDIES ON THE BACTERIOPHAGE OF D'HERELLE : IX. EVIDENCE OF HYDROLYSIS OF BACTERIAL PROTEIN DURING LYSIS.

PubMed

Hetler, D M; Bronfenbrenner, J

1928-07-31

1. During the process of lysis by bacteriophage, there is an appreciable increase in the amount of free amino acid present in the culture. 2. The increase of free amino acid is due to hydrolysis of bacterial protein.

The shells of BMC-type microcompartment organelles in bacteria.

PubMed

Yeates, Todd O; Jorda, Julien; Bobik, Thomas A

2013-01-01

Bacterial microcompartments are large proteinaceous structures that act as metabolic organelles in many bacterial cells. A shell or capsid, which is composed of a few thousand protein subunits, surrounds a series of sequentially acting enzymes and controls the diffusion of substrates and products into and out of the lumen. The carboxysome and the propanediol utilization microcompartment represent two well-studied systems among seven or more distinct types that can be delineated presently. Recent structural studies have highlighted a number of sophisticated mechanisms that underlie the function of bacterial microcompartment shell proteins. This review updates our understanding of bacterial microcompartment shells, how they are assembled, and how they carry out their functions in molecular transport and enzyme organization. Copyright © 2013 S. Karger AG, Basel.

Identification of mycobacterial surface proteins released into subcellular compartments of infected macrophages.

PubMed

Beatty, W L; Russell, D G

2000-12-01

Considerable effort has focused on the identification of proteins secreted from Mycobacterium spp. that contribute to the development of protective immunity. Little is known, however, about the release of mycobacterial proteins from the bacterial phagosome and the potential role of these molecules in chronically infected macrophages. In the present study, the release of mycobacterial surface proteins from the bacterial phagosome into subcellular compartments of infected macrophages was analyzed. Mycobacterium bovis BCG was surface labeled with fluorescein-tagged succinimidyl ester, an amine-reactive probe. The fluorescein tag was then used as a marker for the release of bacterial proteins in infected macrophages. Fractionation studies revealed bacterial proteins within subcellular compartments distinct from mycobacteria and mycobacterial phagosomes. To identify these proteins, subcellular fractions free of bacteria were probed with mycobacterium-specific antibodies. The fibronectin attachment protein and proteins of the antigen 85-kDa complex were identified among the mycobacterial proteins released from the bacterial phagosome.

Bacterial meningitis in solid organ transplant recipients: a population-based prospective study.

PubMed

van Veen, K E B; Brouwer, M C; van der Ende, A; van de Beek, D

2016-10-01

Solid organ transplant (SOT) recipients are at risk of infections of the central nervous system. However, the incidence and clinical course of bacterial meningitis in SOT recipients are unclear. We studied occurrence, disease course, and prognosis of bacterial meningitis in SOT recipients in the Netherlands. All patients with a medical history of solid organ transplantation were selected from our nationwide prospective cohort study on community-acquired bacterial meningitis in patients >16 years old, performed from March 1, 2006 to October 31, 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were collected prospectively. For transplant recipients, additional information was collected retrospectively. We identified 6 SOT recipients, all receiving renal transplants. The annual incidence of bacterial meningitis was 7-fold higher (95% confidence interval [CI] 2.94-17.02, P < 0.001) for renal transplant recipients as compared with the general population (9.56 [95% CI 3.98-22.96] vs. 1.35 [95% CI 1.28-1.43] per 100,000 patients per year). One of the 6 patients (17%) presented with the classic presentation of bacterial meningitis (fever, neck stiffness, and change in mental status). Seizures were common, occurring in 33% of patients. Streptococcus pneumoniae and Listeria monocytogenes were identified in 2 patients each, and Escherichia coli and Pseudomonas aeruginosa were both identified once. Four of 6 patients (67%) had an unfavorable functional outcome. Bacterial meningitis is a rare but devastating complication of solid organ transplantation. SOT recipients are at high risk for developing meningitis, and recognition of this condition may be difficult, owing to atypical clinical manifestation. © 2016 The Authors. Transplant Infectious Disease Published by John Wiley & Sons Ltd.

Molecular characterization of Xanthomonas strains responsible for bacterial leaf spot of tomato in Ethiopia

USDA-ARS?s Scientific Manuscript database

Bacterial spot of tomato (BST) is a major constraint to tomato production in Ethiopia and many other countries leading to significant crop losses. In the present study, using pathogenicity tests, sensitivity to copper and streptomycin, and multilocus sequence analysis, a diverse group of Xanthomonas...

Bacterial Cleanability of Various Types of Eating Surfaces.

ERIC Educational Resources Information Center

Ridenour, Gerald M.; Armbruster, E. H.

1953-01-01

Presents a study of the capability of commercial dishwashers to remove bacteria from various kinds of service plates. Gives an account of preliminary research on the bacterial cleanability of eating surfaces of different materials by two radiological procedures--(1) radiological count, and (2) autoradiographic measurement. Among the factors…

Mathematical Modelling of Bacterial Populations in Bio-remediation Processes

NASA Astrophysics Data System (ADS)

Vasiliadou, Ioanna A.; Vayenas, Dimitris V.; Chrysikopoulos, Constantinos V.

2011-09-01

An understanding of bacterial behaviour concerns many field applications, such as the enhancement of water, wastewater and subsurface bio-remediation, the prevention of environmental pollution and the protection of human health. Numerous microorganisms have been identified to be able to degrade chemical pollutants, thus, a variety of bacteria are known that can be used in bio-remediation processes. In this study the development of mathematical models capable of describing bacterial behaviour considered in bio-augmentation plans, such as bacterial growth, consumption of nutrients, removal of pollutants, bacterial transport and attachment in porous media, is presented. The mathematical models may be used as a guide in designing and assessing the conditions under which areas contaminated with pollutants can be better remediated.

Comparative study of 6-APA production by free and agar immobilized bacteria in nutrient broth culture.

PubMed

Dolui, A K; Das, S

2011-04-01

In the present study different bacterial samples were isolated from soil of different places of Dibrugarh and screened for biotransformation ability to produce 6-Aminopenicillanic acid. Among ten isolated bacterial samples, three gram positive bacterial samples designated as AKDD-2, AKDD-4 and AKDD-6 showed the production of 6-APA from penicillin G. Assessment of production of 6-APA after incubation in penicillin G (2 mg/ml) by three different samples separately in free and agar immobilization state was done by HPLC analysis. Reusability of immobilized cells was found successful up to 14 days.

Use of Natural Antimicrobial Peptides and Bacterial Biopolymers for Cultured Pearl Production

PubMed Central

Simon-Colin, Christelle; Gueguen, Yannick; Bachere, Evelyne; Kouzayha, Achraf; Saulnier, Denis; Gayet, Nicolas; Guezennec, Jean

2015-01-01

Cultured pearls are the product of grafting and rearing of Pinctada margaritifera pearl oysters in their natural environment. Nucleus rejections and oyster mortality appear to result from bacterial infections or from an inappropriate grafting practice. To reduce the impact of bacterial infections, synthetic antibiotics have been applied during the grafting practice. However, the use of such antibiotics presents a number of problems associated with their incomplete biodegradability, limited efficacy in some cases, and an increased risk of selecting for antimicrobial resistant bacteria. We investigated the application of a marine antimicrobial peptide, tachyplesin, which is present in the Japanese horseshoe crab Tachypleus tridentatus, in combination with two marine bacterial exopolymers as alternative treatment agents. In field studies, the combination treatment resulted in a significant reduction in graft failures vs. untreated controls. The combination of tachyplesin (73 mg/L) with two bacterial exopolysaccharides (0.5% w/w) acting as filming agents, reduces graft-associated bacterial contamination. The survival data were similar to that reported for antibiotic treatments. These data suggest that non-antibiotic treatments of pearl oysters may provide an effective means of improving oyster survival following grafting procedures. PMID:26110895

Acute appendicitis presenting with Klebsiella pneumoniae septicemia due to bacterial translocation.

PubMed

Salemis, Nikolaos S

2009-10-01

Bacterial translocation (BT) is defined as the passage of viable bacteria from the gastrointestinal tract, across the intestinal wall, to the mesenteric lymph nodes or other extranodal sites and bloodstream. It has been shown in both animal and human studies and has been implicated as a source of sepsis in susceptible patients. Herein, a rare case of acute appendicitis in a nonimmunocompromised patient who presented with manifestations of Klebsiella pneumoniae septicemia, is described. Translocation of Klebsiella pneumoniae through the compromised appendix mucosa leading in dissemination of the infection into the bloodstream was likely the main causative factor for the atypical and toxic presentation of acute appendicitis. Thorough clinical investigation ruled out other sources of infection. Emergency physicians should be aware that septicemia may be the dominant presentation of acute appendicitis, due to dissemination of the infection into the bloodstream, secondary to bacterial translocation.

Carbohydrate Coating Reduces Adhesion of Biofilm-Forming Bacillus subtilis to Gold Surfaces

PubMed Central

Kesel, S.; Mader, A.; Seeberger, P. H.; Lieleg, O.

2014-01-01

The growth of bacterial biofilms in pipes and food tanks causes severe problems in industry. Biofilms growing on medical implants or catheters are of great concern, as they can cause serious infections and decrease the functionality of the medical device. The prevention of bacterial adhesion—the first step in colonization and biofilm formation—is therefore very important. Current research comprises alterations in surface properties, the prevention of adhesin biosynthesis, inhibition with receptor analogs, or the development of anti-adhesive vaccines. We present a new approach that allows us to study bacterial adhesion with high sensitivity in real-time while testing several different surfaces in parallel. Using the cantilever-array technique we demonstrate that coating of gold surfaces with mono- or disaccharides results in a reduction of the bacterial adhesion of the biofilm-forming bacterium Bacillus subtilis NCIB 3610 to these gold surfaces. This reduction in bacterial adhesion is independent of the studied carbohydrate. Using several mutant strains, we investigate the underlying molecular interactions, and our results suggest that adhesion to gold surfaces is mediated by thiol groups present in proteins of the bacterial cell membrane or biofilm matrix proteins expressed at low levels by the wild-type strain. Furthermore, our data indicate that the adhesion of B. subtilis NCIB 3610 to carbohydrate-coated gold surfaces is facilitated by interactions between carbohydrates installed on the cantilever gold surface and an exopolysaccharide expressed by this strain. Understanding general and specific contributions of molecular interactions mediating bacterial adhesion will enable its prevention in the future. PMID:25038098

Community-Acquired Bacterial Meningitis in Alcoholic Patients

PubMed Central

Weisfelt, Martijn; de Gans, Jan; van der Ende, Arie; van de Beek, Diederik

2010-01-01

Background Alcoholism is associated with susceptibility to infectious disease, particularly bacterial pneumonia. In the present study we described characteristics in alcoholic patients with bacterial meningitis and delineate the differences with findings in non-alcoholic adults with bacterial meningitis. Methods/Principal Findings This was a prospective nationwide observational cohort study including patients aged >16 years who had bacterial meningitis confirmed by culture of cerebrospinal fluid (696 episodes of bacterial meningitis occurring in 671 patients). Alcoholism was present in 27 of 686 recorded episodes of bacterial meningitis (4%) and alcoholics were more often male than non-alcoholics (82% vs 48%, P = 0.001). A higher proportion of alcoholics had underlying pneumonia (41% vs 11% P<0.001). Alcoholics were more likely to have meningitis due to infection with Streptococcus pneumoniae (70% vs 50%, P = 0.01) and Listeria monocytogenes (19% vs 4%, P = 0.005), whereas Neisseria meningitidis was more common in non-alcoholic patients (39% vs 4%, P = 0.01). A large proportion of alcoholics developed complications during clinical course (82% vs 62%, as compared with non-alcoholics; P = 0.04), often cardiorespiratory failure (52% vs 28%, as compared with non-alcoholics; P = 0.01). Alcoholic patients were at risk for unfavourable outcome (67% vs 33%, as compared with non-alcoholics; P<0.001). Conclusions/Significance Alcoholic patients are at high risk for complications resulting in high morbidity and mortality. They are especially at risk for cardiorespiratory failure due to underlying pneumonia, and therefore, aggressive supportive care may be crucial in the treatment of these patients. PMID:20161709

Incidence of bacterial respiratory pathogens and their susceptibility to common antibacterial agents.

PubMed Central

Qadri, S. M.; Lee, G. C.; Ueno, Y.; Burdette, J. M.

1993-01-01

Although most respiratory tract infections are caused by viruses, bacterial pathogens are responsible for higher morbidity and mortality. Because virtually nothing is known about the etiology of bacterial respiratory pathogens in Saudi Arabia, this study examined the incidence of these organisms in 5426 patients over a 1-year period. Of the bacterial pathogens isolated from 904 patients, the most common organism was Hemophilus influenzae (31%), followed by pneumococci (22%), Pseudomonas aeruginosa (16%), and others (31%). Because the first two organisms accounted for more than 50% of isolates, their susceptibility to commonly used antibiotics was also reviewed. The results are presented here. PMID:8496993

Effect of oral bacterial lysates on serum immunoglobulins.

PubMed

Palma-Carlos, A G; Palma-Carlos, M L

1989-11-01

The level of serum immunoglobulins IgG, IgA, IgM and IgE has been studied before and after oral immunotherapy with a bacterial lysate in 88 patients with bronchial asthma, repeated respiratory infection and 12 cases of IgA deficiency. A significant increase in IgA has been observed in 9 patients presenting initially a decreased IgA serum level. In 3 patients without response to the standard treatment an increase in IgA was achieved increasing the dosage of oral bacterial lysate. Oral bacterial lysates could be an useful immunomodulating agent in repeated respiratory infections associated or not with IgA deficiency.

Pediatric bacterial meningitis in French Guiana.

PubMed

Elenga, N; Sicard, S; Cuadro-Alvarez, E; Long, L; Njuieyon, F; Martin, E; Kom-Tchameni, R; Balcaen, J; Moreau, B; Boukhari, R

2015-01-01

Controlling vaccine-preventable infectious diseases is a public health priority in French Guiana but there is currently no epidemiological data on pediatric bacterial meningitis in this overseas department. Our aim was to describe data related to pediatric bacterial meningitis in French Guiana and compare it with that of metropolitan France. We conducted a multicenter retrospective study from 2000 to 2010 to describe the clinical picture, biological data, epidemiology, and outcome of pediatric bacterial meningitis case patients in French Guiana. The median age of bacterial meningitis patients was 6months [0-15] and the sex ratio 1.06. We observed a total of 60 bacterial meningitis case patients. Most presented with pneumococcal meningitis (24 patients; 40%); 11 with Haemophilus influenzae type b meningitis (23%), five with group B streptococcal meningitis (8.5%), and five others (8.5%) with staphylococcal meningitis (three patients presented with coagulase-negative staphylococci and two with Staphylococcus aureus). Only one patient presented with group B meningococcal meningitis, an 18-month-old infant. We recorded 14 deaths (overall case fatality: 23%); eight were due to Streptococcus pneumoniae (case fatality: 33%). The overall sequelae rate was 28%. It was 32% for patients presenting with pneumococcal meningitis. We observed that 38% of children who had never been vaccinated were infected by a vaccine-preventable bacterium. We observed many differences in the distribution of the bacteria and in the patients' prognosis when comparing the French Guiana data with that of metropolitan France. Improving vaccination coverage would decrease the incidence of H. influenzae meningitis. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

The Epidemiology, Management, and Outcomes of Bacterial Meningitis in Infants.

PubMed

Ouchenir, Lynda; Renaud, Christian; Khan, Sarah; Bitnun, Ari; Boisvert, Andree-Anne; McDonald, Jane; Bowes, Jennifer; Brophy, Jason; Barton, Michelle; Ting, Joseph; Roberts, Ashley; Hawkes, Michael; Robinson, Joan L

2017-07-01

The pathogens that cause bacterial meningitis in infants and their antimicrobial susceptibilities may have changed in this era of increasing antimicrobial resistance, use of conjugated vaccines, and maternal antibiotic prophylaxis for group B Streptococcus (GBS). The objective was to determine the optimal empirical antibiotics for bacterial meningitis in early infancy. This was a cohort study of infants <90 days of age with bacterial meningitis at 7 pediatric tertiary care hospitals across Canada in 2013 and 2014. There were 113 patients diagnosed with proven meningitis ( n = 63) or suspected meningitis ( n = 50) presented at median 19 days of age, with 63 patients (56%) presenting a diagnosis from home. Predominant pathogens were Escherichia coli ( n = 37; 33%) and GBS ( n = 35; 31%). Two of 15 patients presenting meningitis on day 0 to 6 had isolates resistant to both ampicillin and gentamicin ( E coli and Haemophilus influenzae type B). Six of 60 infants presenting a diagnosis of meningitis from home from day 7 to 90 had isolates, for which cefotaxime would be a poor choice ( Listeria monocytogenes [ n = 3], Enterobacter cloacae , Cronobacter sakazakii , and Pseudomonas stutzeri ). Sequelae were documented in 84 infants (74%), including 8 deaths (7%). E coli and GBS remain the most common causes of bacterial meningitis in the first 90 days of life. For empirical therapy of suspected bacterial meningitis, one should consider a third-generation cephalosporin (plus ampicillin for at least the first month), potentially substituting a carbapenem for the cephalosporin if there is evidence for Gram-negative meningitis. Copyright © 2017 by the American Academy of Pediatrics.

Absence of bacterial DNA in culture-negative urine from cats with and without lower urinary tract disease.

PubMed

Lund, Heidi Sjetne; Skogtun, Gaute; Sørum, Henning; Eggertsdóttir, Anna Vigdís

2015-10-01

A diagnosis of bacterial cystitis commonly relies on a positive microbiological culture demonstrating the presence of a significant number of colony-forming units/ml urine, as urine within the upper urinary tract, bladder and proximal urethra generally is considered sterile. Recent studies from human and veterinary medicine indicate the presence of non-culturable bacteria in culture-negative urine samples. The aim of the present study was to determine the occurrence of bacterial DNA in culture-negative urine samples from cats with signs of feline lower urinary tract disease (FLUTD) and healthy control cats by 16S ribosomal DNA PCR and subsequent sequencing. The study sample included 38 culture-negative urine samples from cats with FLUTD and 43 culture-negative samples from control cats. Eight culture-positive urine samples from cats with FLUTD were included as external positive controls in addition to negative reaction controls. Of possible methodological limitations, degradation of DNA due to storage, the use of non-sedimented urine for DNA isolation and lack of internal positive reaction controls should be mentioned. The positive controls were recognised, but occurrence of bacterial DNA in culture-negative urine from cats with or without signs of lower urinary tract disease was not demonstrated. However, considering the possible methodological limitations, the presence of bacterial DNA in the urine of culture-negative FLUTD cats cannot be excluded based on the present results alone. Therefore, a prospective study reducing the possibility of degradation of DNA due to storage, in combination with modifications enhancing the chance of detecting even lower levels of bacterial DNA in culture-negative samples, seems warranted. © ISFM and AAFP 2014.

A Mach-Zender digital holographic microscope with sub-micrometer resolution for imaging and tracking of marine micro-organisms

NASA Astrophysics Data System (ADS)

Kühn, Jonas; Niraula, Bimochan; Liewer, Kurt; Kent Wallace, J.; Serabyn, Eugene; Graff, Emilio; Lindensmith, Christian; Nadeau, Jay L.

2014-12-01

Digital holographic microscopy is an ideal tool for investigation of microbial motility. However, most designs do not exhibit sufficient spatial resolution for imaging bacteria. In this study we present an off-axis Mach-Zehnder design of a holographic microscope with spatial resolution of better than 800 nm and the ability to resolve bacterial samples at varying densities over a 380 μm × 380 μm × 600 μm three-dimensional field of view. Larger organisms, such as protozoa, can be resolved in detail, including cilia and flagella. The instrument design and performance are presented, including images and tracks of bacterial and protozoal mixed samples and pure cultures of six selected species. Organisms as small as 1 μm (bacterial spores) and as large as 60 μm (Paramecium bursaria) may be resolved and tracked without changes in the instrument configuration. Finally, we present a dilution series investigating the maximum cell density that can be imaged, a type of analysis that has not been presented in previous holographic microscopy studies.

Outcome in patients with bacterial meningitis presenting with a minimal Glasgow Coma Scale score

PubMed Central

Lucas, Marjolein J.; Brouwer, Matthijs C.; van der Ende, Arie

2014-01-01

Objective: In bacterial meningitis, a decreased level of consciousness is predictive for unfavorable outcome, but the clinical features and outcome in patients presenting with a minimal score on the Glasgow Coma Scale are unknown. Methods: We assessed the incidence, clinical characteristics, and outcome of patients with bacterial meningitis presenting with a minimal score on the Glasgow Coma Scale from a nationwide cohort study of adults with community-acquired bacterial meningitis in the Netherlands from 2006 to 2012. Results: Thirty of 1,083 patients (3%) presented with a score of 3 on the Glasgow Coma Scale. In 22 of 30 patients (73%), the minimal Glasgow Coma Scale score could be explained by use of sedative medication or complications resulting from meningitis such as seizures, cerebral edema, and hydrocephalus. Systemic (86%) and neurologic (47%) complications occurred frequently, leading to a high proportion of patients with unfavorable outcome (77%). However, 12 of 30 patients (40%) survived and 7 patients (23%) had a good functional outcome, defined as a score of 5 on the Glasgow Outcome Scale. Patients presenting with a minimal Glasgow Coma Scale score on admission and bilaterally absent pupillary light responses, bilaterally absent corneal reflexes, or signs of septic shock on admission all died. Conclusions: Patients with community-acquired bacterial meningitis rarely present with a minimal score on the Glasgow Coma Scale, but this condition is associated with high rates of morbidity and mortality. However, 1 out of 5 of these severely ill patients will make a full recovery, stressing the continued need for aggressive supportive care in these patients. PMID:25340065

Increased electrical output when a bacterial ABTS oxidizer is used in a microbial fuel cell

USDA-ARS?s Scientific Manuscript database

Microbial fuel cells (MFCs) are a technology that provides electrical energy from the microbial oxidation of organic compounds. Most MFCs use oxygen as the oxidant in the cathode chamber. The present study examined the formation in culture of an unidentified bacterial oxidant and investigated the ...

The Gut Microbiomes of Two Pachysoma MacLeay Desert Dung Beetle Species (Coleoptera: Scarabaeidae: Scarabaeinae) Feeding on Different Diets.

PubMed

Franzini, Philippa Z N; Ramond, Jean-Baptiste; Scholtz, Clarke H; Sole, Catherine L; Ronca, Sandra; Cowan, Don A

2016-01-01

Micro-organisms inhabiting animal guts benefit from a protected and nutrient-rich environment while assisting the host with digestion and nutrition. In this study we compare, for the first time, the bacterial and fungal gut communities of two species of the small desert dung beetle genus Pachysoma feeding on different diets: the detritivorous P. endroedyi and the dry-dung-feeding P. striatum. Whole-gut microbial communities from 5 individuals of each species were assessed using 454 pyrosequencing of the bacterial 16S rRNA gene and fungal ITS gene regions. The two bacterial communities were significantly different, with only 3.7% of operational taxonomic units shared, and displayed intra-specific variation. The number of bacterial phyla present within the guts of P. endroedyi and P. striatum individuals ranged from 6-11 and 4-7, respectively. Fungal phylotypes could only be detected within the gut of P. striatum. Although the role of host phylogeny in Pachysoma microbiome assembly remains unknown, evidence presented in this study suggests that host diet may be a deterministic factor.

Bacterial plaque colonization around dental implant surfaces.

PubMed

Covani, Ugo; Marconcini, Simone; Crespi, Roberto; Barone, Antonio

2006-09-01

To examine the distribution of bacteria into the internal and external surfaces of failed implants using histologic analysis. There were 10 failed pure titanium and 5 failed hydroxyapatite-coated titanium implants consecutively removed various years after their placement. Criteria for fixture removal were peri-implant radiolucency and clinical mobility. The mobile fixtures were retrieved with the patients under local anesthesia. Fixtures were removed maintaining the abutments with the aim to observe the bacterial infiltration at the level of abutment/implant interface and on the implant surface. A thin radiolucent space was always present around all the failed implants. The abutments screws were tightly secured in all clinical cases. The bacterial cells were composed of cocci and filaments, which were adherent to the implant surface with an orientation perpendicular to the long axis of the implant. All the specimens included in this study showed bacteria at the level of implant/abutment interface. Histologic analysis at the level of abutment/implant interface in 2-stage implants identified heavy bacterial colonization. These findings appear to support those studies showing bacteria penetration at the level of the micro-gap, which can legitimate the hypothesis that the micro-gap at the bone level could present a risk for bone loss caused by bacterial colonization.

Biliary bacterial factors determine the path of gallstone formation.

PubMed

Stewart, Lygia; Grifiss, J McLeod; Jarvis, Gary A; Way, Lawrence W

2006-11-01

Bacteria cause pigment gallstones and can act as a nidus for cholesterol gallstone formation. Bacterial factors that facilitate gallstone formation include beta-glucuronidase (bG), phospholipase (PhL), and slime. The current study sought to determine whether bacterial factors influence the path of gallstone formation. A total of 382 gallstones were cultured and/or examined using scanning electron microscopy (SEM). Bacteria were tested for bG and slime production. Gallstone composition was determined using infrared spectrography. Ca-palmitate presence documented bacterial PhL production. Groups were identified based upon bacterial factors present: slime and bGPhL (slime/bGPhL), bGPhL only, and slime only. Influence of bacterial stone-forming factors on gallstone composition and morphology was analyzed. Bacteria were present in 75% of pigment, 76% of mixed, and 20% of cholesterol stones. Gallstones with bGPhL producing bacteria contained more pigment (71% vs. 26%, P < .0001). The slime/bGPhL group was associated (79%) with pigment stones, bGPhL was associated (56%) with mixed stones, while slime (or none) only was associated (67%) with cholesterol stones (P < .031, all comparisons). Bacterial properties determined the path of gallstone formation. Bacteria that produced all stone-forming factors promoted pigment stone formation, while those that produced only bGPhL promoted mixed stone formation. Bacteria that only produced slime lacked the ability to generate pigment solids, and consequently were more common in the centers of cholesterol stones. This shows how bacterial characteristics may govern the process of gallstone formation.

Community-acquired bacterial meningitis in adults with cancer or a history of cancer.

PubMed

Costerus, Joost M; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

2016-03-01

To study the incidence, clinical presentation, causative bacteria, and outcome of community-acquired bacterial meningitis in adults with cancer. We evaluated incidence and characteristics of patients with cancer included in a nationwide prospective cohort study of adults with community-acquired meningitis performed in the Netherlands from March 1, 2006, to September 31, 2014. All patients underwent a neurologic examination at hospital discharge, and outcome was graded using the Glasgow Outcome Scale. Active cancer was identified in 68 of 1,351 episodes (5%) and a history of cancer in 87 (6%). The annual incidence of community-acquired bacterial meningitis was 2.71-fold (95% confidence interval [CI] 1.68-4.36, p < 0.001) increased for patients with cancer compared to patients without cancer in 2010, and 3.52-fold (95% CI 2.16-5.73, p < 0.001) in 2013. The clinical presentation of bacterial meningitis in patients with cancer compared to patients without cancer was similar. Patients with active cancer presented with lower leukocyte count in blood (12.1 × 10(9) cells/L vs 17.3 × 10(9) cells/L, p < 0.001) and CSF (670 cells/mm(3) vs 2,567 cells/mm(3), p < 0.001) and were more likely to be infected with Listeria monocytogenes (21% vs 5%, p < 0.001) than patients without cancer. Active cancer was identified as an independent risk factor for unfavorable outcome in bacterial meningitis (odds ratio 1.85, 95% CI 1.09-3.13). One of 8 patients with community-bacterial meningitis was identified to have a history of cancer and cancer was considered active in half of these patients. Patients with active cancer present with lower CSF leukocyte counts, are more likely to be infected with L monocytogenes, and are at high risk of unfavorable outcome. © 2016 American Academy of Neurology.

Different bacterial communities in ectomycorrhizae and surrounding soil

PubMed Central

Vik, Unni; Logares, Ramiro; Blaalid, Rakel; Halvorsen, Rune; Carlsen, Tor; Bakke, Ingrid; Kolstø, Anne-Brit; Økstad, Ole Andreas; Kauserud, Håvard

2013-01-01

Several eukaryotic symbioses have shown to host a rich diversity of prokaryotes that interact with their hosts. Here, we study bacterial communities associated with ectomycorrhizal root systems of Bistorta vivipara compared to bacterial communities in bulk soil using pyrosequencing of 16S rRNA amplicons. A high richness of Operational Taxonomic Units (OTUs) was found in plant roots (3,571 OTUs) and surrounding soil (3,476 OTUs). The community composition differed markedly between these two environments. Actinobacteria, Armatimonadetes, Chloroflexi and OTUs unclassified at phylum level were significantly more abundant in plant roots than in soil. A large proportion of the OTUs, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomycorrhizae. Furthermore, the bacterial communities of the plant roots were spatially structured up to a distance of 60 cm, which may be explained by bacteria using fungal hyphae as a transport vector. The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis. PMID:24326907

Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands.

PubMed

Arroyo, Paula; Sáenz de Miera, Luis E; Ansola, Gemma

2015-02-15

Bacteria are key players in wetland ecosystems, however many essential aspects regarding the ecology of wetland bacterial communities remain unknown. The present study characterizes soil bacterial communities from natural and constructed wetlands through the pyrosequencing of 16S rDNA genes in order to evaluate the influence of wetland variables on bacterial community composition and structure. The results show that the composition of soil bacterial communities was significantly associated with the wetland type (natural or constructed wetland), the type of environment (lagoon, Typha or Salix) and three continuous parameters (SOM, COD and TKN). However, no clear associations were observed with soil pH. Bacterial diversity values were significantly lower in the constructed wetland with the highest inlet nutrient concentrations. The abundances of particular metabolic groups were also related to wetland characteristics. Copyright © 2014 Elsevier B.V. All rights reserved.

Detection and quantification of intracellular bacterial colonies by automated, high-throughput microscopy.

PubMed

Ernstsen, Christina L; Login, Frédéric H; Jensen, Helene H; Nørregaard, Rikke; Møller-Jensen, Jakob; Nejsum, Lene N

2017-08-01

To target bacterial pathogens that invade and proliferate inside host cells, it is necessary to design intervention strategies directed against bacterial attachment, cellular invasion and intracellular proliferation. We present an automated microscopy-based, fast, high-throughput method for analyzing size and number of intracellular bacterial colonies in infected tissue culture cells. Cells are seeded in 48-well plates and infected with a GFP-expressing bacterial pathogen. Following gentamicin treatment to remove extracellular pathogens, cells are fixed and cell nuclei stained. This is followed by automated microscopy and subsequent semi-automated spot detection to determine the number of intracellular bacterial colonies, their size distribution, and the average number per host cell. Multiple 48-well plates can be processed sequentially and the procedure can be completed in one working day. As a model we quantified intracellular bacterial colonies formed by uropathogenic Escherichia coli (UPEC) during infection of human kidney cells (HKC-8). Urinary tract infections caused by UPEC are among the most common bacterial infectious diseases in humans. UPEC can colonize tissues of the urinary tract and is responsible for acute, chronic, and recurrent infections. In the bladder, UPEC can form intracellular quiescent reservoirs, thought to be responsible for recurrent infections. In the kidney, UPEC can colonize renal epithelial cells and pass to the blood stream, either via epithelial cell disruption or transcellular passage, to cause sepsis. Intracellular colonies are known to be clonal, originating from single invading UPEC. In our experimental setup, we found UPEC CFT073 intracellular bacterial colonies to be heterogeneous in size and present in nearly one third of the HKC-8 cells. This high-throughput experimental format substantially reduces experimental time and enables fast screening of the intracellular bacterial load and cellular distribution of multiple bacterial isolates. This will be a powerful experimental tool facilitating the study of bacterial invasion, drug resistance, and the development of new therapeutics. Copyright © 2017 Elsevier B.V. All rights reserved.

Principal coordinate analysis assisted chromatographic analysis of bacterial cell wall collection: A robust classification approach.

PubMed

Kumar, Keshav; Cava, Felipe

2018-04-10

In the present work, Principal coordinate analysis (PCoA) is introduced to develop a robust model to classify the chromatographic data sets of peptidoglycan sample. PcoA captures the heterogeneity present in the data sets by using the dissimilarity matrix as input. Thus, in principle, it can even capture the subtle differences in the bacterial peptidoglycan composition and can provide a more robust and fast approach for classifying the bacterial collection and identifying the novel cell wall targets for further biological and clinical studies. The utility of the proposed approach is successfully demonstrated by analysing the two different kind of bacterial collections. The first set comprised of peptidoglycan sample belonging to different subclasses of Alphaproteobacteria. Whereas, the second set that is relatively more intricate for the chemometric analysis consist of different wild type Vibrio Cholerae and its mutants having subtle differences in their peptidoglycan composition. The present work clearly proposes a useful approach that can classify the chromatographic data sets of chromatographic peptidoglycan samples having subtle differences. Furthermore, present work clearly suggest that PCoA can be a method of choice in any data analysis workflow. Copyright © 2018 Elsevier Inc. All rights reserved.

Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment.

PubMed

Störmer, Rebecca; Wichels, Antje; Gerdts, Gunnar

2013-12-15

The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring. Copyright © 2013 Elsevier Ltd. All rights reserved.

Interactome of E. piscicida and grouper liver proteins reveals strategies of bacterial infection and host immune response.

PubMed

Li, Hui; Zhu, Qing-Feng; Peng, Xuan-Xian; Peng, Bo

2017-01-03

The occurrence of infectious diseases is related to heterogeneous protein interactions between a host and a microbe. Therefore, elucidating the host-pathogen interplay is essential. We previously revealed the protein interactome between Edwardsiella piscicida and fish gill cells, and the present study identified the protein interactome between E. piscicida and E. drummondhayi liver cells. E. drummondhayi liver cells and bacterial pull-down approaches were used to identify E. piscicida outer membrane proteins that bind to liver cells and fish liver cell proteins that interact with bacterial cells, respectively. Eight bacterial proteins and 11 fish proteins were characterized. Heterogeneous protein-protein interactions between these bacterial cells and fish liver cells were investigated through far-Western blotting and co-immunoprecipitation. A network was constructed based on 42 heterogeneous protein-protein interactions between seven bacterial proteins and 10 fish proteins. A comparison of the new interactome with the previously reported interactome showed that four bacterial proteins overlapped, whereas all of the identified fish proteins were new, suggesting a difference between bacterial tricks for evading host immunity and the host strategy for combating bacterial infection. Furthermore, these bacterial proteins were found to regulate the expression of host innate immune-related proteins. These findings indicate that the interactome contributes to bacterial infection and host immunity.

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

NASA Astrophysics Data System (ADS)

Coelho, Francisco J. R. C.; Louvado, António; Domingues, Patrícia M.; Cleary, Daniel F. R.; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R.; Cunha, Ângela; Gomes, Newton C. M.

2016-10-01

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

PubMed Central

Coelho, Francisco J. R. C.; Louvado, António; Domingues, Patrícia M.; Cleary, Daniel F. R.; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R.; Cunha, Ângela; Gomes, Newton C. M.

2016-01-01

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults. PMID:27762306

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz.

PubMed

Coelho, Francisco J R C; Louvado, António; Domingues, Patrícia M; Cleary, Daniel F R; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R; Cunha, Ângela; Gomes, Newton C M

2016-10-20

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.

First report of bacterial community from a Bat Guano using Illumina next-generation sequencing.

PubMed

De Mandal, Surajit; Zothansanga; Panda, Amritha Kumari; Bisht, Satpal Singh; Senthil Kumar, Nachimuthu

2015-06-01

V4 hypervariable region of 16S rDNA was analyzed for identifying the bacterial communities present in Bat Guano from the unexplored cave - Pnahkyndeng, Meghalaya, Northeast India. Metagenome comprised of 585,434 raw Illumina sequences with a 59.59% G+C content. A total of 416,490 preprocessed reads were clustered into 1282 OTUs (operational taxonomical units) comprising of 18 bacterial phyla. The taxonomic profile showed that the guano bacterial community is dominated by Chloroflexi, Actinobacteria and Crenarchaeota which account for 70.73% of all sequence reads and 43.83% of all OTUs. Metagenome sequence data are available at NCBI under the accession no. SRP051094. This study is the first to characterize Bat Guano bacterial community using next-generation sequencing approach.

First report of bacterial community from a Bat Guano using Illumina next-generation sequencing

PubMed Central

De Mandal, Surajit; Zothansanga; Panda, Amritha Kumari; Bisht, Satpal Singh; Senthil Kumar, Nachimuthu

2015-01-01

V4 hypervariable region of 16S rDNA was analyzed for identifying the bacterial communities present in Bat Guano from the unexplored cave — Pnahkyndeng, Meghalaya, Northeast India. Metagenome comprised of 585,434 raw Illumina sequences with a 59.59% G+C content. A total of 416,490 preprocessed reads were clustered into 1282 OTUs (operational taxonomical units) comprising of 18 bacterial phyla. The taxonomic profile showed that the guano bacterial community is dominated by Chloroflexi, Actinobacteria and Crenarchaeota which account for 70.73% of all sequence reads and 43.83% of all OTUs. Metagenome sequence data are available at NCBI under the accession no. SRP051094. This study is the first to characterize Bat Guano bacterial community using next-generation sequencing approach. PMID:26484190

Vulvovaginal symptoms in women with bacterial vaginosis.

PubMed

Klebanoff, Mark A; Schwebke, Jane R; Zhang, Jun; Nansel, Tonja R; Yu, Kai-Fun; Andrews, William W

2004-08-01

A substantial, but highly variable, percentage of women with bacterial vaginosis are said to be asymptomatic. The purpose of this study was to estimate the prevalence of symptoms among women with bacterial vaginosis compared with women without bacterial vaginosis by direct, explicit, and detailed questioning of these women. Women presenting for a routine health care visit at 12 health department clinics in Birmingham, Alabama, were recruited to participate in a longitudinal study of vaginal flora. At the first visit, they underwent a pelvic examination, lower genital tract microbiological evaluation, and an interview that included detailed questions regarding lower genital tract symptoms. The prevalence of symptoms among women with and without bacterial vaginosis (Gram stain score 7 or higher) was compared. Among 2,888 women without gonorrhea, Chlamydia, or trichomonas, 75% of women with and 82% of women without bacterial vaginosis never noted any vaginal odor in the past 6 months (P <.001). The corresponding values were 63% and 65% for never noting vaginal "wetness" (P =.02); 58% and 57% for vaginal discharge (P =.65); 91% and 86% for irritation (P =.004); 88% and 85% for itching (P =.64); and 96% and 94% for dysuria (P =.002), respectively. Cumulatively, 58% of women with bacterial vaginosis noted odor, discharge, and/or wetness in the past 6 months compared with 57% of women without bacterial vaginosis (P =.70). The 2 classic symptoms of bacterial vaginosis discharge and odor are each reported by a minority of women with bacterial vaginosis and are only slightly more prevalent than among women without bacterial vaginosis.

Probing the substrate specificity of the bacterial Pnkp/Hen1 RNA repair system using synthetic RNAs

PubMed Central

Zhang, Can; Chan, Chio Mui; Wang, Pei; Huang, Raven H.

2012-01-01

Ribotoxins cleave essential RNAs involved in protein synthesis as a strategy for cell killing. RNA repair systems exist in nature to counteract the lethal actions of ribotoxins, as first demonstrated by the RNA repair system from bacteriophage T4 25 yr ago. Recently, we found that two bacterial proteins, named Pnkp and Hen1, form a stable complex and are able to repair ribotoxin-cleaved tRNAs in vitro. However, unlike the well-studied T4 RNA repair system, the natural RNA substrates of the bacterial Pnkp/Hen1 RNA repair system are unknown. Here we present comprehensive RNA repair assays with the recombinant Pnkp/Hen1 proteins from Anabaena variabilis using a total of 33 different RNAs as substrates that might mimic various damaged forms of RNAs present in living cells. We found that unlike the RNA repair system from bacteriophage T4, the bacterial Pnkp/Hen1 RNA repair system exhibits broad substrate specificity. Based on the experimental data presented here, a model of preferred RNA substrates of the Pnkp/Hen1 repair system is proposed. PMID:22190744

Challenges of bacterial meningitis case management in low income settings: an experience from Ethiopia.

PubMed

Gudina, Esayas Kebede; Tesfaye, Markos; Adane, Aynishet; Lemma, Kinfe; Shibiru, Tamiru; Pfister, Hans-Walter; Klein, Matthias

2016-07-01

To investigate the current diagnostic and therapeutic strategies used in the care of patients with suspected bacterial meningitis at teaching hospitals in Ethiopia. This was a hospital-based retrospective study conducted at four teaching hospitals in different regions of Ethiopia. Participants were patients aged 14 years and older treated for suspected bacterial meningitis. Presenting complaints, diagnostic strategies used and treatments given were obtained from clinical records. A total of 425 patients were included in the study; 52.7% were men and 83.8% were younger than 50 years. Fever, headache, neck stiffness and impaired consciousness were the most common clinical presentations; 55.5% underwent lumbar puncture. Overall, only 96 (22.6%) patients had cerebrospinal fluid abnormalities compatible with bacterial meningitis. A causative bacterium was identified in only 14 cases. Ceftriaxone was used as the empiric treatment of choice, either alone or in combination with other antibiotics; 17.6% of patients were also given vancomycin. Adjunctive dexamethasone was given to 50.4%. Most patients treated as bacterial meningitis did not receive a proper diagnostic workup. The choice of antibiotic was not tailored to the specific clinical condition of the patient. Such an approach may result in poor treatment outcomes and lead to antibiotic resistance. Management of patients with suspected bacterial meningitis should be supported by analysis of cerebrospinal fluid, and treatment should be tailored to local evidence and current evidence-based recommendations. © 2016 John Wiley & Sons Ltd.

Bacterial meningitis in alcoholic patients: A population-based prospective study.

PubMed

van Veen, Kiril E B; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

2017-04-01

To study clinical features and outcome of community-acquired bacterial meningitis in alcoholic patients. Patients with a history of alcoholism were selected from our nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 2006 to October 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were prospectively collected. Of 1359 included episodes, 88 episodes (6%) occurred in 88 alcoholic patients. Seizures as presenting symptom were present in 18% alcoholic patients, and 23% presented with co-existing pneumonia. Causative organisms were Streptococcus pneumoniae in 76%, Listeria monocytogenes in 8%, and Neisseria meningitidis in 6% of patients. A high rate of systemic complications occurred with respiratory failure in 40% and endocarditis in 9% of patients. Outcome was unfavorable in 58% of alcoholic patients, and 25% died. Alcoholism was associated with unfavorable outcome in a multivariate analysis (OR 1.96; 95% CI 1.12-3.46; P = 0.019), but not with death (OR 0.76; 95% CI 0.35-1.68; P = 0.762). Alcoholic bacterial meningitis patients often have an unfavorable outcome, which appears to result from a high rate of systemic complications, mainly respiratory failure. Seizures are common in alcoholic patients and warrant caution of development of an alcohol withdrawal syndrome. Copyright © 2017. Published by Elsevier Ltd.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments.

PubMed

Rocha, Lidianne L; Colares, Geórgia B; Nogueira, Vanessa L R; Paes, Fernanda A; Melo, Vânia M M

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

PubMed Central

Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors.

PubMed

Chehoud, Christel; Stieh, Daniel J; Bailey, Aubrey G; Laughlin, Alice L; Allen, Shannon A; McCotter, Kerrie L; Sherrill-Mix, Scott A; Hope, Thomas J; Bushman, Frederic D

2017-04-24

We sought to investigate the effects of HIV infection on the vaginal microbiota and associations with treatment and demographic factors. We thus compared vaginal microbiome samples from HIV-infected (HIV+) and HIV-uninfected (HIV-) women collected at two Chicago area hospitals. We studied vaginal microbiome samples from 178 women analyzed longitudinally (n = 324 samples) and collected extensive data on clinical status and demographic factors. We used 16S rRNA gene sequencing to characterize the bacterial lineages present, then UniFrac, Shannon diversity, and other measures to compare community structure with sample metadata. Differences in microbiota measures were modest in the comparison of HIV+ and HIV- samples, in contrast to several previous studies, consistent with effective antiretroviral therapy. Proportions of healthy Lactobacillus species were not higher in HIV- patients overall, but were significantly higher when analyzed within each hospital in isolation. Rates of bacterial vaginosis were higher among African-American women and HIV+ women. Bacterial vaginosis was associated with higher frequency of HIV+. Unexpectedly, African-American women were more likely to switch bacterial vaginosis status between sampling times; switching was not associated with HIV+ status. The influence of HIV infection on the vaginal microbiome was modest for this cohort of well suppressed urban American women, consistent with effective antiretroviral therapy. HIV+ was found to be associated with bacterial vaginosis. Although bacterial vaginosis has previously been associated with HIV transmission, most of the women studied here became HIV+ many years before our test for bacterial vaginosis, thus implicating additional mechanisms linking HIV infection and bacterial vaginosis.

Cerebrospinal fluid ferritin in children with viral and bacterial meningitis.

PubMed

Rezaei, M; Mamishi, S; Mahmoudi, S; Pourakbari, B; Khotaei, G; Daneshjou, K; Hashemi, N

2013-01-01

Despite the fact that the prognosis of bacterial meningitis has been improved by the influence of antibiotics, this disease is still one of the significant causes of morbidity and mortality in children. Rapid differentiation between bacterial and aseptic meningitis, and the need for immediate antibiotic treatment in the former, is crucial in the prognosis of these patients. Ferritin is one of the most sensitive biochemical markers investigated in cerebrospinal fluid (CSF) for the early diagnosis of bacterial meningitis. The present study aims to evaluate the diagnostic capability of CSF ferritin in differentiating bacterial and viral meningitis in the paediatric setting. A cross-sectional study was carried out in the referral Children's Medical Center Hospital, Tehran, during 2008 and 2009. According to the inclusion criteria, CSF samples from 42 patients with suspected meningitis were obtained and divided into two meningitis groups, bacterial (n = 18) and viral (n = 24). Ferritin and other routine determinants (i.e., leucocytes, protein and glucose) were compared between the two groups. Ferritin concentration in the bacterial meningitis group was 106.39 +/- 86.96 ng/dL, which was considerably higher than in the viral meningitis group (10.17 +/- 14.09, P < 0.001). Mean CSF protein concentration and cell count were significantly higher in the bacterial meningitis group and showed a positive correlation with CSF ferritin. In conclusion, this study suggests that CSF ferritin concentration is an accurate test for the early differentiation of bacterial and aseptic meningitis; however, further investigation on a larger cohort of patients is required to confirm this finding.

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.

PubMed

Luo, Gang; Angelidaki, Irini

2014-09-01

The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. Copyright © 2014 Elsevier Ltd. All rights reserved.

Viral-bacterial associations in acute apical abscesses.

PubMed

Ferreira, Dennis C; Rôças, Isabela N; Paiva, Simone S M; Carmo, Flávia L; Cavalcante, Fernanda S; Rosado, Alexandre S; Santos, Kátia R N; Siqueira, José F

2011-08-01

Viral-bacterial and bacterial synergism have been suggested to contribute to the pathogenesis of several human diseases. This study sought to investigate the possible associations between 9 candidate endodontic bacterial pathogens and 9 human viruses in samples from acute apical abscesses. DNA extracts from purulent exudate aspirates of 33 cases of acute apical abscess were surveyed for the presence of 9 selected bacterial species using a 16S ribosomal RNA gene-based nested polymerase chain reaction (PCR) approach. Single or nested PCR assays were used for detection of the human papillomavirus (HPV) and herpesviruses types 1 to 8. Two-thirds of the abscess samples were positive for at least one of the target viruses. Specifically, the most frequently detected viruses were HHV-8 (54.5%); HPV (9%); and varicella zoster virus (VZV), Epstein-Barr virus (EBV), and HHV-6 (6%). Bacterial DNA was present in all cases and the most prevalent bacterial species were Treponema denticola (70%), Tannerella forsythia (67%), Porphyromonas endodontalis (67%), Dialister invisus (61%), and Dialister pneumosintes (57.5%). HHV-8 was positively associated with 7 of the target bacterial species and HPV with 4, but all these associations were weak. Several bacterial pairs showed a moderate positive association. Viral coinfection was found in 6 abscess cases, but no significant viral association could be determined. Findings demonstrated that bacterial and viral DNA occurred concomitantly in two-thirds of the samples from endodontic abscesses. Although this may suggest a role for viruses in the etiology of apical abscesses, the possibility also exists that the presence of viruses in abscess samples is merely a consequence of the bacterially induced disease process. Further studies are necessary to clarify the role of these viral-bacterial interactions, if any, in the pathogenesis of acute apical abscesses. Copyright © 2011 Mosby, Inc. All rights reserved.

Bacterial communities in soil samples from the Mingyong Glacier of southwestern China.

PubMed

Li, Haoyu; Taj, Muhammad Kamran; Ji, Xiuling; Zhang, Qi; Lin, Liangbing; Zhou, Zhimei; Wei, Yunlin

2017-05-01

The present study was an effort to determine the bacterial diversity of soils in Mingyong Glacier located at the Meili Snow Mountains of southwestern China. Mingyong Glacier has different climatic zones within a very narrow area, and bacterial community diversity in this low temperature area remains largely unknown. In this study, soil samples were collected from four different climatic zones: M11A (dry warm valley), M14 (forest), M15 (grass land), and M16 (glacier zones). Phylogenetic analysis based on 16S rRNA gene V6 hypervariable region showed high bacterial abundance in the glacier. The number of Operational Taxonomic Units ranged from 2.24×10 3 to 5.56×10 3 in soil samples. Statistical analysis of 16S rRNA gene clone libraries results showed that bacterial diversity in zones M11A，M14 and M16 are higher than in zone M15. The bacterial community structures are clearly distinguishable, and phylogenetic analysis showed that the predominant phyla were Proteobacteria, Deinococcus-Thermus, Firmicutes, Actinobacteria, and Nitrospirae in Mingyong Glacier. Seventy-nine different orders from four zones have been isolated. Bacterial diversity and distribution of bacterial communities related to the anthropogenic perturbations in zone (M15) were confirmed by diversity index analysis, and the diversity index of other three zones was satisfactory through this analysis software. The results suggest that bacterial diversity and distribution analyses using bacterial 16S rRNA gene V6 hypervariable region were successful, and bacterial communities in this area not only had the same bacterial phyla compared to other glaciers but also had their own rare species.

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

DOE PAGES

Linz, Alexandra M.; Crary, Benjamin C.; Shade, Ashley; ...

2017-06-28

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likelymore » reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “CandidatusOmnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.« less

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

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

Linz, Alexandra M.; Crary, Benjamin C.; Shade, Ashley

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likelymore » reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “CandidatusOmnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.« less

Anti-bacterial activity of some Brazilian medicinal plants.

PubMed

de Lima, Maria Raquel Ferreira; de Souza Luna, Josiane; dos Santos, Aldenir Feitosa; de Andrade, Maria Cristina Caño; Sant'Ana, Antônio Euzébio Goulart; Genet, Jean-Pierre; Marquez, Béatrice; Neuville, Luc; Moreau, Nicole

2006-04-21

Extracts from various organs of 25 plants of Brazilian traditional medicine were assayed with respect to their anti-bacterial activities against Escherichia coli, a susceptible strain of Staphylococcus aureus and two resistant strains of Staphylococcus aureus harbouring the efflux pumps NorA and MsrA. Amongst the 49 extracts studied, 14 presented anti-bacterial activity against Staphylococcus aureus, including the ethanolic extracts from the rhizome of Jatropha elliptica, from the stem barks of Schinus terebinthifolius and Erythrina mulungu, from the stems and leaves of Caesalpinia pyramidalis and Serjania lethalis, and from the stem bark and leaves of Lafoensia pacari. The classes of compounds present in the active extracts were determined as a preliminary step towards their bioactivity-guided separation. No extracts were active against Escherichia coli.

Identification of Mycobacterial Surface Proteins Released into Subcellular Compartments of Infected Macrophages

PubMed Central

Beatty, Wandy L.; Russell, David G.

2000-01-01

Considerable effort has focused on the identification of proteins secreted from Mycobacterium spp. that contribute to the development of protective immunity. Little is known, however, about the release of mycobacterial proteins from the bacterial phagosome and the potential role of these molecules in chronically infected macrophages. In the present study, the release of mycobacterial surface proteins from the bacterial phagosome into subcellular compartments of infected macrophages was analyzed. Mycobacterium bovis BCG was surface labeled with fluorescein-tagged succinimidyl ester, an amine-reactive probe. The fluorescein tag was then used as a marker for the release of bacterial proteins in infected macrophages. Fractionation studies revealed bacterial proteins within subcellular compartments distinct from mycobacteria and mycobacterial phagosomes. To identify these proteins, subcellular fractions free of bacteria were probed with mycobacterium-specific antibodies. The fibronectin attachment protein and proteins of the antigen 85-kDa complex were identified among the mycobacterial proteins released from the bacterial phagosome. PMID:11083824

Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing.

PubMed

Tzanetakis, Giorgos N; Azcarate-Peril, M Andrea; Zachaki, Sophia; Panopoulos, Panos; Kontakiotis, Evangelos G; Madianos, Phoebus N; Divaris, Kimon

2015-08-01

Elucidating the microbial ecology of endodontic infections (EIs) is a necessary step in developing effective intracanal antimicrobials. The aim of the present study was to investigate the bacterial composition of symptomatic and asymptomatic primary and persistent infections in a Greek population using high-throughput sequencing methods. 16S amplicon pyrosequencing of 48 root canal bacterial samples was conducted, and sequencing data were analyzed using an oral microbiome-specific and a generic (Greengenes) database. Bacterial abundance and diversity were examined by EI type (primary or persistent), and statistical analysis was performed by using non-parametric and parametric tests accounting for clustered data. Bacteroidetes was the most abundant phylum in both infection groups. Significant, albeit weak associations of bacterial diversity were found, as measured by UniFrac distances with infection type (analyses of similarity, R = 0.087, P = .005) and symptoms (analyses of similarity, R = 0.055, P = .047). Persistent infections were significantly enriched for Proteobacteria and Tenericutes compared with primary ones; at the genus level, significant differences were noted for 14 taxa, including increased enrichment of persistent infections for Lactobacillus, Streptococcus, and Sphingomonas. More but less abundant phyla were identified using the Greengenes database; among those, Cyanobacteria (0.018%) and Acidobacteria (0.007%) were significantly enriched among persistent infections. Persistent infections showed higher phylogenetic diversity (PD) (asymptomatic: PD = 9.2, standard error [SE] = 1.3; symptomatic: PD = 8.2, SE = 0.7) compared with primary infections (asymptomatic: PD = 5.9, SE = 0.8; symptomatic: PD = 7.4, SE = 1.0). The present study revealed a high bacterial diversity of EI and suggests that persistent infections may have more diverse bacterial communities than primary infections. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Micro-leakage at the implant-abutment interface with different tightening torques in vitro.

PubMed

Silva-Neto, João Paulo da; Prudente, Marcel Santana; Carneiro, Thiago de Almeida Prado Naves; Nóbilo, Mauro Antônio de Arruda; Penatti, Mario Paulo Amante; Neves, Flávio Domingues das

2012-01-01

This study evaluated the microleakage at the implant/abutment interface of external hexagon (eH) implants and abutments with different amounts of bacteria and tightening torques. A bacterial suspension was prepared to inoculate the implants. The first phase of this study used nine EH implants and abutments that were divided into three groups with different amounts of bacterial suspension (n=3): V0.5: 0.5 µL; V1.0: 1.0 µL e V1.5: 1.5 µL, and tightened to the manufacturer's recommended torque. The second phase of this experiment used 27 assemblies that were similar to those used in the first phase. These samples were inoculated with 0.5 µL of bacterial suspension and divided into three groups (n=9). T10: 10 Ncm; T20: 20 Ncm and T32: 32 Ncm. The samples were evaluated according to the turbidity of the broth every 24 hours for 14 days, and the bacteria viability was tested after that period. The statistical evaluation was conducted by Kruskal-Wallis testing (p<.05). During the first phase, groups V1.0 and V1.5 was presented with bacterial contamination in all samples after 24 h. During the second phase, two samples from group T10 and one from T20 presented positive results for bacterial contamination. Different amounts of bacterial solution led to overflow and contamination during the first 24 h of the experiment. The tightening torques did not statistically affect the microleakage in the assemblies. However, the group that was tightened to 32 Ncm torque did not show any bacterial contamination. After 14 days of experimentation, the bacteria were proven to remain viable inside the implant internal cavity.

Micro-leakage at the implant-abutment interface with different tightening torques in vitro

PubMed Central

da SILVA-NETO, João Paulo; PRUDENTE, Marcel Santana; CARNEIRO, Thiago de Almeida Prado Naves; NÓBILO, Mauro Antônio de Arruda; PENATTI, Mario Paulo Amante; NEVES, Flávio Domingues das

2012-01-01

Objectives This study evaluated the microleakage at the implant/abutment interface of external hexagon (EH) implants and abutments with different amounts of bacteria and tightening torques. Material and Methods A bacterial suspension was prepared to inoculate the implants. The first phase of this study used nine EH implants and abutments that were divided into three groups with different amounts of bacterial suspension (n=3): V0.5: 0.5 µL; V1.0: 1.0 µL e V1.5: 1.5 µL, and tightened to the manufacturer's recommended torque. The second phase of this experiment used 27 assemblies that were similar to those used in the first phase. These samples were inoculated with 0.5 µL of bacterial suspension and divided into three groups (n=9). T10: 10 Ncm; T20: 20 Ncm and T32: 32 Ncm. The samples were evaluated according to the turbidity of the broth every 24 hours for 14 days, and the bacteria viability was tested after that period. The statistical evaluation was conducted by Kruskal-Wallis testing (p<.05). Results During the first phase, groups V1.0 and V1.5 was presented with bacterial contamination in all samples after 24 h. During the second phase, two samples from group T10 and one from T20 presented positive results for bacterial contamination. Different amounts of bacterial solution led to overflow and contamination during the first 24 h of the experiment. The tightening torques did not statistically affect the microleakage in the assemblies. However, the group that was tightened to 32 Ncm torque did not show any bacterial contamination. Conclusion After 14 days of experimentation, the bacteria were proven to remain viable inside the implant internal cavity. PMID:23138747

[Features of interaction bacterial strains Micrococcus luteus LBK1 from plants varieties/hybrids cucumber and sweet pepper and with fungus Fusarium oxysporum Scelecht].

PubMed

Parfeniuk, A; Sterlikova, O; Beznosko, I; Krut', V

2014-01-01

The article presents the results of studying the impact of bacterial strain M. luteus LBK1, stimulating the growth and development of plant varieties/hybrids of cucumber and sweet pepper on the intensity of sporulation of the fungus F. oxysporum Scelecht--fusariose rot pathogen.

Dynamics of indigenous bacterial communities associated with crude oil degradation in soil microcosms during nutrient-enhanced bioremediation.

PubMed

Chikere, Chioma B; Surridge, Karen; Okpokwasili, Gideon C; Cloete, Thomas E

2012-03-01

Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The present study therefore demonstrated that the soil investigated harbours hydrocarbon-degrading bacterial populations which can be biostimulated to achieve effective bioremediation of oil-contaminated soil.

The Skin-Mucus Microbial Community of Farmed Atlantic Salmon (Salmo salar)

PubMed Central

Minniti, Giusi; Hagen, Live Heldal; Porcellato, Davide; Jørgensen, Sven Martin; Pope, Phillip B.; Vaaje-Kolstad, Gustav

2017-01-01

The skin of the teleost is a flexible and scaled structure that protects the fish toward the external environment. The outermost surface of the skin is coated with mucus, which is believed to be colonized by a diverse bacterial community (commensal and/or opportunistic). Little is known about such communities and their role in fish welfare. In aquaculture, fish seem to be more susceptible to pathogens compared to wild fish. Indeed common fish farming practices may play important roles in promoting their vulnerability, possibly by causing changes to their microbiomes. In the present study, 16S rRNA gene amplicon sequencing was employed to analyze the composition of the farmed Salmo salar skin-mucus microbiome before and after netting and transfer. The composition of the bacterial community present in the rearing water was also investigated in order to evaluate its correlation with the community present on the fish skin. Our results reveal variability of the skin-mucus microbiome among the biological replicates before fish handling. On the contrary, after fish handling, the skin-mucus community exhibited structural similarity among the biological replicates and significant changes were observed in the bacterial composition compared to the fish analyzed prior to netting and transfer. Limited correlation was revealed between the skin-mucus microbiome and the bacterial community present in the rearing water. Finally, analysis of skin-mucus bacterial biomasses indicated low abundance for some samples, highlighting the need of caution when interpreting community data due to the possible contamination of water-residing bacteria. PMID:29104567

THE OCCURRENCE OF POLYGLYCEROPHOSPHATE AS AN ANTIGENIC COMPONENT OF VARIOUS GRAM-POSITIVE BACTERIAL SPECIES

PubMed Central

McCarty, Maclyn

1959-01-01

A bacterial substance has been described which gives a precipitin reaction with certain antisera to Group A streptococci. The precipitating antigen is present in various Gram-positive bacteria, including most hemolytic streptococci, staphylococci, and aerobic sporulating bacilli. It is not present in any of the Gram-negative species examined or in pneumococci, clostridia, or corynebacteria. Analysis of purified preparations obtained from Group A streptococci indicates that the antigen is a simple polymer of glycerophosphate. The identification has been confirmed by immunochemical studies, including precipitin tests and specific inhibition with synthetic polyglycerophosphates. In addition, the infrared spectra of bacterial and synthetic polyglycerophosphate are shown to be closely similar. Immunochemical analysis suggests that the amount of polyglycerophosphate present in Group A streptococci and staphylococci is approximately 1 per cent of the dry weight of the cells. The cellular localization and function of the polyglycerophosphate have not been established. PMID:13641562

Culturable microbiota of ranched southern bluefin tuna (Thunnus maccoyii Castelnau).

PubMed

Valdenegro-Vega, V; Naeem, S; Carson, J; Bowman, J P; Tejedor del Real, J L; Nowak, B

2013-10-01

The Australian tuna industry is based on the ranching of wild southern bluefin tuna (SBT, Thunnus maccoyii). Within this industry, only opportunistic pathogens have been reported infecting external wounds of fish. This study aimed to identify different culturable bacteria present in three cohorts of SBT and to determine normal bacteria and potential pathogens in isolates from harvest fish and moribund/dead fish. Post-mortem changes in the microbiota were also studied. Moribund/dead showed a greater proportion of members from the family Vibrionaceae than harvested fish; the latter presented mainly non-Vibrio species. In harvested fish spleens, Vibrio splendidus I complex was the most commonly identified group among Vibrio isolates, while most groups from the family Vibrionaceae were isolated from gills. For moribund/dead, Vibrio chagasii and Photobacterium damselae subsp. damselae were common in gill, spleen and kidney samples. Non-Vibrio isolates from gills were characterized using 16S rRNA sequencing as Flavobacteriaceae and classes Gammaproteobacteria and Alphaproteobacteria, mainly from the genera Winogradskyella and Tenacibaculum. Post-mortem changes showed dynamic shifts in bacterial dominance in gills, with Vibrionaceae and non-Vibrio spp. found in similar proportions initially and types related to Pseudoalteromonas ruthenica prevailing after 27 h. Spleen samples showed little bacterial growth until 5 h post-mortem, while various Vibrio-associated species were isolated 27 h post-mortem. Bacterial isolates found include a range of potentially pathogenic bacteria that should be monitored though most of them have yet to be associated with disease in tuna. This study forms a foundation for future research into the bacterial population dynamics under different culture conditions of SBT. An understanding of the bacterial compositions in SBT is necessary to evaluate the effects of some bacterial species on their health. © 2013 The Society for Applied Microbiology.

How conserved are the bacterial communities associated with aphids? A detailed assessment of the Brevicoryne brassicae (Hemiptera: Aphididae) using 16S rDNA.

PubMed

Clark, E L; Daniell, T J; Wishart, J; Hubbard, S F; Karley, A J

2012-12-01

Aphids harbor a community of bacteria that include obligate and facultative endosymbionts belonging to the Enterobacteriaceae along with opportunistic, commensal, or pathogenic bacteria. This study represents the first detailed analysis of the identity and diversity of the bacterial community associated with the cabbage aphid, Brevicoryne brassicae (L.). 16S rDNA sequence analysis revealed that the community of bacteria associated with B. brassicae was diverse, with at least four different bacterial community types detected among aphid lines, collected from widely dispersed sites in Northern Britain. The bacterial sequence types isolated from B. brassicae showed little similarity to any bacterial endosymbionts characterized in insects; instead, they were closely related to free-living extracellular bacterial species that have been isolated from the aphid gut or that are known to be present in the environment, suggesting that they are opportunistic bacteria transmitted between the aphid gut and the environment. To quantify variation in bacterial community between aphid lines, which was driven largely by differences in the proportions of two dominant bacterial orders, the Pseudomonales and the Enterobacteriales, we developed a novel real-time (Taqman) qPCR assay. By improving our knowledge of aphid microbial ecology, and providing novel molecular tools to examine the presence and function of the microbial community, this study forms the basis of further research to explore the influence of the extracellular bacterial community on aphid fitness, pest status, and susceptibility to control by natural enemies.

Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582

NASA Astrophysics Data System (ADS)

Florea, Michael; Reeve, Benjamin; Abbott, James; Freemont, Paul S.; Ellis, Tom

2016-03-01

Bacterial cellulose is a strong, highly pure form of cellulose that is used in a range of applications in industry, consumer goods and medicine. Gluconacetobacter hansenii ATCC 53582 is one of the highest reported bacterial cellulose producing strains and has been used as a model organism in numerous studies of bacterial cellulose production and studies aiming to increased cellulose productivity. Here we present a high-quality draft genome sequence for G. hansenii ATCC 53582 and find that in addition to the previously described cellulose synthase operon, ATCC 53582 contains two additional cellulose synthase operons and several previously undescribed genes associated with cellulose production. In parallel, we also develop optimized protocols and identify plasmid backbones suitable for transformation of ATCC 53582, albeit with low efficiencies. Together, these results provide important information for further studies into cellulose synthesis and for future studies aiming to genetically engineer G. hansenii ATCC 53582 for increased cellulose productivity.

Effect of γ irradiation on poly(vinyl alcohol) and bacterial cellulose composites used as packaging materials

NASA Astrophysics Data System (ADS)

Stoica-Guzun, Anicuta; Stroescu, Marta; Jipa, Iuliana; Dobre, Loredana; Zaharescu, Traian

2013-03-01

The aim of this paper is to present the influence of bacterial cellulose microfibrils and γ-radiation dose on poly(vinyl alcohol) (PVA)-bacterial cellulose (BC) composites. Two composite materials were obtained: the first one from PVA aqueous solution 4% and 5% wet bacterial cellulose and the second from the same PVA solution and 10% wet bacterial cellulose. In terms of PVA/dry BC ratios (w/w) for these films the ratios are 1/0.025 and 1/0.050. The obtained composite materials were characterized by infrared spectroscopy with Fourier transform (FT-IR) and UV-vis spectroscopy in order to evaluate the irradiation effect on their stability. The swelling behavior of the polymeric composites was also studied. The composite materials were compared with a film of pure PVA and a dry BC membrane.

Probing Prokaryotic Social Behaviors with Bacterial “Lobster Traps”

PubMed Central

Connell, Jodi L.; Wessel, Aimee K.; Parsek, Matthew R.; Ellington, Andrew D.; Whiteley, Marvin; Shear, Jason B.

2010-01-01

Bacteria are social organisms that display distinct behaviors/phenotypes when present in groups. These behaviors include the abilities to construct antibiotic-resistant sessile biofilm communities and to communicate with small signaling molecules (quorum sensing [QS]). Our understanding of biofilms and QS arises primarily from in vitro studies of bacterial communities containing large numbers of cells, often greater than 108 bacteria; however, in nature, bacteria often reside in dense clusters (aggregates) consisting of significantly fewer cells. Indeed, bacterial clusters containing 101 to 105 cells are important for transmission of many bacterial pathogens. Here, we describe a versatile strategy for conducting mechanistic studies to interrogate the molecular processes controlling antibiotic resistance and QS-mediated virulence factor production in high-density bacterial clusters. This strategy involves enclosing a single bacterium within three-dimensional picoliter-scale microcavities (referred to as bacterial “lobster traps”) defined by walls that are permeable to nutrients, waste products, and other bioactive small molecules. Within these traps, bacteria divide normally into extremely dense (1012 cells/ml) clonal populations with final population sizes similar to that observed in naturally occurring bacterial clusters. Using these traps, we provide strong evidence that within low-cell-number/high-density bacterial clusters, QS is modulated not only by bacterial density but also by population size and flow rate of the surrounding medium. We also demonstrate that antibiotic resistance develops as cell density increases, with as few as ~150 confined bacteria exhibiting an antibiotic-resistant phenotype similar to biofilm bacteria. Together, these findings provide key insights into clinically relevant phenotypes in low-cell-number/high-density bacterial populations. PMID:21060734

The diagnostic value of CRP, IL-8, PCT, and sTREM-1 in the detection of bacterial infections in pediatric oncology patients with febrile neutropenia.

PubMed

Miedema, Karin G E; de Bont, Eveline S J M; Elferink, Rob F M Oude; van Vliet, Michel J; Nijhuis, Claudi S M Oude; Kamps, Willem A; Tissing, Wim J E

2011-10-01

In this study, we evaluated C-reactive protein (CRP), interleukin (IL)-8, procalcitonin (PCT), and soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) as predictors for bacterial infection in febrile neutropenia, plus their usefulness in febrile neutropenia during chemotherapy-induced gastrointestinal mucositis. Plasma was obtained from pediatric oncology patients at presentation with febrile neutropenia (n = 43) and 24-48 h later (n = 17). The patients were classified as having or not having a bacterial infection. Plasma was also obtained of patients in the absence and in the presence of mucositis (n = 26). At presentation with febrile neutropenia, median IL-8 and PCT levels were significantly increased in patients with a bacterial infection, in contrast to CRP and sTREM-1. IL-8 was the most sensitive marker for the early detection of bacterial infection, in combination with clinical parameters or PCT the sensitivity reached 100%. After 24-48 h, only PCT was significantly elevated during bacterial infection. IL-8 levels were significantly increased during mucositis. Mucositis did not cause considerable changes in PCT levels. IL-8 is the most useful marker for the early detection of bacterial infections, compared with CRP, PCT, and sTREM-1. IL-8 in combination with clinical parameters or PCT might be even more useful. Gastrointestinal mucositis alone does not affect PCT levels, in contrast to IL-8 levels, and therefore, PCT might be more useful for the detection of bacterial infections during mucositis than IL-8.

Raised Proinflammatory Cytokine Production Within Cerebrospinal Fluid Precedes Fever Onset in Patients With Neurosurgery-Associated Bacterial Meningitis.

PubMed

Liu, Zhuo-Hao; Tu, Po-Hsun; Chen, Nan-Yu; Yip, Ping K; Bowes, Amy L; Lee, Cheng-Chi; Chan, She-Hung; Kung, Chua-Chi; Wang, Alvin Yi-Chou; Wu, Chieh-Tsai; Lee, Shih-Tseng

2015-11-01

The objective of the present study was to determine whether selective inflammatory cytokine concentrations within cerebrospinal fluid are useful markers for the differential diagnosis of aseptic and bacterial meningitis within neurosurgical patients. Prospective, open-label, observational, cohort study. Neurosurgical ICU, Chang Gung Memorial Hospital. Thirty-two consecutive neurosurgical patients who had postoperative fever following external ventricular drain insertion for the treatment of brain injury underwent serial cerebrospinal fluid cytokine analysis pre and post fever to determine the value of such markers in ascertaining the differential diagnosis of meningitis. Cerebrospinal fluid samples were collected on the day of fever onset, as well as on day 2 and 4 pre and post fever development. Tumor necrosis factor-α, interleukin-1β, interleukin-6, interleukin-8, transforming growth factor-β, and procalcitonin were subsequently analyzed using enzyme-linked immunosorbent assay analysis techniques. Inflammatory marker levels were compared among febrile aseptic, bacterial, and nonmeningitis patients to determine cerebrospinal fluid inflammatory changes over time. Significant increases in cerebrospinal fluid tumor necrosis factor -α, interleukin-1β, interleukin-6, and interleukin-8 levels were observed within patients with bacterial meningitis at fever onset, which was not evident in aseptic or nonmeningitis patients. Furthermore, significant increases in cerebrospinal fluid tumor necrosis factor-α, interleukin-1β, interleukin-6, and interleukin-8 levels were detected as early as 4 days prior to fever onset within patients with bacterial meningitis when compared with both aseptic and nonmeningitis groups. Interestingly, procalcitonin was only significantly increased in patients with bacterial meningitis on the fourth day post fever. The present study suggests that raised cerebrospinal fluid tumor necrosis factor -α, interleukin-1β, and interleukin-8 in a temporal manner may indicate early bacterial meningitis development in neurosurgical patients, enabling earlier diagnostic certainty and improved patient outcomes.

A comparative study of fungal and bacterial biofiltration treating a VOC mixture.

PubMed

Estrada, José M; Hernández, Sergio; Muñoz, Raúl; Revah, Sergio

2013-04-15

Bacterial biofilters usually exhibit a high microbial diversity and robustness, while fungal biofilters have been claimed to better withstand low moisture contents and pH values, and to be more efficient coping with hydrophobic volatile organic compounds (VOCs). However, there are only few systematic evaluations of both biofiltration technologies. The present study compared fungal and bacterial biofiltration for the treatment of a VOC mixture (propanal, methyl isobutyl ketone-MIBK, toluene and hexanol) under the same operating conditions. Overall, fungal biofiltration supported lower elimination capacities than its bacterial counterpart (27.7 ± 8.9 vs 40.2 ± 5.4 gCm(-3) reactor h(-1)), which exhibited a final pressure drop 60% higher than that of the bacterial biofilter due to mycelial growth. The VOC mineralization ratio was also higher in the bacterial bed (≈ 63% vs ≈ 43%). However, the substrate biodegradation preference order was similar for both biofilters (propanal>hexanol>MIBK>toluene) with propanal partially inhibiting the consumption of the rest of the VOCs. Both systems supported an excellent robustness versus 24h VOC starvation episodes. The implementation of a fungal/bacterial coupled system did not significantly improve the VOC removal performance compared to the individual biofilter performances. Copyright © 2013 Elsevier B.V. All rights reserved.

The epidemiology of bacterial meningitis in Kosovo.

PubMed

Namani, Sadie A; Koci, Remzie A; Qehaja-Buçaj, Emine; Ajazaj-Berisha, Lindita; Mehmeti, Murat

2014-07-14

The purpose of this study was to present the epidemiologic features of bacterial meningitis in the developing country of Kosovo. Data were collected from active surveillance of bacterial meningitis cases treated at the University Clinical Center of Kosovo in the years 2000 (first post-war year) and 2010. Meningitis cases in 2000 compared with 2010 showed a 35.5% decline in incidence (from 4.8 to 3.1 cases per 100,000 population) and a decrease in the case fatality rate from 10% to 5%. In children, there was a lower mortality rate (5% versus 2%) and a lower incidence of neurological complications (13% versus 16%) as compared to adults (32% versus 10% and 16% versus 35%, respectively). Neisseria meningitidis was the most common pathogen of bacterial meningitis in both study periods. Bacterial meningitis was most prevalent in the pediatric population, and showed an increase in the median age, from three years in 2000 to seven years in 2010. A steady number of bacterial meningitis cases in adults throughout last decade (around 20 cases per year) was recorded. During the last decade, gradual changes have been observed in the epidemiology of bacterial meningitis that are unrelated to the introduction of new vaccines, but are partly due to the improvement of living conditions.

Characterizing the bacterial communities in retail stores in the United States.

PubMed

Hoisington, A; Maestre, J P; Kinney, K A; Siegel, J A

2016-12-01

The microorganisms present in retail environments have not been studied in detail despite the fact that these environments represent a potentially important location for exposure. In this study, HVAC filter dust samples in 13 US retail stores were collected and analyzed via pyrosequencing to characterize the indoor bacterial communities and to explore potential relationships between these communities and building and environmental parameters. Although retail stores contained a diverse bacterial community of 788 unique genera, over half of the nearly 118K sequences were attributed to the Proteobacteria phylum. Streptophyta, Bacillus, Corynebacterium, Pseudomonas, and Acinetobacter were the most prevalent genera detected. The recovered indoor airborne microbial community was statistically associated with both human oral and skin microbiota, indicating occupants are important contributors, despite a relatively low occupant density per unit volume in retail stores. Bacteria generally associated with outdoor environments were present in the indoor communities with no obvious association with air exchange rate, even when considering relative abundance. No significant association was observed between the indoor bacterial community recovered and store location, store type, or season. However, predictive functional gene profiling showed significant associations between the indoor community and season. The microbiome recovered from multiple samples collected months apart from the same building varied significantly indicating that caution is warranted when trying to characterize the bacterial community with a single sampling event. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Soft Lithography and Minimally Human Invasive Technique for Rapid Screening of Oral Biofilm Formation on New Microfabricated Dental Material Surfaces

PubMed Central

Alvarez-Escobar, Marta; Hansford, Derek; Monteiro, Fernando J.

2018-01-01

Introduction Microfabrication offers opportunities to study surface concepts focused to reduce bacterial adhesion on implants using human minimally invasive rapid screening (hMIRS). Wide information is available about cell/biomaterial interactions using eukaryotic and prokaryotic cells on surfaces of dental materials with different topographies, but studies using human being are still limited. Objective To evaluate a synergy of microfabrication and hMIRS to study the bacterial adhesion on micropatterned surfaces for dental materials. Materials and Methods Micropatterned and flat surfaces on biomedical PDMS disks were produced by soft lithography. The hMIRS approach was used to evaluate the total oral bacterial adhesion on PDMS surfaces placed in the oral cavity of five volunteers (the study was approved by the University Ethical Committee). After 24 h, the disks were analyzed using MTT assay and light microscopy. Results In the present pilot study, microwell structures were microfabricated on the PDMS surface via soft lithography with a spacing of 5 µm. Overall, bacterial adhesion did not significantly differ between the flat and micropatterned surfaces. However, individual analysis of two subjects showed greater bacterial adhesion on the micropatterned surfaces than on the flat surfaces. Significance Microfabrication and hMIRS might be implemented to study the cell/biomaterial interactions for dental materials. PMID:29593793

Statin Treatment and Mortality in Bacterial Infections – A Systematic Review and Meta-Analysis

PubMed Central

Björkhem-Bergman, Linda; Bergman, Peter; Andersson, Jan; Lindh, Jonatan D.

2010-01-01

Background Several studies have reported improved survival in severe bacterial infections among statin treated patients. In addition, statins have been ascribed beneficial anti-inflammatory effects. The aim of this study was to evaluate the effect of statin-treatment on mortality in patients with bacterial infections, by means of a systematic review and a meta-analysis. Methodology and Principal Findings Studies investigating the association between statin use and mortality in patients with bacterial disease were identified in a systematic literature review and a meta-analysis was performed to calculate the overall odds ratio of mortality in statin users. The literature search identified 947 citations from which 40 relevant studies were extracted. In all, 15 studies comprising 113 910 patients were included in the final analysis. Statin use was associated with a significantly (p<0.0001) reduced mortality in patients suffering from bacterial infections (OR 0.52, 95% CI 0.42–0.66). However, all studies included were of observational design and funnel plot analyses indicated influence by a possible publication bias (Egger's bias test p<0.05). When a precision estimate test was used to adjust for publication bias the effect of statin treatment was no longer significant, with an OR of 0.79 (95% CI 0.58–1.07). Conclusion/Significance According to the meta-analysis of observational studies presented here, patients on statin therapy seem to have a better outcome in bacterial infections. However, the association did not reach statistical significance after adjustment for apparent publication bias. Thus, there is a great need for randomised controlled trials investigating the possible beneficial effect of statins in bacterial infections. PMID:20502712

Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile).

PubMed

Leon, Carla G; Moraga, Ruben; Valenzuela, Cristian; Gugliandolo, Concetta; Lo Giudice, Angelina; Papale, Maria; Vilo, Claudia; Dong, Qunfeng; Smith, Carlos T; Rossello-Mora, Ramon; Yañez, Jorge; Campos, Victor L

2018-01-01

Arsenic (As), a highly toxic metalloid, naturally present in Camarones River (Atacama Desert, Chile) is a great health concern for the local population and authorities. In this study, the taxonomic and functional characterization of bacterial communities associated to metal-rich sediments from three sites of the river (sites M1, M2 and M3), showing different arsenic concentrations, were evaluated using a combination of approaches. Diversity of bacterial communities was evaluated by Illumina sequencing. Strains resistant to arsenic concentrations varying from 0.5 to 100 mM arsenite or arsenate were isolated and the presence of genes coding for enzymes involved in arsenic oxidation (aio) or reduction (arsC) investigated. Bacterial communities showed a moderate diversity which increased as arsenic concentrations decreased along the river. Sequences of the dominant taxonomic groups (abundances ≥1%) present in all three sites were affiliated to Proteobacteria (range 40.3-47.2%), Firmicutes (8.4-24.8%), Acidobacteria (10.4-17.1%), Actinobacteria (5.4-8.1%), Chloroflexi (3.9-7.5%), Planctomycetes (1.2-5.3%), Gemmatimonadetes (1.2-1.5%), and Nitrospirae (1.1-1.2%). Bacterial communities from sites M2 and M3 showed no significant differences in diversity between each other (p = 0.9753) but they were significantly more diverse than M1 (p<0.001 and p<0.001, respectively). Sequences affiliated with Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi and Actinobacteria at M1 accounted for more than 89% of the total classified bacterial sequences present but these phyla were present in lesser proportions in M2 and M3 sites. Strains isolated from the sediment of sample M1, having the greatest arsenic concentration (498 mg kg-1), showed the largest percentages of arsenic oxidation and reduction. Genes aio were more frequently detected in isolates from M1 (54%), whereas arsC genes were present in almost all isolates from all three sediments, suggesting that bacterial communities play an important role in the arsenic biogeochemical cycle and detoxification of arsenical compounds. Overall, results provide further knowledge on the microbial diversity of arsenic contaminated fresh-water sediments.

Molecular identification and quantification of bacteria from endodontic infections using real-time polymerase chain reaction.

PubMed

Blome, B; Braun, A; Sobarzo, V; Jepsen, S

2008-10-01

It was the aim of the present study to evaluate root canal samples for the presence and numbers of specific species as well as for total bacterial load in teeth with chronic apical periodontitis using quantitative real-time polymerase chain reaction (PCR). Forty adult patients with one radiographically documented periapical lesion were included. Twenty teeth presented with primary infections and 20 with secondary infections, requiring retreatment. After removal of necrotic pulp tissue or root canal filling, a first bacterial sample was obtained. Following chemo-mechanical root canal preparation a second sample was taken and a third sample was obtained after 14 days of intracanal dressing with calcium hydroxide. Analysis by real-time PCR enabled the quantification of total bacterial counts and of nine selected species. Root canals with primary infections harbored significantly more bacteria (by total bacterial count) than teeth with secondary infections (P < 0.05). Mean total bacterial count in the retreatment group was 2.1 x 10(6) and was significantly reduced following root canal preparation (3.6 x 10(4)) and intracanal dressing (1.4 x 10(5)). Corresponding values for primary infections were: 4.6 x 10(7), 3.6 x 10(4), and 6.9 x 10(4). The numbers of the selected bacteria and their detection frequency were also significantly reduced. Root canals with primary infections contained a higher bacterial load. Chemo-mechanical root canal preparation reduced bacterial counts by at least 95%.

Investigation of subcellular localization and dynamics of membrane proteins in living bacteria by combining optical micromanipulation and high-resolution microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Barroso Peña, Álvaro; Nieves, Marcos; Teper, Konrad; Wedlich-Soldner, Roland; Denz, Cornelia

2016-09-01

The plasma membrane serves as protective interface between cells and their environment. It also constitutes a hub for selective nutrient uptake and signal transduction. Increasing evidence over the last years indicates that, similar to eukaryotic cells, lateral membrane organization plays an important role in the regulation of prokaryotic signaling pathways. However, the mechanisms underlying this phenomenon are still poorly understood. Spatiotemporal characterization of bacterial signal transduction demands very sensitive high-resolution microscopy techniques due to the low expression levels of most signaling proteins and the small size of bacterial cells. In addition, direct study of subcellular confinement and dynamics of bacterial signaling proteins during the different stages of the signal transduction also requires immobilization in order to avoid cell displacement caused by Brownian motion, local fluid flows and bacterial self-propulsion. In this work we present a novel approach based on the combination of high resolution imaging and optical manipulation that enables the investigation of the distribution and dynamics of proteins at the bacterial plasma membrane. For this purpose, we combine the versatility of holographic optical tweezers (HOT) with the sensitivity and resolution of total internal reflection fluorescence (TIRF) microscopy. Furthermore, we discuss the implementation of microfluidic devices in our integrated HOT+TIRF system for the control of growth conditions of bacterial cells. The capabilities of our workstation provides thus new valuable insights into the fundamental cellular and physical mechanisms underlying the regulation of bacterial signal transduction.

Evaluating the effects of variable water chemistry on bacterial transport during infiltration.

PubMed

Zhang, Haibo; Nordin, Nahjan Amer; Olson, Mira S

2013-07-01

Bacterial infiltration through the subsurface has been studied experimentally under different conditions of interest and is dependent on a variety of physical, chemical and biological factors. However, most bacterial transport studies fail to adequately represent the complex processes occurring in natural systems. Bacteria are frequently detected in stormwater runoff, and may present risk of microbial contamination during stormwater recharge into groundwater. Mixing of stormwater runoff with groundwater during infiltration results in changes in local solution chemistry, which may lead to changes in both bacterial and collector surface properties and subsequent bacterial attachment rates. This study focuses on quantifying changes in bacterial transport behavior under variable solution chemistry, and on comparing the influences of chemical variability and physical variability on bacterial attachment rates. Bacterial attachment rate at the soil-water interface was predicted analytically using a combined rate equation, which varies temporally and spatially with respect to changes in solution chemistry. Two-phase Monte Carlo analysis was conducted and an overall input-output correlation coefficient was calculated to quantitatively describe the importance of physiochemical variation on the estimates of attachment rate. Among physical variables, soil particle size has the highest correlation coefficient, followed by porosity of the soil media, bacterial size and flow velocity. Among chemical variables, ionic strength has the highest correlation coefficient. A semi-reactive microbial transport model was developed within HP1 (HYDRUS1D-PHREEQC) and applied to column transport experiments with constant and variable solution chemistries. Bacterial attachment rates varied from 9.10×10(-3)min(-1) to 3.71×10(-3)min(-1) due to mixing of synthetic stormwater (SSW) with artificial groundwater (AGW), while bacterial attachment remained constant at 9.10×10(-3)min(-1) in a constant solution chemistry (AGW only). The model matched observed bacterial breakthrough curves well. Although limitations exist in the application of a semi-reactive microbial transport model, this method represents one step towards a more realistic model of bacterial transport in complex microbial-water-soil systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterization of a novel high-pH-tolerant laccase-like multicopper oxidase and its sequence diversity in Thioalkalivibrio sp.

PubMed

Ausec, Luka; Črnigoj, Miha; Šnajder, Marko; Ulrih, Nataša Poklar; Mandic-Mulec, Ines

2015-12-01

Laccases are oxidoreductases mostly studied in fungi, while bacterial laccases remain poorly studied despite their high genetic diversity and potential for biotechnological application. Our previous bioinformatic analysis identified alkaliphilic bacterial strains Thioalkalivibrio sp. as potential sources of robust bacterial laccases that would be stable at high pH. In the present work, a gene for a laccase-like enzyme from Thioalkalivibrio sp. ALRh was cloned and expressed as a 6× His-tagged protein in Escherichia coli. The purified enzyme was a pH-tolerant laccase stable in the pH range between 2.1 and 9.9 at 20 °C as shown by intrinsic fluorescence emission spectrometry. It had optimal activities at pH 5.0 and pH 9.5 with the laccase substrates 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 2,6-dimethoxyphenol, respectively. In addition, it could oxidize several other monophenolic compounds and potassium hexacyanoferrate(II) but not tyrosine. It showed highest activity at 50 °C, making it suitable for prolonged incubations at this temperature. The present study shows that Thioalkalivibrio sp. encodes an active, alkaliphilic, and thermo-tolerant laccase and contributes to our understanding of the versatility of bacterial laccase-like multicopper oxidases in general.

Towards in vivo bacterial detection in human lung(Conference Presentation)

NASA Astrophysics Data System (ADS)

Choudhary, Tushar R.; Bradley, Mark; Duncan, Rory R.; Dhaliwal, Kevin

2017-04-01

Antibiotic resistance is a serious global concern. One way to tackle this problem is to develop new and sensitive approaches to diagnose bacterial infections and prevent unnecessary antibiotic use. With recent developments in optical molecular imaging, we are one step closer to in situ rapid detection of bacterial infections. We present here bespoke fluorescent probes for bacterial detection in ex vivo human lung tissue using fluorescence lifetime imaging microscopy (FLIM). Two in-house synthesised bespoke probes were used in this study to detect and differentiate between Gram positive and Gram negative bacterial strain using their fluorescence lifetime in the ex vivo human lung tissue. The average fluorescence lifetime of Gram positive probe (n=12) was 2.40 ± 0.25 ns and Gram negative (n=12) was 6.73 ± 0.49 ns. The human lung tissue (n=12) average fluorescence lifetime value was found to be 3.43 ± 0.19 ns. Furthermore we were also able to distinguish between dead or alive bacteria in ex vivo lung tissue based on difference in their lifetime. We have developped Fibre-FLIM methods to enable clinical translation within the Proteus Project (www.proteus.ac.uk).

Utility of Lumbar Puncture in Children Presenting With Status Epilepticus.

PubMed

Michelson, Kenneth A; Lyons, Todd W; Johnson, Kara B; Nigrovic, Lise E; Harper, Marvin B; Kimia, Amir A

2017-08-01

Because meningitis may trigger seizures, we sought to determine its frequency in children with first-time status epilepticus (SE). We performed a retrospective cross-sectional study of children aged 1 month to 21 years who presented to a single pediatric emergency department between 1995 and 2012 with SE and who had a lumbar puncture (LP) performed as part of the diagnostic evaluation. We defined bacterial meningitis as a cerebrospinal fluid (CSF) culture positive for a bacterial pathogen or CSF pleocytosis (CSF white blood cells ≥10 cells/mm) with a blood culture positive for a bacterial pathogen. We defined viral meningitis or encephalitis using a positive enterovirus or herpes simplex virus polymerase chain reaction test. Among 126 children with SE who had an LP performed, 8 (6%) had CSF pleocytosis. Of these, 5 had received antibiotics before performance of a diagnostic LP. One child in the cohort was proven to have bacterial meningitis (0.8%; 95% confidence interval [CI], 0%-6%). Two other children had enteroviral meningitis (2/13 tested, 15%; 95% CI, 3%-51%), and 1 had a herpes simplex virus infection (1/47, 2%; 95% CI, 0%-15%). Bacterial meningitis is an uncommon cause of SE.

Role of quorum sensing in bacterial infections

PubMed Central

Castillo-Juárez, Israel; Maeda, Toshinari; Mandujano-Tinoco, Edna Ayerim; Tomás, María; Pérez-Eretza, Berenice; García-Contreras, Silvia Julieta; Wood, Thomas K; García-Contreras, Rodolfo

2015-01-01

Quorum sensing (QS) is cell communication that is widely used by bacterial pathogens to coordinate the expression of several collective traits, including the production of multiple virulence factors, biofilm formation, and swarming motility once a population threshold is reached. Several lines of evidence indicate that QS enhances virulence of bacterial pathogens in animal models as well as in human infections; however, its relative importance for bacterial pathogenesis is still incomplete. In this review, we discuss the present evidence from in vitro and in vivo experiments in animal models, as well as from clinical studies, that link QS systems with human infections. We focus on two major QS bacterial models, the opportunistic Gram negative bacteria Pseudomonas aeruginosa and the Gram positive Staphylococcus aureus, which are also two of the main agents responsible of nosocomial and wound infections. In addition, QS communication systems in other bacterial, eukaryotic pathogens, and even immune and cancer cells are also reviewed, and finally, the new approaches proposed to combat bacterial infections by the attenuation of their QS communication systems and virulence are also discussed. PMID:26244150

Temporal and Spatial Dynamics of Sediment Anaerobic Ammonium Oxidation (Anammox) Bacteria in Freshwater Lakes.

PubMed

Yang, Yuyin; Dai, Yu; Li, Ningning; Li, Bingxin; Xie, Shuguang; Liu, Yong

2017-02-01

Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake. Dianchi Lake had greater anammox bacterial abundance than Erhai Lake. In both Dianchi Lake and Erhai Lake, anammox bacteria were much more abundant in summer than in spring. Anammox bacterial community richness, diversity, and structure in these two freshwater lakes were subjected to temporal and spatial variations. Sediment anammox bacterial communities in Dianchi Lake and Erhai Lake were dominated by Candidatus Brocadia and a novel phylotype followed by Candidatus Kuenenia; however, these two lakes had distinct anammox bacterial community structure. In addition, trophic status determined sediment anammox bacterial community structure.

Bacterial Community Succession in Pine-Wood Decomposition.

PubMed

Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Bacterial Community Succession in Pine-Wood Decomposition

PubMed Central

Kielak, Anna M.; Scheublin, Tanja R.; Mendes, Lucas W.; van Veen, Johannes A.; Kuramae, Eiko E.

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities. PMID:26973611

A new method for concentration analysis of bacterial endotoxins in perfluorocarbon

NASA Astrophysics Data System (ADS)

Chen, Dan-Dan; Feng, Xiao-Ming; Wang, Chun-Ren; Huang, Qing-Quan; Yang, Zhao-Peng; Meng, Qing-Yuan

2014-12-01

This communication demonstrates the feasibility of the gel-clot method for the analysis of bacterial endotoxins in water extracts of perfluorocarbon which is a water insoluble liquid medical device. Perfluorocarbon (10 mL) was shaken with 10mL water for 15 min at 2000 r/min and the endotoxin present was extracted to the aqueous phase without interference inhibition/enhancement of the product and the recovery of endotoxin added to perfluorocarbon was determined. A validation study confirmed that endotoxins presented in perfluorocarbon pass over into the aqueous phase at concentrations of 20, 10 and 5 EU/mL with recoveries from 86.8% to 96.8%. Therefore, the gel-clot test is suitable for detecting bacterial endotoxins in perfluorocarbon which is a water insoluble medical device.

Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis

PubMed Central

Tyx, Robert E.; Stanfill, Stephen B.; Keong, Lisa M.; Rivera, Angel J.; Satten, Glen A.; Watson, Clifford H.

2016-01-01

The bacterial communities present in smokeless tobacco (ST) products have not previously reported. In this study, we used Next Generation Sequencing to study the bacteria present in U.S.-made dry snuff, moist snuff and Sudanese toombak. Sample diversity and taxonomic abundances were investigated in these products. A total of 33 bacterial families from four phyla, Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, were identified. U.S.-produced dry snuff products contained a diverse distribution of all four phyla. Moist snuff products were dominated by Firmicutes. Toombak samples contained mainly Actinobacteria and Firmicutes (Aerococcaceae, Enterococcaceae, and Staphylococcaceae). The program PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to impute the prevalence of genes encoding selected bacterial toxins, antibiotic resistance genes and other pro-inflammatory molecules. PICRUSt also predicted the presence of specific nitrate reductase genes, whose products can contribute to the formation of carcinogenic nitrosamines. Characterization of microbial community abundances and their associated genomes gives us an indication of the presence or absence of pathways of interest and can be used as a foundation for further investigation into the unique microbiological and chemical environments of smokeless tobacco products. PMID:26784944

Numerical studies of bacterial-carpet microflows

NASA Astrophysics Data System (ADS)

Huber, Greg; Tillberg, Dan; Powers, Thomas R.

2004-03-01

Bacterial carpets are arrays of motile bacteria attached to two-dimensional surfaces. Improved understanding of carpet flows is important in the design of microfluidic devices and transport systems powered by bacterial flagellar motion. In recent experiments by the group of Howard Berg, cells of swarming S. marcescens are stuck to the surface, with most of their flagella free to rotate in the fluid. These studies show modified transport and greatly enhanced diffusion near the active carpet surface. We present theoretical models of the flagella-driven flow, bridging the nano- to the macro-scale, simulate the diffusion and advection of passive tracers, and compare the numerical results with the tracking data of Berg et al.

Microbial analysis in primary and persistent endodontic infections by using pyrosequencing.

PubMed

Hong, Bo-Young; Lee, Tae-Kwon; Lim, Sang-Min; Chang, Seok Woo; Park, Joonhong; Han, Seung Hyun; Zhu, Qiang; Safavi, Kamran E; Fouad, Ashraf F; Kum, Kee Yeon

2013-09-01

The aim of this study was to investigate the bacterial community profile of intracanal microbiota in primary and persistent endodontic infections associated with asymptomatic chronic apical periodontitis by using GS-FLX Titanium pyrosequencing. The null hypothesis was that there is no difference in diversity of overall bacterial community profiles between primary and persistent infections. Pyrosequencing analysis from 10 untreated and 8 root-filled samples was conducted. Analysis from 18 samples yielded total of 124,767 16S rRNA gene sequences (with a mean of 6932 reads per sample) that were taxonomically assigned into 803 operational taxonomic units (3% distinction), 148 genera, and 10 phyla including unclassified. Bacteroidetes was the most abundant phylum in both primary and persistent infections. There were no significant differences in bacterial diversity between the 2 infection groups (P > .05). The bacterial community profile that was based on dendrogram showed that bacterial population in both infections was not significantly different in their structure and composition (P > .05). The present pyrosequencing study demonstrates that persistent infections have as diverse bacterial community as primary infections. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Is Drosophila-microbe association species-specific or region specific? A study undertaken involving six Indian Drosophila species.

PubMed

Singhal, Kopal; Khanna, Radhika; Mohanty, Sujata

2017-06-01

The present work aims to identify the microbial diversity associated with six Indian Drosophila species using next generation sequencing (NGS) technology and to discover the nature of their distribution across species and eco-geographic regions. Whole fly gDNA of six Drosophila species were used to generate sequences in an Illumina platform using NGS technology. De novo based assembled raw reads were blasted against the NR database of NCBI using BLASTn for identification of their bacterial loads. We have tried to include Drosophila species from different taxonomical groups and subgroups and from three different eco-climatic regions India; four species belong to Central India, while the rest two, D. melanogaster and D. ananassae, belong to West and South India to determine both their species-wise and region-wide distribution. We detected the presence of 33 bacterial genera across all six study species, predominated by the class Proteobacteria. Amongst all, D. melanogaster was found to be the most diverse by carrying around 85% of the bacterial diversity. Our findings infer both species-specific and environment-specific nature of the bacterial species inhabiting the Drosophila host. Though the present results are consistent with most of the earlier studies, they also remain incoherent with some. The present study outcome on the host-bacteria association and their species specific adaptation may provide some insight to understand the host-microbial interactions and the phenotypic implications of microbes on the host physiology. The knowledge gained may be importantly applied into the recent insect and pest population control strategy going to implement through gut microflora in India and abroad.

The diagnostic value of cytokine and nitric oxide concentrations in cerebrospinal fluid for the differential diagnosis of meningitis.

PubMed

Bociąga-Jasik, M; Garlicki, A; Cieśla, A; Kalinowska-Nowak, A; Sobczyk-Krupiarz, I; Mach, T

2012-06-01

In several cases of meningitis routinely used diagnostic procedures are unable to identify the cause of this disease. The objective of the present study was to determine whether proinflammatory cytokine (tumour necrosis factor (TNF-α), interleukin-1β (IL-1β), interleukin-8 (IL-8)) and nitric oxide (NO) concentrations in the CSF are useful markers for the differential diagnosis of meningitis. Sixty-seven patients (42 patients with bacterial meningitis and 25 patients with viral meningitis) were included in the present study. In the investigated group, the TNF-α, IL-1β and IL-8 concentrations in the CSF samples collected on the day of admission were assessed. Furthermore, the NO concentrations were assessed in 23 patients. The results revealed that the measurement of proinflammatory cytokines in CSF can aid in a differential diagnosis. In particular, a high concentration of TNF-α may be a sensitive and specific marker of a bacterial aetiology of the neuroinfection. In the present study, TNF-α concentrations greater than 75.8 pg/ml differentiated between bacterial and viral meningitis with 100% sensitivity and specificity. The NO concentration in the CSF was also significantly greater in patients with bacterial meningitis than in those with viral meningitis. The assessment of TNF-α, IL-1β and IL-8 concentrations in the CSF is useful in the differential diagnosis of neuroinfection. Because many factors may influence NO production in the central nervous system (CNS), it is not clear whether NO values can be used for the differential diagnosis of meningitis, and further studies are required.

[Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)].

PubMed

Zakhia, Frédéric; de Lajudie, Philippe

2006-03-01

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.

Impact of disinfection on drinking water biofilm bacterial community.

PubMed

Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-11-01

Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination. Copyright © 2015. Published by Elsevier B.V.

Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan.

PubMed

Tandon, Kshitij; Yang, Shan-Hua; Wan, Min-Tao; Yang, Chia-Chin; Baatar, Bayanmunkh; Chiu, Chih-Yu; Tsai, Jeng-Wei; Liu, Wen-Cheng; Tang, Sen-Lin

2018-04-21

Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes-located 21 km apart and with disparate trophic characteristics-and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time. However, airborne bacterial communities were diverse and displayed spatial and temporal variance. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were dominant in both lakes, with different relative abundances between lakes, and Parcubacteria (OD1) was dominant in air samples for all sampling times, except two. We also identified certain shared taxa between lake water and the air above it. The results obtained on these communities in the present study provide putative candidates to study how airborne communities shape lake water bacterial compositions and vice versa.

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

PubMed Central

Wright, Justin; Kirchner, Veronica; Bernard, William; Ulrich, Nikea; McLimans, Christopher; Campa, Maria F.; Hazen, Terry; Macbeth, Tamzen; Marabello, David; McDermott, Jacob; Mackelprang, Rachel; Roth, Kimberly; Lamendella, Regina

2017-01-01

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios. PMID:29213257

Characteristics of airborne bacteria in Mumbai urban environment.

PubMed

Gangamma, S

2014-08-01

Components of biological origin constitute small but a significant proportion of the ambient airborne particulate matter (PM). However, their diversity and role in proinflammatory responses of PM are not well understood. The present study characterizes airborne bacterial species diversity in Mumbai City and elucidates the role of bacterial endotoxin in PM induced proinflammatory response in ex vivo. Airborne bacteria and endotoxin samples were collected during April-May 2010 in Mumbai using six stage microbial impactor and biosampler. The culturable bacterial species concentration was measured and factors influencing the composition were identified by principal component analysis (PCA). The biosampler samples were used to stimulate immune cells in whole blood assay. A total of 28 species belonging to 17 genera were identified. Gram positive and spore forming groups of bacteria dominated the airborne culturable bacterial concentration. The study indicated the dominance of spore forming and human or animal flora derived pathogenic/opportunistic bacteria in the ambient air environment. Pathogenic and opportunistic species of bacteria were also present in the samples. TNF-α induction by PM was reduced (35%) by polymyxin B pretreatment and this result was corroborated with the results of blocking endotoxin receptor cluster differentiation (CD14). The study highlights the importance of airborne biological particles and suggests need of further studies on biological characterization of ambient PM. Copyright © 2014 Elsevier B.V. All rights reserved.

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety.

PubMed

Li, Qi; Yu, Shuili; Li, Lei; Liu, Guicai; Gu, Zhengyang; Liu, Minmin; Liu, Zhiyuan; Ye, Yubing; Xia, Qing; Ren, Liumo

2017-01-01

Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health.

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety

PubMed Central

Li, Qi; Yu, Shuili; Li, Lei; Liu, Guicai; Gu, Zhengyang; Liu, Minmin; Liu, Zhiyuan; Ye, Yubing; Xia, Qing; Ren, Liumo

2017-01-01

Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health. PMID:29312177

The antimicrobial effectiveness of 25% propolis extract in root canal irrigation of primary teeth.

PubMed

Verma, Manjesh Kumar; Pandey, Ramesh Kumar; Khanna, Richa; Agarwal, Jyotsna

2014-01-01

The choice of irrigating solution used in root canals of primary teeth is complicated by their complex morphology and paucity of associated literature. Propolis is a natural product that has gained interest in this context due to its antibacterial effectiveness against several endodontic pathogens. The present study was undertaken to assess the potential of water-soluble 25% propolis extract against microorganisms present in root canals of primary teeth during endodontic procedures. The child patients in the age group of 4-7 years with radiographic evidence of carious pulp exposure were included in the study. Definitive selection was done after gaining access into the pulp chamber and root canals of the selected teeth. The clinical and radiographic evidence of pathosis was ruled out for inclusion in the study. The selected teeth were divided into two groups randomly. In Group A 0.9% isotonic saline and in Group B 25% extract water-soluble propolis were used as irrigating solution, respectively. The bacterial samples were collected both pre- and post-irrigation and were transferred for microbial assay. STAISTISTICAL ANALYSIS: Wilcoxon matched signed rank test was used to compare the pre-and post-irrigation bacterial counts. Mann-Whitney test was used to compare the mean change (pre-post) in bacterial colony counts of groups in the study. Antimicrobial effectiveness of 25% water-soluble extract of propolis in the root canals of primary teeth was confirmed in the present study. The reduction in the mean bacterial colony counts of all the isolated bacteria was noticed higher in Group B than Group A. The results of the present study have confirmed that the antibacterial effectiveness of water-soluble extract of propolis in the root canals of primary teeth in vivo. Considering the low toxicity concerns and antibacterial effectiveness, water-soluble extract of 25% propolis can be advocated as a root canal irrigant in endodontic treatment of primary teeth.

Vaginal toxic shock reaction triggering desquamative inflammatory vaginitis.

PubMed

Pereira, Nigel; Edlind, Thomas D; Schlievert, Patrick M; Nyirjesy, Paul

2013-01-01

The study aimed to report 2 cases of desquamative inflammatory vaginitis associated with toxic shock syndrome toxin 1 (TSST-1)-producing Staphylococcus aureus strains. Case report of 2 patients, 1 with an acute and 1 with a chronic presentation, diagnosed with desquamative inflammatory vaginitis on the basis of clinical findings and wet mount microscopy. Pretreatment and posttreatment vaginal bacterial and yeast cultures were obtained. Pretreatment vaginal bacterial cultures from both patients grew TSST-1-producing S. aureus. Subsequent vaginal bacterial culture results after oral antibiotic therapy were negative. Desquamative inflammatory vaginitis may be triggered through TSST-1-mediated vaginal toxic shock reaction.

Bacterial enzymes involved in lignin degradation.

PubMed

de Gonzalo, Gonzalo; Colpa, Dana I; Habib, Mohamed H M; Fraaije, Marco W

2016-10-20

Lignin forms a large part of plant biomass. It is a highly heterogeneous polymer of 4-hydroxyphenylpropanoid units and is embedded within polysaccharide polymers forming lignocellulose. Lignin provides strength and rigidity to plants and is rather resilient towards degradation. To improve the (bio)processing of lignocellulosic feedstocks, more effective degradation methods of lignin are in demand. Nature has found ways to fully degrade lignin through the production of dedicated ligninolytic enzyme systems. While such enzymes have been well thoroughly studied for ligninolytic fungi, only in recent years biochemical studies on bacterial enzymes capable of lignin modification have intensified. This has revealed several types of enzymes available to bacteria that enable them to act on lignin. Two major classes of bacterial lignin-modifying enzymes are DyP-type peroxidases and laccases. Yet, recently also several other bacterial enzymes have been discovered that seem to play a role in lignin modifications. In the present review, we provide an overview of recent advances in the identification and use of bacterial enzymes acting on lignin or lignin-derived products. Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.

Individual based simulations of bacterial growth on agar plates

NASA Astrophysics Data System (ADS)

Ginovart, M.; López, D.; Valls, J.; Silbert, M.

2002-03-01

The individual based simulator, INDividual DIScrete SIMulations (INDISIM) has been used to study the behaviour of the growth of bacterial colonies on a finite dish. The simulations reproduce the qualitative trends of pattern formation that appear during the growth of Bacillus subtilis on an agar plate under different initial conditions of nutrient peptone concentration, the amount of agar on the plate, and the temperature. The simulations are carried out by imposing closed boundary conditions on a square lattice divided into square spatial cells. The simulator studies the temporal evolution of the bacterial population possible by setting rules of behaviour for each bacterium, such as its uptake, metabolism and reproduction, as well as rules for the medium in which the bacterial cells grow, such as concentration of nutrient particles and their diffusion. The determining factors that characterize the structure of the bacterial colony patterns in the presents simulations, are the initial concentrations of nutrient particles, that mimic the amount of peptone in the experiments, and the set of values for the microscopic diffusion parameter related, in the experiments, to the amount of the agar medium.

Bioremediation and reclamation of soil contaminated with petroleum oil hydrocarbons by exogenously seeded bacterial consortium: a pilot-scale study.

PubMed

Mukherjee, Ashis K; Bordoloi, Naba K

2011-03-01

Spillage of petroleum hydrocarbons causes significant environmental pollution. Bioremediation is an effective process to remediate petroleum oil contaminant from the ecosystem. The aim of the present study was to reclaim a petroleum oil-contaminated soil which was unsuitable for the cultivation of crop plants by using petroleum oil hydrocarbon-degrading microbial consortium. Bacterial consortium consisting of Bacillus subtilis DM-04 and Pseudomonas aeruginosa M and NM strains were seeded to 20% (v/w) petroleum oil-contaminated soil, and bioremediation experiment was carried out for 180 days under laboratory condition. The kinetics of hydrocarbon degradation was analyzed using biochemical and gas chromatographic (GC) techniques. The ecotoxicity of the elutriates obtained from petroleum oil-contaminated soil before and post-treatment with microbial consortium was tested on germination and growth of Bengal gram (Cicer aretinum) and green gram (Phaseolus mungo) seeds. Bacterial consortium showed a significant reduction in total petroleum hydrocarbon level in contaminated soil (76% degradation) as compared to the control soil (3.6% degradation) 180 days post-inoculation. The GC analysis confirmed that bacterial consortium was more effective in degrading the alkane fraction compared to aromatic fraction of crude petroleum oil hydrocarbons in soil. The nitrogen, sulfur, and oxygen compounds fraction was least degraded. The reclaimed soil supported the germination and growth of crop plants (C. aretinum and P. mungo). In contrast, seeds could not be germinated in petroleum oil-contaminated soil. The present study reinforces the application of bacterial consortium rather than individual bacterium for the effective bioremediation and reclamation of soil contaminated with petroleum oil.

Endosymbiont Dominated Bacterial Communities in a Dwarf Spider

PubMed Central

Vanthournout, Bram; Hendrickx, Frederik

2015-01-01

The microbial community of spiders is little known, with previous studies focussing primarily on the medical importance of spiders as vectors of pathogenic bacteria and on the screening of known cytoplasmic endosymbiont bacteria. These screening studies have been performed by means of specific primers that only amplify a selective set of endosymbionts, hampering the detection of unreported species in spiders. In order to have a more complete overview of the bacterial species that can be present in spiders, we applied a combination of a cloning assay, DGGE profiling and high-throughput sequencing on multiple individuals of the dwarf spider Oedothorax gibbosus. This revealed a co-infection of at least three known (Wolbachia, Rickettsia and Cardinium) and the detection of a previously unreported endosymbiont bacterium (Rhabdochlamydia) in spiders. 16S rRNA gene sequences of Rhabdochlamydia matched closely with those of Candidatus R. porcellionis, which is currently only reported as a pathogen from a woodlouse and with Candidatus R. crassificans reported from a cockroach. Remarkably, this bacterium appears to present in very high proportions in one of the two populations only, with all investigated females being infected. We also recovered Acinetobacter in high abundance in one individual. In total, more than 99% of approximately 4.5M high-throughput sequencing reads were restricted to these five bacterial species. In contrast to previously reported screening studies of terrestrial arthropods, our results suggest that the bacterial communities in this spider species are dominated by, or even restricted to endosymbiont bacteria. Given the high prevalence of endosymbiont species in spiders, this bacterial community pattern could be widespread in the Araneae order. PMID:25706947

Bridging the knowledge gap: from microbiome composition to function.

PubMed

Faith, Jeremiah J

2015-03-01

Despite the wealth of metagenomic sequencing data, the functions of most bacterial genes from the mammalian microbiota have remained poorly understood. In their recent study (Yaung et al 2015), Wang, Gerber, and colleagues present a platform which allows functional mining of bacterial genomes for genes that contribute to fitness in vivo and holds great potential for forward engineering microbes with enhanced colonization abilities in the microbiota.

Bacterial vaginosis in threatened preterm, preterm and term labour.

PubMed

Chawanpaiboon, Saifon; Pimol, Kanjana

2010-12-01

To present the prevalence of bacterial vaginosis in threatened preterm, preterm, and term labor and results after treatment. Forty-four, 50, and 56 pregnant women with threatened preterm, preterm, and term labor respectively were participated. Bacterial vaginosis was diagnosed by Amsel's criteria. Treatment by metronidazole or clindamycin was used. A case record form recorded maternal age, obstetric history, gestational age at admission and delivery, examination data, the route of delivery, and the newborn birth weight and conditions. The patients in threatened preterm labor group had significantly positive bacterial vaginosis when compared to those in the term labor group. Prevalence of bacterial vaginosis in threatened preterm, preterm, and term labor were presented The prevalence of bacterial vaginosis in both preterm labor groups was higher than in the term labor group.

Putative bacterial volatile-mediated growth in soybean (Glycine max L. Merrill) and expression of induced proteins under salt stress.

PubMed

Vaishnav, A; Kumari, S; Jain, S; Varma, A; Choudhary, D K

2015-08-01

Plant root-associated rhizobacteria elicit plant immunity referred to as induced systemic tolerance (IST) against multiple abiotic stresses. Among multibacterial determinants involved in IST, the induction of IST and promotion of growth by putative bacterial volatile compounds (VOCs) is reported in the present study. To characterize plant proteins induced by putative bacterial VOCs, proteomic analysis was performed by MALDI-MS/MS after exposure of soybean seedlings to a new strain of plant growth promoting rhizobacteria (PGPR) Pseudomonas simiae strain AU. Furthermore, expression analysis by Western blotting confirmed that the vegetative storage protein (VSP), gamma-glutamyl hydrolase (GGH) and RuBisCo large chain proteins were significantly up-regulated by the exposure to AU strain and played a major role in IST. VSP has preponderant roles in N accumulation and mobilization, acid phosphatase activity and Na(+) homeostasis to sustain plant growth under stress condition. More interestingly, plant exposure to the bacterial strain significantly reduced Na(+) and enhanced K(+) and P content in root of soybean seedlings under salt stress. In addition, high accumulation of proline and chlorophyll content also provided evidence of protection against osmotic stress during the elicitation of IST by bacterial exposure. The present study reported for the first time that Ps. simiae produces a putative volatile blend that can enhance soybean seedling growth and elicit IST against 100 mmol l(-1) NaCl stress condition. The identification of such differentially expressed proteins provide new targets for future studies that will allow assessment of their physiological roles and significance in the response of glycophytes to stresses. Further work should uncover more about the chemical side of VOC compounds and a detailed study about their molecular mechanism responsible for plant growth. © 2015 The Society for Applied Microbiology.

Characterization of small microfluidic valves for studies of mechanical properties of bacteria

DOE PAGES

Yang, Da; Greer, Clayton M.; Jones, Branndon P.; ...

2015-09-02

Lab-on-a-chip platforms present many new opportunities to study bacterial cells and cellular assemblies. Here, the authors describe a new platform that allows us to apply uniaxial stress to individual bacterial cells while observing the cell and its subcellular assemblies using a high resolution optical microscope. The microfluidic chip consists of arrays of miniature pressure actuated valves. By placing a bacterium under one of such valves and partially closing the valve by externally applied pressure, the cell can be deformed. Although large pressure actuated valves used in integrated fluidic circuits have been extensively studied previously, here the authors downsize those microfluidicmore » valves and use flow channels with rectangular cross-sections to maintain the bacteria in contact with cell culture medium during the experiments. The closure of these valves has not been characterized before. First, these valves are modeled using finite element analysis, and then compared the modeling results with the actual closing profiles of the valves, which is determined from absorption measurements. The measurements and modeling show with good agreement that the deflection of valves is a linear function of externally applied pressure and the deflection scales proportionally to the width of the flow channel. In addition to characterizing the valve, the authors show at a proof-of-principle level that it can be used to deform a bacterial cell at considerable magnitude. They found the largest deformations in 5 μm wide channels where the bacterial width and length increase by 1.6 and 1.25 times, respectively. Narrower and broader channels are less optimal for these studies. Finally, the platform presents a promising approach to probe, in a quantitative and systematic way, the mechanical properties of not only bacterial cells but possibly also yeast and other single-celled organisms.« less

Effect of NaCl induced floc disruption on biological disintegration of sludge for enhanced biogas production.

PubMed

Kavitha, S; Kaliappan, S; Adish Kumar, S; Yeom, Ick Tae; Rajesh Banu, J

2015-09-01

In the present study, the influence of NaCl mediated bacterial disintegration of waste activated sludge (WAS) was evaluated in terms of disintegration and biodegradability of WAS. Floc disruption was efficient at 0.03 g/g SS of NaCl, promoting the shifts of extracellular proteins and carbohydrates from inner layers to extractable--soluble layers (90 mg/L), respectively. Outcomes of sludge disintegration reveal that the maximum solubilization achieved was found to be 23%, respectively. The model elucidating the parameter evaluation, explicates that floc disrupted--bacterially disintegrated sludge (S3) showed superior biodegradability of about 0.23 (gCOD/gCOD) than the bacterially disintegrated (S2) and control (S3) sludges of about 0.13 (gCOD/gCOD) and 0.05 (gCOD/gCOD), respectively. Cost evaluation of the present study affords net profits of approximately 2.5 USD and -21.5 USD in S3 and S2 sludge. Copyright © 2015 Elsevier Ltd. All rights reserved.

Application of a Human Fecal Marker Assay to Diverse Coastal Environments in California and Hawaii

NASA Astrophysics Data System (ADS)

Layton, B.; Boehm, A.

2007-05-01

Bacterial pollution at beaches is a growing problem of increasing national concern. Currently, the EPA uses Enterococcus as one measure of water quality for recreational contact. Recent work has suggested that rather than indicating anthropogenic pollution, enterococci may be indigenous to the environment. A human-specific gene marker for Enterococcus faecium (known as esp) was recently proposed as a molecular test for bacterial contamination of human origin. The present study applied the esp gene assay to a variety of coastal environments in California and Hawaii, including groundwater, sand, freshwater creeks, estuaries, and the surf zone. Results indicate that enterococci of human origin are present in many of these environments, suggesting that at least a portion of the bacterial pollution at these sites is a result of anthropogenic inputs rather than autochthonous microbial populations.

Chronic bacterial prostatitis in men with spinal cord injury.

PubMed

Krebs, Jörg; Bartel, Peter; Pannek, Jürgen

2014-12-01

Recurrent urinary tract infections (UTI) are a major problem affecting spinal cord injury (SCI) patients and may stem from chronic bacterial prostatitis. We have therefore investigated the presence of chronic bacterial prostatitis and its role in the development of recurrent symptomatic UTI in SCI men. This study is a prospective cross-sectional investigation of bacterial prostatitis in SCI men in a single SCI rehabilitation center. In 50 men with chronic SCI presenting for a routine urologic examination, urine samples before and after prostate massage were taken for microbiologic investigation and white blood cell counting. Furthermore, patient characteristics, bladder diary details, and the annual rate of symptomatic UTI were collected retrospectively. No participant reported current symptoms of UTI or prostatitis. In most men (39/50, 78 %), the microbiologic analysis of the post-massage urine sample revealed growth of pathogenic bacteria. The majority of these men (32/39, 82 %) also presented with mostly (27/39, 69 %) the same pathogenic bacteria in the pre-massage sample. There was no significant (p = 0.48) difference in the number of symptomatic UTI in men with a positive post-massage culture compared with those with a negative culture. No significant (p = 0.67) difference in the frequency distribution of positive versus negative post-massage cultures was detected between men with recurrent and sporadic UTI. Most SCI men are affected by asymptomatic bacterial prostatitis; however, bacterial prostatitis does not play a major role in the development of recurrent UTI. The indication for antibiotic treatment of chronic bacterial prostatitis in asymptomatic SCI men with recurrent UTI is questionable.

Bacterial meningitis in patients with HIV: A population-based prospective study.

PubMed

van Veen, Kiril E B; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

2016-03-01

We studied occurrence, disease course, and prognosis of community-acquired bacterial meningitis in HIV-infected adults in the Netherlands. We performed a nationwide, prospective cohort study. Patients over 16 years old with bacterial meningitis were included. Data on patient history, symptoms and signs on admission, laboratory findings, radiologic examination, treatment, and outcome were collected prospectively. For HIV-positive patients additional information was collected retrospectively. From March 2006 to December 2013, 1354 episodes of community-acquired meningitis were included in the cohort. Thirteen patients were HIV-infected (1.0%). The annual incidence of bacterial meningitis was 8.3-fold higher (95%CI 4.6-15.1, P < 0.001) among HIV-infected patients as compared to the general population (10.79 [95%CI 5.97-19.48] vs 1.29 [95%CI 1.22-1.37] per 100.000 patients per year). Predisposing factors (other than HIV), clinical symptoms and signs, ancillary investigations, causative organisms and outcome were comparable between HIV-infected and patients without HIV infection. HIV-infected patients in the Netherlands have a 8.3-fold higher risk for bacterial meningitis as compared to the general population despite cART therapy. Clinical presentation and outcome of patients with acute bacterial meningitis with and without HIV are similar. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

The use of bacterial bioremediation of metals in aquatic environments in the twenty-first century: a systematic review.

PubMed

de Alencar, Feliphe Lacerda Souza; Navoni, Julio Alejandro; do Amaral, Viviane Souza

2017-07-01

Metal pollution is a current environmental issue as a consequence of unregulated anthropic activiy. A wide range of bioremediation strategies have been successfully implemented to recover contaminated areas. Among them, bacterial bioremediation stands out as a promising tool to confront these types of concerns. This study aimed to compare and discuss worldwide scientific evolution of bacterial potential for metal bioremediation in aquatic ecosystems. The study consisted of a systematic review, elaborated through a conceptual hypothesis model, during the period from 2000 to 2016, using PubMed, MEDLINE, and SciELO databases as data resources. The countries with the largest number of reports included in this work were India and the USA. Industrial wastewater discharge was the main subject associated to metal contamination/pollution and where bacterial bioremediations have mostly been applied. Biosorption is the main bioremediation mechanism described. Bacterial adaptation to metal presence was discussed in all the selected studies, and chromium was the most researched bioremedied substrate. Gram-negative Pseudomonas aeruginosas and the Gram-positive Bacillus subtilis bacteria were microorganisms with the greatest applicability for metal bioremediation. Most reports involved the study of genes and/or proteins related to metal metabolism and/or resistence, and Chromobacterium violaceum was the most studied. The present work shows the relevance of metal bacterial bioremediation through the high number of studies aimed at understanding the microbiological mechanisms involved. Moreover, the developed processes applied in removal and/or reducing the resulting environmental metal contaminant/pollutant load have become a current and increasingly biotechnological issue for recovering impacted areas.

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food).

PubMed

Riquelme, Cristina; Câmara, Sandra; Dapkevicius, Maria de Lurdes N Enes; Vinuesa, Pablo; da Silva, Célia Costa Gomes; Malcata, F Xavier; Rego, Oldemiro A

2015-01-02

This work presents the first study on the bacterial communities in Pico cheese, a traditional cheese of the Azores (Portugal), made from raw cow's milk. Pyrosequencing of tagged amplicons of the V3-V4 regions of the 16S rDNA and Operational Taxonomic Unit-based (OTU-based) analysis were applied to obtain an overall idea of the microbiota in Pico cheese and to elucidate possible differences between cheese-makers (A, B and C) and maturation times. Pyrosequencing revealed a high bacterial diversity in Pico cheese. Four phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) and 54 genera were identified. The predominant genus was Lactococcus (77% of the sequences). Sequences belonging to major cheese-borne pathogens were not found. Staphylococcus accounted for 0.5% of the sequences. Significant differences in bacterial community composition were observed between cheese-maker B and the other two units that participated in the study. However, OTU analysis identified a set of taxa (Lactococcus, Streptococcus, Acinetobacter, Enterococcus, Lactobacillus, Staphylococcus, Rothia, Pantoea and unclassified genera belonging to the Enterobacteriaceae family) that would represent the core components of artisanal Pico cheese microbiota. A diverse bacterial community was present at early maturation, with an increase in the number of phylotypes up to 2 weeks, followed by a decrease at the end of ripening. The most remarkable trend in abundance patterns throughout ripening was an increase in the number of sequences belonging to the Lactobacillus genus, with a concomitant decrease in Acinetobacter, and Stenotrophomonas. Microbial rank abundance curves showed that Pico cheese's bacterial communities are characterized by a few dominant taxa and many low-abundance, highly diverse taxa that integrate the so-called "rare biosphere". Copyright © 2014 Elsevier B.V. All rights reserved.

Estimation of the Incidence of Bacterial Vaginosis and other Vaginal Infections and its Consequences on Maternal/Fetal Outcome in Pregnant Women Attending an Antenatal Clinic in a Tertiary Care Hospital in North India

PubMed Central

Lata, Indu; Pradeep, Yashodhara; Sujata; Jain, Amita

2010-01-01

Aims: This study was undertaken to estimate the incidence of bacterial vaginosis (BV) and other vaginal infections during pregnancy and its association with urinary tract infections (UTI) and its consequences on pregnancy outcome, maternal and fetal morbidity and mortality. Settings and Design: Prospective cohort study. Materials and Methods: The present prospective cohort study was conducted on 200 women attending the antenatal clinic (ANC) of a tertiary hospital. All pertinent obstetric and neonatal data covering antenatal events during the course of pregnancy, delivery, puerperium and condition of each newborn at the time of birth were collected. BV was detected by both Gram stain and gold standard clinical criteria (Amsel’s composite criteria). Statistical analysis used: Data were analyzed using SPSS version 9. Fischer’s exact test, chi square tests and Student’s’ test has been used for analysis. The probability of 5% was considered as significant for continuous variables such as age, period of gestation and birth weight. Odds ratio (OR) and confidence interval (CI) with 95% probability were determined. Results: The incidence of bacterial vaginosis was 41 in 200 patients. Adverse outcomes such as preterm labor, PROM and fetal complications were found more in pregnant women who had bacterial vaginosis (N=41), bacterial vaginosis with UTI (N=14) as compared to those without bacterial vaginosis (N=118). Conclusions: The incidence of poor pregnancy outcome was higher in bacterial vaginosis with UTI. Prevention of BV and UTI is cost effective to minimize the pregnancy-related complications and preterm labor to decrease in perinatal and maternal mortality and morbidity. We recommend all antenatal patients should be screened for the presence of bacterial vaginosis, other infections and UTI. PMID:20922108

Estimation of the Incidence of Bacterial Vaginosis and other Vaginal Infections and its Consequences on Maternal/Fetal Outcome in Pregnant Women Attending an Antenatal Clinic in a Tertiary Care Hospital in North India.

PubMed

Lata, Indu; Pradeep, Yashodhara; Sujata; Jain, Amita

2010-04-01

This study was undertaken to estimate the incidence of bacterial vaginosis (BV) and other vaginal infections during pregnancy and its association with urinary tract infections (UTI) and its consequences on pregnancy outcome, maternal and fetal morbidity and mortality. Prospective cohort study. The present prospective cohort study was conducted on 200 women attending the antenatal clinic (ANC) of a tertiary hospital. All pertinent obstetric and neonatal data covering antenatal events during the course of pregnancy, delivery, puerperium and condition of each newborn at the time of birth were collected. BV was detected by both Gram stain and gold standard clinical criteria (Amsel's composite criteria). Data were analyzed using SPSS version 9. Fischer's exact test, chi square tests and Student's' test has been used for analysis. The probability of 5% was considered as significant for continuous variables such as age, period of gestation and birth weight. Odds ratio (OR) and confidence interval (CI) with 95% probability were determined. The incidence of bacterial vaginosis was 41 in 200 patients. Adverse outcomes such as preterm labor, PROM and fetal complications were found more in pregnant women who had bacterial vaginosis (N=41), bacterial vaginosis with UTI (N=14) as compared to those without bacterial vaginosis (N=118). The incidence of poor pregnancy outcome was higher in bacterial vaginosis with UTI. Prevention of BV and UTI is cost effective to minimize the pregnancy-related complications and preterm labor to decrease in perinatal and maternal mortality and morbidity. We recommend all antenatal patients should be screened for the presence of bacterial vaginosis, other infections and UTI.

Bacterial diversity at different stages of the composting process

PubMed Central

2010-01-01

Background Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA. Results Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts. Conclusions Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants. PMID:20350306

Bacterial isolates from equine infections in western Canada (1998–2003)

PubMed Central

Clark, Chris; Greenwood, Sarah; Boison, Joe O.; Chirino-Trejo, Manuel; Dowling, Patricia M.

2008-01-01

All bacterial samples of equine origin submitted to the diagnostic laboratory at the Western College of Veterinary Medicine from January 1998 to December 2003 from either “in-clinic” or Field Service cases were accessed (1323 submissions). The most common bacterial isolates from specific presenting signs were identified, along with their in vitro antimicrobial susceptibility patterns. The most common site from which significant bacterial isolates were recovered was the respiratory tract, followed by wounds. Streptococcus zooepidemicus was the most common isolate from most infections, followed by Escherichia coli. Antimicrobial resistance was not common in the isolates and acquired antimicrobial resistance to multiple drugs was rare. The results are compared with previous published studies from other institutions and used to suggest appropriate antimicrobial treatments for equine infections in western Canada. PMID:18309745

The intrinsic resistome of bacterial pathogens

PubMed Central

Olivares, Jorge; Bernardini, Alejandra; Garcia-Leon, Guillermo; Corona, Fernando; B. Sanchez, Maria; Martinez, Jose L.

2013-01-01

Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyze recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice. PMID:23641241

The intrinsic resistome of bacterial pathogens.

PubMed

Olivares, Jorge; Bernardini, Alejandra; Garcia-Leon, Guillermo; Corona, Fernando; B Sanchez, Maria; Martinez, Jose L

2013-01-01

Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyze recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice.

Bacterial meningitis in adults in Iceland, 1995-2010.

PubMed

Thornórðardóttir, Asgerður; Erlendsdóttir, Helga; Sigurðardóttir, Bryndís; Harðardóttir, Hjördís; Reynisson, Ingi Karl; Gottfreðsson, Magnús; Guðmundsson, Sigurður

2014-05-01

Bacterial meningitis is a serious disease with a mortality rate of 15-20% in adults. We conducted a population-based study of bacterial meningitis in adults (≥ 16 y) in Iceland, 1995-2010. Cases were identified based on positive bacterial cultures from cerebrospinal fluid (CSF) and/or the ICD codes for bacterial meningitis. Medical charts were reviewed and outcomes were assessed using the national population registry. The study period was divided into 2 equal parts, 1995-2002 and 2003-2010, before and after implementation of routine childhood vaccination against serogroup C meningococci, respectively. In total, 111 episodes occurred in 110 individuals. The most common causative organisms were Neisseria meningitidis (41%) and Streptococcus pneumoniae (30%). Only 30% of the patients presented with the classical symptom triad of fever, neck stiffness, and an altered mental status. The overall incidence was 3.2/100,000 inhabitants/y, and dropped significantly between the first and second halves of the study (p = 0.03). This drop was due to a reduced incidence of N. meningitidis meningitis: 34 and 12 cases in the first and second periods, respectively (p = 0.006). The incidence of meningitis caused by S. pneumoniae remained unchanged. The case fatality rates were 18% and 13% in the first and second halves of the study, respectively (difference not significant). The incidence of bacterial meningitis has decreased since the implementation of meningococcal C vaccination in 2002. However, the case fatality rate has remained unchanged.

Picornaviruses in cerebrospinal fluid of children with meningitis in Luanda, Angola.

PubMed

Pelkonen, Tuula; Roine, Irmeli; Anjos, Elizabete; Kaijalainen, Svetlana; Roivainen, Merja; Peltola, Heikki; Pitkäranta, Anne

2012-07-01

Human enteroviruses are the most common cause of viral meningitis. Viral-bacterial interaction may affect the clinical course and outcome of bacterial meningitis. In Africa, viruses might be responsible for 14-25% of all meningitis cases. However, only few studies from Africa have reported detection of viruses in the cerebrospinal fluid (CSF) or mixed viral-bacterial infections of the central nervous system (CNS). The aim of the present study was to investigate the presence of picornaviruses in the CSF of children suffering from meningitis in Luanda, Angola. The study included 142 consecutive children enrolled in a prospective study of bacterial meningitis in Luanda between 2005 and 2006, from whom a CSF sample was available. CSF samples were obtained at hospital admission, stored in a deep-freeze, and transported to Finland for testing by real-time PCR for picornaviruses. Enteroviruses were detected in 4 (3%) of 142 children with presumed bacterial meningitis. A 5-month-old girl with rhinovirus and Haemophilus influenzae meningitis recovered uneventfully. An 8-year-old girl with human enterovirus and pneumococcal meningitis developed no sequelae. A 2-month-old girl with human enterovirus and malaria recovered quickly. A 7-month-old girl with human enterovirus was treated for presumed tuberculous meningitis and survived with severe sequelae. Mixed infections of the CNS with picornaviruses and bacteria are rare. Detection of an enterovirus does not affect the clinical picture and outcome of bacterial meningitis. Copyright © 2012 Wiley Periodicals, Inc.

Culture-positive sepsis in neonatal camelids: 21 cases.

PubMed

Dolente, Brett A; Lindborg, Susan; Palmer, Jonathan E; Wilkins, Pamela A

2007-01-01

There is limited literature on neonatal bacterial sepsis in New World (NW) camelids. Bacterial culture-positive crias have clinical differences based on the specific bacterial genera isolated. Bacterial culture-positive NW camelid crias <21 days of age from 1990 to 2005 were included. Historic physical examination and cliniopathologic data were retrieved from medical records as were the identity and antibiograms of bacterial isolates. Cases were categorized by outcome (survival versus nonsurvival) and type of sepsis (gram-negative or gram-positive). Kruskal-Wallis and chi-square testing were used to evaluate differences between groups. Twenty-one crias met the inclusion criteria. Median age was 2 days. Failure of passive transfer was common. There were few differences identified on the basis of outcome or type of sepsis. Crias without gastrointestinal or central nervous system involvement survived in greater numbers. Forty-six percent of isolates were gram-positive. The most common isolates were the following: Escherichia coli, Enterococcus spp., Listeria monocytogenes, and Citrobacter spp. Overall survival was 67% (14/21). Crias with sepsis do not appear to present with major biochemical, hematologic, or blood gas abnormalities, potentially complicating diagnosis. Affected crias may not have localizing signs at presentation and are not usually febrile, although hypothermia, tachypnea, and tachycardia are relatively common. Total protein concentration was not a substitute for immunoglobulin G measurement in septic crias in this study. Familiarity with the clinical presentation and common pathogens isolated should improve early recognition and treatment and ultimately outcome of crias with sepsis.

Bacteria Present in Comadia redtenbacheri Larvae (Lepidoptera: Cossidae).

PubMed

Hernández-Flores, L; Llanderal-Cázares, C; Guzmán-Franco, A W; Aranda-Ocampo, S

2015-09-01

The external and internal culturable bacterial community present in the larvae of Comadia redtenbacheri Hammerschmidt, an edible insect, was studied. Characterization of the isolates determined the existence of 18 morphotypes and phylogenetic analysis of the 16S rRNA gene revealed the existence of Paenibacillus sp., Bacillus safensis, Pseudomonas sp., Bacillus pseudomycoides, Corynebacterium variabile, Enterococcus sp., Gordonia sp., Acinetobacter calcoaceticus, Arthrobacter sp., Micrococcus sp., and Bacillus cereus. Greater diversity of bacteria was found in those larvae obtained from vendors than in those directly taken from Agave plants in nature. Many of the larvae obtained from vendors presented signs of potential disease, and after the analysis, results showed a greater bacterial community compared with the larvae with a healthy appearance. This indicates that bacterial flora can vary in accordance with how the larvae are handled during extraction, collection, and transport. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Evolvable social agents for bacterial systems modeling.

PubMed

Paton, Ray; Gregory, Richard; Vlachos, Costas; Saunders, Jon; Wu, Henry

2004-09-01

We present two approaches to the individual-based modeling (IbM) of bacterial ecologies and evolution using computational tools. The IbM approach is introduced, and its important complementary role to biosystems modeling is discussed. A fine-grained model of bacterial evolution is then presented that is based on networks of interactivity between computational objects representing genes and proteins. This is followed by a coarser grained agent-based model, which is designed to explore the evolvability of adaptive behavioral strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of the two proposed individual-based bacterial models are discussed, and some results from simulation experiments are presented, illustrating their adaptive properties.

Adjunctive dexamethasone therapy in unconfirmed bacterial meningitis in resource limited settings: is it a risk worth taking?

PubMed

Gudina, Esayas Kebede; Tesfaye, Markos; Adane, Aynishet; Lemma, Kinfe; Shibiru, Tamiru; Wieser, Andreas; Pfister, Hans-Walter; Klein, Matthias

2016-08-26

Bacterial meningitis is associated with significant morbidity and mortality despite advances in medical care. The main objective of this study was to assess the association of adjunctive dexamethasone treatment with discharge outcome of patients treated as bacterial meningitis in low income setting. A retrospective study was conducted at four teaching hospitals across Ethiopia. Patients of age 14 years and older treated as cases of bacterial meningitis between January 1, 2011 and April 30, 2015 were included in this study. Information regarding sociodemographic data, clinical presentations, laboratory data, treatments given and status at hospital discharge were retrieved from patients' medical records using a structured questionnaire. Predefined outcome variables at discharge were analysed using descriptive statistics. Multivariable logistic regression was used to identify factors independently associated with poor outcome. A total of 425 patients treated with the presumptive clinical diagnosis of bacterial meningitis were included in this study (lumbar puncture done in 56 %; only 19 % had CSF findings compatible with bacterial meningitis, and only 3 % had proven etiology). The overall in hospital mortality rate was 20.2 %. Impaired consciousness, aspiration pneumonia, and cranial nerve palsy at admission were independently associated with increased mortality. Adjuvant dexamethasone, which was used in 50.4 % of patients, was associated with increased in-hospital mortality (AOR = 3.38; 95 % CI 1.87-6.12, p < 0.001) and low Glasgow outcome scale (GOS) at discharge (AOR = 4.46 (95 % CI 1.98-10.08). This association between dexamethasone and unfavorable outcome was found to be more pronounced in suspected but unproven cases and in those without CSF alterations compatible with bacterial meningitis. Most patients treated for suspected bacterial meningitis did not receive proper diagnostic workup. Adjuvant dexamethasone use in clinically suspected but unproven cases of bacterial meningitis was associated with an increased mortality and poor discharge GOS. These findings show that there are potential deleterious effects in unconfirmed cases in this setting. Physicians practising under such circumstances should thus abide with the current recommendation and defer the use of adjuvant corticosteroid in suspected cases of bacterial meningitis.

Radiolabel ratio method for measuring pulmonary clearance of intratracheal bacterial challenges

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

LaForce, F.M.; Boose, D.S.

Calculation of bacterial clearance is a fundamental step in any study of in situ lung antibacterial defenses. A method is described whereby about 85% of a radiolabeled bacterial inoculum was consistently introduced into the bronchopulmonary tree of a mouse by the intratracheal route. Mice were then killed 1 and 4 hours later; their lungs were removed aseptically and homogenized, and viable bacteria and radiolabel counts were determined. Radiolabel counts fell slowly, and more than 80% of the original radiolabel was still present in homogenized lung samples from animals sacrificed 4 hours after challenge. Bacteria/isotope ratios for the bacterial inoculum andmore » homogenized lung samples from animals sacrificed immediately after challenge were very similar. Bacterial clearance values were the same whether computed from bacterial counts alone or according to a radiolabel ratio method whereby the change in the bacteria/isotope ratio in ground lung aliquots was divided by a similar ratio from bacteria used to inoculate animals. Some contamination resulted from oral streptococci being swept into the bronchopulmonary free during the aspiration process. This contamination was not a problem when penicillin was incorporated into the agar and penicillin-resistant strains were used for the bacterial challenges.« less

CHANGES IN BACTERIAL COMPOSITION OF BIOFILM IN A ...

EPA Pesticide Factsheets

This study examined the development of bacterial biofilms within a metropolitan distribution system. The distribution system is fed with different source water (i.e., groundwater, GW and surface water, SW) and undergoes different treatment processes in separate facilities. The biofilm community was characterized using 16S rRNA gene clone libraries and functional potential analysis, generated from total DNA extracted from coupons in biofilm annular reactors fed with onsite drinking water for up to eighteen months. Significant differences in the bacterial community structure were observed between GW and SW. Representatives that explained the dissimilarity between service areas were associated with Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Gammaproteobacteria, and Firmicutes. After nine months the biofilm bacterial community from both areas were dominated by Mycobacterium species. The distribution of the dominant OTU (Mycobacterium) positively correlated with the drinking water distribution system (DWDS) temperature, but no clear relationship was seen with free chlorine residual, pH, turbidity or total organic carbon (TOC). The results suggest that biofilm microbial communities harbor distinct and diverse bacterial communities, and that source water, treatment processes and environmental conditions may play an important role in shaping the bacterial community in the distribution system. On the other hand, several bacterial groups were present i

National survey of molecular bacterial diversity of New Zealand groundwater: relationships between biodiversity, groundwater chemistry and aquifer characteristics.

PubMed

Sirisena, Kosala A; Daughney, Christopher J; Moreau-Fournier, Magali; Ryan, Ken G; Chambers, Geoffrey K

2013-12-01

Groundwater is a vital component of rural and urban water supplies in New Zealand. Although extensive monitoring of chemical and physical properties is conducted due to the high demand for this valuable resource, current information on its bacterial content is limited. However, bacteria provide an immense contribution to drive the biogeochemical processes in the groundwater ecosystem as in any other ecosystem. Therefore, a proper understanding of bacterial diversity is crucial to assess the effectiveness of groundwater management policies. In this study, we investigated the bacterial community structure in NZ groundwater at a national scale using the terminal restriction fragment length polymorphism (T-RFLP) molecular profiling tool and determined the relationships between bacterial diversity and groundwater chemistry, geological parameters and human impact. Considerable bacterial diversity was present and the community structures were strongly related to groundwater chemistry, and in particular to redox potential and human impact, reflecting their potential influence on determination of bacterial diversity. Further, the mean residence time of groundwater also showed relationships with bacterial community structure. These novel findings pertaining to community composition and its relationships with environmental parameters will provide a strong foundation for qualitative exploration of the bacterial diversity in NZ groundwater in relation to sustainable management of this valuable resource. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Development of a restricted state space stochastic differential equation model for bacterial growth in rich media.

PubMed

Møller, Jan Kloppenborg; Bergmann, Kirsten Riber; Christiansen, Lasse Engbo; Madsen, Henrik

2012-07-21

In the present study, bacterial growth in a rich media is analysed in a Stochastic Differential Equation (SDE) framework. It is demonstrated that the SDE formulation and smoothened state estimates provide a systematic framework for data driven model improvements, using random walk hidden states. Bacterial growth is limited by the available substrate and the inclusion of diffusion must obey this natural restriction. By inclusion of a modified logistic diffusion term it is possible to introduce a diffusion term flexible enough to capture both the growth phase and the stationary phase, while concentration is restricted to the natural state space (substrate and bacteria non-negative). The case considered is the growth of Salmonella and Enterococcus in a rich media. It is found that a hidden state is necessary to capture the lag phase of growth, and that a flexible logistic diffusion term is needed to capture the random behaviour of the growth model. Further, it is concluded that the Monod effect is not needed to capture the dynamics of bacterial growth in the data presented. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bacterial membrane proteomics.

PubMed

Poetsch, Ansgar; Wolters, Dirk

2008-10-01

About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

Prevalence and Bacterial Isolates of Mastitis in Dairy Farms in Selected Districts of Eastern Harrarghe Zone, Eastern Ethiopia

PubMed Central

Abera, Gerema

2017-01-01

The study was conducted from November 2015 to April 2016 to estimate the prevalence of clinical and subclinical mastitis in lactating cows, to assess the associated risk factors, and to isolate the major bacterial pathogens in dairy farms in selected district of Eastern Harrarghe Zone, Eastern Ethiopia. The study was carried out in 384 dairy cows based on data collection, farm visit, animal examination, California mastitis test (CMT), and isolation bacterial pathogens using standard techniques. In the present study the overall mastitis at cow level was 247 (64.3%). The prevalence of clinical and subclinical mastitis and quarter level prevalence for clinical and subclinical mastitis were 12.5% and 51.8% at cow level and 10.7% and 46.4% at quarter level, respectively. Clinically, 101 (6.6%) quarters which belong to 75 (19.5%) animals were found to be with blind teat. In the present study prevalence of mastitis was significantly associated with parity and age (p < 0.05). Bacteriological examination of milk sample revealed 187 isolates where coagulase negative Staphylococcus species (CNS) (34.2%) was the predominant species while Streptococcus faecalis (2.1%) was identified as the least bacteria. The present study concluded that prevalence of mastitis particularly the subclinical mastitis was major problem of dairy cows in the area and hence warrants serious attention. PMID:28352648

Bacterial diversity in different regions of gastrointestinal tract of Giant African snail (Achatina fulica).

PubMed

Pawar, Kiran D; Banskar, Sunil; Rane, Shailendra D; Charan, Shakti S; Kulkarni, Girish J; Sawant, Shailesh S; Ghate, Hemant V; Patole, Milind S; Shouche, Yogesh S

2012-12-01

The gastrointestinal (GI) tract of invasive land snail Achatina fulica is known to harbor metabolically active bacterial communities. In this study, we assessed the bacterial diversity in the different regions of GI tract of Giant African snail, A. fulica by culture-independent and culture-dependent methods. Five 16S rRNA gene libraries from different regions of GI tract of active snails indicated that sequences affiliated to phylum γ-Proteobacteria dominated the esophagus, crop, intestine, and rectum libraries, whereas sequences affiliated to Tenericutes dominated the stomach library. On phylogenetic analysis, 30, 27, 9, 27, and 25 operational taxonomic units (OTUs) from esophagus, crop, stomach, intestine, and rectum libraries were identified, respectively. Estimations of the total bacterial diversity covered along with environmental cluster analysis showed highest bacterial diversity in the esophagus and lowest in the stomach. Thirty-three distinct bacterial isolates were obtained, which belonged to 12 genera of two major bacterial phyla namely γ-Proteobacteria and Firmicutes. Among these, Lactococcus lactis and Kurthia gibsonii were the dominant bacteria present in all GI tract regions. Quantitative real-time polymerase chain reaction (qPCR) analysis indicated significant differences in bacterial load in different GI tract regions of active and estivating snails. The difference in the bacterial load between the intestines of active and estivating snail was maximum. Principal component analysis (PCA) of terminal restriction fragment length polymorphism suggested that bacterial community structure changes only in intestine when snail enters estivation state. © 2012 The Authors. Published by Blackwell Publishing Ltd.

Bacterial diversity in different regions of gastrointestinal tract of Giant African Snail (Achatina fulica)

PubMed Central

Pawar, Kiran D; Banskar, Sunil; Rane, Shailendra D; Charan, Shakti S; Kulkarni, Girish J; Sawant, Shailesh S; Ghate, Hemant V; Patole, Milind S; Shouche, Yogesh S

2012-01-01

The gastrointestinal (GI) tract of invasive land snail Achatina fulica is known to harbor metabolically active bacterial communities. In this study, we assessed the bacterial diversity in the different regions of GI tract of Giant African snail, A. fulica by culture-independent and culture-dependent methods. Five 16S rRNA gene libraries from different regions of GI tract of active snails indicated that sequences affiliated to phylum γ-Proteobacteria dominated the esophagus, crop, intestine, and rectum libraries, whereas sequences affiliated to Tenericutes dominated the stomach library. On phylogenetic analysis, 30, 27, 9, 27, and 25 operational taxonomic units (OTUs) from esophagus, crop, stomach, intestine, and rectum libraries were identified, respectively. Estimations of the total bacterial diversity covered along with environmental cluster analysis showed highest bacterial diversity in the esophagus and lowest in the stomach. Thirty-three distinct bacterial isolates were obtained, which belonged to 12 genera of two major bacterial phyla namely γ-Proteobacteria and Firmicutes. Among these, Lactococcus lactis and Kurthia gibsonii were the dominant bacteria present in all GI tract regions. Quantitative real-time polymerase chain reaction (qPCR) analysis indicated significant differences in bacterial load in different GI tract regions of active and estivating snails. The difference in the bacterial load between the intestines of active and estivating snail was maximum. Principal component analysis (PCA) of terminal restriction fragment length polymorphism suggested that bacterial community structure changes only in intestine when snail enters estivation state. PMID:23233413

Bridging the knowledge gap: from microbiome composition to function

PubMed Central

Faith, Jeremiah J

2015-01-01

Despite the wealth of metagenomic sequencing data, the functions of most bacterial genes from the mammalian microbiota have remained poorly understood. In their recent study (Yaung et al 2015), Wang, Gerber, and colleagues present a platform which allows functional mining of bacterial genomes for genes that contribute to fitness in vivo and holds great potential for forward engineering microbes with enhanced colonization abilities in the microbiota. PMID:26148349

Fusobacterium nucleatum in endodontic flare-ups.

PubMed

Chávez de Paz Villanueva, Luis Eduardo

2002-02-01

The extent to which Fusobacterium nucleatum is recovered from root canals of teeth that present with an interappointment flare-up following endodontic instrumentation was investigated. Included in the study were 28 patients that sought emergency treatment after initiation of root canal therapy. Only non-painful teeth that had been treated because of a necrotic pulp and periapical inflammatory lesion were studied. Root canal samples for bacterial analysis were taken, transported to a bacteriological laboratory, and processed for a semiquantitative assessment of bacterial isolates. Bacterial findings were correlated with self-assessed pain intensity as recorded by means of a Visual Analogue Scale. Clinical presentation of swelling and presence of exudate in the treated root canals were also linked. Bacteria were recovered from all teeth examined. Gram-negative anaerobic coccoid rods (Prevotella species and Porphyromonas species) were frequent isolates. All teeth in patients who were reported to be in severe pain (Visual Analogue Scale > or = 6) displayed F nucleatum. Nine out of 10 of these teeth also had swelling and exudate in the root canals. Samples from the remaining patients that had teeth with less pain score showed a variable bacterial recovery. None of these teeth displayed F nucleatum. F nucleatum appears to be associated with the development of the most severe forms of interappointment endodontic flare-ups.

Impact of Hydraulic Well Restoration on Native Bacterial Communities in Drinking Water Wells

PubMed Central

Karwautz, Clemens; Lueders, Tillmann

2014-01-01

The microbial monitoring of drinking water production systems is essential to assure water quality and minimize possible risks. However, the comparative impact of microbes from the surrounding aquifer and of those established within drinking water wells on water parameters remains poorly understood. High pressure jetting is a routine method to impede well clogging by fine sediments and also biofilms. In the present study, bacterial communities were investigated in a drinking water production system before, during, and after hydraulic purging. Variations were observed in bacterial communities between different wells of the same production system before maintenance, despite them having practically identical water chemistries. This may have reflected the distinct usage practices of the different wells, and also local aquifer heterogeneity. Hydraulic jetting of one well preferentially purged a subset of the dominating taxa, including lineages related to Diaphorobacter, Nitrospira, Sphingobium, Ralstonia, Alkanindiges, Janthinobacterium, and Pseudomonas spp, suggesting their tendency for growth in well-associated biofilms. Lineages of potential drinking water concern (i.e. Legionellaceae, Pseudomonadaceae, and Acinetobacter spp.) reacted distinctly to hydraulic jetting. Bacterial diversity was markedly reduced in drinking water 2 weeks after the cleaning procedure. The results of the present study provide a better understanding of drinking water wells as a microbial habitat, as well as their role in the microbiology of drinking water systems. PMID:25273229

Impact of hydraulic well restoration on native bacterial communities in drinking water wells.

PubMed

Karwautz, Clemens; Lueders, Tillmann

2014-01-01

The microbial monitoring of drinking water production systems is essential to assure water quality and minimize possible risks. However, the comparative impact of microbes from the surrounding aquifer and of those established within drinking water wells on water parameters remains poorly understood. High pressure jetting is a routine method to impede well clogging by fine sediments and also biofilms. In the present study, bacterial communities were investigated in a drinking water production system before, during, and after hydraulic purging. Variations were observed in bacterial communities between different wells of the same production system before maintenance, despite them having practically identical water chemistries. This may have reflected the distinct usage practices of the different wells, and also local aquifer heterogeneity. Hydraulic jetting of one well preferentially purged a subset of the dominating taxa, including lineages related to Diaphorobacter, Nitrospira, Sphingobium, Ralstonia, Alkanindiges, Janthinobacterium, and Pseudomonas spp, suggesting their tendency for growth in well-associated biofilms. Lineages of potential drinking water concern (i.e. Legionellaceae, Pseudomonadaceae, and Acinetobacter spp.) reacted distinctly to hydraulic jetting. Bacterial diversity was markedly reduced in drinking water 2 weeks after the cleaning procedure. The results of the present study provide a better understanding of drinking water wells as a microbial habitat, as well as their role in the microbiology of drinking water systems.

Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

PubMed

Wu, Huiting; Zhang, Jingxu; Mi, Zilong; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-02-01

Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson's correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

Early Bacterial Pneumonia After Hepatic Transplantation: Epidemiologic Profile.

PubMed

Prieto Amorin, J; Lopez, M; Rando, K; Castelli, J; Medina Presentado, J

2018-03-01

Postoperative pulmonary complications are major cause of morbidity and mortality in patients receiving liver transplantation (LT), particularly bacterial pneumonia occurring within the first 100 days after transplantation. Our aim in this study was to determine the incidence, microorganisms involved, associated factors, and morbidity of bacterial pneumonia presenting in the first 100 days posttransplant. We performed a cohort study in which patients receiving liver transplantation were included prospectively in our national database (Database of Infections in Transplantation of Solid Organs). The study period was from July 14, 2009 to July 24, 2015. One hundred six patients were transplanted during the 6-year period. We documented 9 bacterial pneumonia cases with an incidence of 8.5 per 100 patients; 2 patients had hospital-acquired pneumonia (HAP) and 7 had ventilator-associated pneumonia (VAP). In 4 of the 9 bacterial pneumonia cases, patients presented with bacteremia. Eleven microorganisms were isolated these 9 patients. Microbiologic diagnosis methods included 5 cases of alveolar bronchoalveolar lavage (BAL), 1 case of BAL and pleural fluid puncture, 1 case of pleural fluid puncture, and 1 case through sputum study. Of the 11 isolated organisms, 9 corresponded to Gram-negative bacilli (GNB): Klebsiella spp, n = 3; Acinetobacter baumannii, n = 4; Morganella morganii, n = 1; and Pseudomonas aeruginosa, n = 1. Regarding the resistance profile, 7 presented with a multiresistance profile (MDR) and extreme resistance (XDR). Univariate analysis identified the Model for End-Stage Liver Disease (MELD) pretransplant score as a factor associated with developing pneumonia (P < .001, 95% confidence interval [CI] 2.872-10.167), and early extubation, before 8 hours posttransplant, as a protective factor (P = .008; relative risk [RR] 0.124; 95% CI 0 .041-0.377). Hospital stay was longer in patients with pneumonia compared to those without pneumonia (P < .0001, 95% CI 17.79-43.11 days). There was also an increased risk of death in patients with pneumonia (RR 17.963; 95% CI 5106-63,195). Early bacterial pneumonia after hepatic transplantation is associated with higher morbidity and mortality. At our center, 4 of 9 patients had bacteremia. GNB cases with MDR and XDR profiles are predominant. Early extubation is a protective factor. Copyright © 2017 Elsevier Inc. All rights reserved.

Bacterial reproductive pathogens of cats and dogs.

PubMed

Graham, Elizabeth M; Taylor, David J

2012-05-01

With the notable exception of Brucella canis, exogenous bacterial pathogens are uncommon causes of reproductive disease in cats and dogs. Most bacterial reproductive infections are endogenous, and predisposing factors for infection are important. This article reviews the etiology, pathogenesis, clinical presentation, diagnosis, treatment, and public health significance of bacterial reproductive pathogens in cats and dogs.

Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile)

PubMed Central

Leon, Carla G.; Moraga, Ruben; Valenzuela, Cristian; Gugliandolo, Concetta; Lo Giudice, Angelina; Papale, Maria; Vilo, Claudia; Dong, Qunfeng; Smith, Carlos T.; Rossello-Mora, Ramon; Yañez, Jorge

2018-01-01

Arsenic (As), a highly toxic metalloid, naturally present in Camarones River (Atacama Desert, Chile) is a great health concern for the local population and authorities. In this study, the taxonomic and functional characterization of bacterial communities associated to metal-rich sediments from three sites of the river (sites M1, M2 and M3), showing different arsenic concentrations, were evaluated using a combination of approaches. Diversity of bacterial communities was evaluated by Illumina sequencing. Strains resistant to arsenic concentrations varying from 0.5 to 100 mM arsenite or arsenate were isolated and the presence of genes coding for enzymes involved in arsenic oxidation (aio) or reduction (arsC) investigated. Bacterial communities showed a moderate diversity which increased as arsenic concentrations decreased along the river. Sequences of the dominant taxonomic groups (abundances ≥1%) present in all three sites were affiliated to Proteobacteria (range 40.3–47.2%), Firmicutes (8.4–24.8%), Acidobacteria (10.4–17.1%), Actinobacteria (5.4–8.1%), Chloroflexi (3.9–7.5%), Planctomycetes (1.2–5.3%), Gemmatimonadetes (1.2–1.5%), and Nitrospirae (1.1–1.2%). Bacterial communities from sites M2 and M3 showed no significant differences in diversity between each other (p = 0.9753) but they were significantly more diverse than M1 (p<0.001 and p<0.001, respectively). Sequences affiliated with Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi and Actinobacteria at M1 accounted for more than 89% of the total classified bacterial sequences present but these phyla were present in lesser proportions in M2 and M3 sites. Strains isolated from the sediment of sample M1, having the greatest arsenic concentration (498 mg kg-1), showed the largest percentages of arsenic oxidation and reduction. Genes aio were more frequently detected in isolates from M1 (54%), whereas arsC genes were present in almost all isolates from all three sediments, suggesting that bacterial communities play an important role in the arsenic biogeochemical cycle and detoxification of arsenical compounds. Overall, results provide further knowledge on the microbial diversity of arsenic contaminated fresh-water sediments. PMID:29715297

Sequelae due to bacterial meningitis among African children: a systematic literature review

PubMed Central

Ramakrishnan, Meenakshi; Ulland, Aaron J; Steinhardt, Laura C; Moïsi, Jennifer C; Were, Fred; Levine, Orin S

2009-01-01

Background African children have some of the highest rates of bacterial meningitis in the world. Bacterial meningitis in Africa is associated with high case fatality and frequent neuropsychological sequelae. The objective of this study is to present a comprehensive review of data on bacterial meningitis sequelae in children from the African continent. Methods We conducted a systematic literature search to identify studies from Africa focusing on children aged between 1 month to 15 years with laboratory-confirmed bacterial meningitis. We extracted data on neuropsychological sequelae (hearing loss, vision loss, cognitive delay, speech/language disorder, behavioural problems, motor delay/impairment, and seizures) and mortality, by pathogen. Results A total of 37 articles were included in the final analysis representing 21 African countries and 6,029 children with confirmed meningitis. In these studies, nearly one fifth of bacterial meningitis survivors experienced in-hospital sequelae (median = 18%, interquartile range (IQR) = 13% to 27%). About a quarter of children surviving pneumococcal meningitis and Haemophilus influenzae type b (Hib) meningitis had neuropsychological sequelae by the time of hospital discharge, a risk higher than in meningococcal meningitis cases (median = 7%). The highest in-hospital case fatality ratios observed were for pneumococcal meningitis (median = 35%) and Hib meningitis (median = 25%) compared to meningococcal meningitis (median = 4%). The 10 post-discharge studies of children surviving bacterial meningitis were of varying quality. In these studies, 10% of children followed-up post discharge died (range = 0% to 18%) and a quarter of survivors had neuropsychological sequelae (range = 3% to 47%) during an average follow-up period of 3 to 60 months. Conclusion Bacterial meningitis in Africa is associated with high mortality and risk of neuropsychological sequelae. Pneumococcal and Hib meningitis kill approximately one third of affected children and cause clinically evident sequelae in a quarter of survivors prior to hospital discharge. The three leading causes of bacterial meningitis are vaccine preventable, and routine use of conjugate vaccines could provide substantial health and economic benefits through the prevention of childhood meningitis cases, deaths and disability. PMID:19751516

[Antibiotic therapy of hospital-acquired pneumonia and its pharmacoeconomics].

PubMed

Kolář, Milan; Htoutou Sedláková, Miroslava; Urbánek, Karel; Uvízl, Radomír; Adamus, Milan; Imwensi, O P

2016-03-01

Important hospital-acquired infections include pneumonia, mainly because of the increasing resistance of bacterial pathogens to antimicrobials and the associated potential failure of antibiotic therapy. The present study aimed at determining the most frequent etiological agents of hospital-acquired pneumonia (HAP) and assessing the relationship between 30-day mortality and adequacy of antibiotic therapy. Based on the obtained information, optimal patterns of antibiotic therapy were to be defined, including a pharmacoeconomic perspective. In patients with clinically confirmed HAP, bacterial etiological agents were identified, their susceptibility to antimicrobials was determined and statistical methods were used to assess the relationship between adequacy of antibiotic therapy and 30-day mortality. The study comprised 68 patients with clinically confirmed HAP. The most common etiological agents were strains of Pseudomonas aeruginosa (30.8 %), Klebsiella pneumoniae (23.1 %) and Burkholderia cepacia complex (15.4 %). Gram-negative bacteria accounted for 86.5 % of all bacterial pathogens. The overall mortality reached 42.5 %. In the subgroup of patients with inadequate antibiotic therapy, 30-day mortality was significantly higher (83.3 %) than in the subgroup with adequate therapy (30.0 %; p = 0.002). The risk for 30-day mortality was 2.78 times higher in case of inadequate antibiotic therapy (95%CI: 1.52-5.07). The proportion of Pseudomonas aeruginosa strains was significantly higher in the subgroup of patients with inadequate antibiotic therapy than in those with adequate therapy (67 % vs. 27 %; p = 0.032). Results of the present study suggest a significant relationship between mortality of patients with HAP and ineffective antibiotic therapy due to resistance of the bacterial pathogen. Thus, it is clear that initial antibiotic therapy must be based on qualified assumption of sufficient activity against the most common bacterial pathogens and results of surveillance of bacterial resistance in the relevant epidemiological unit. At the same time, however, it must be stressed that it is impossible to cover all potential variants of the etiological agents and their resistance phenotypes.

Antibacterial activity of glass-ionomer restorative cements exposed to cavity-producing microorganisms.

PubMed

Herrera, M; Castillo, A; Baca, P; Carrión, P

1999-01-01

The antibacterial activity of the glass-ionomer restorative cements Ketac-Fil, Ketac-Silver, Fuji II LC, and Vitremer was studied in vitro, in conjunction with a total of 32 strains of five bacterial genera that may be associated with dental caries: Streptococcus spp, Lactobacillus spp, Actinomyces spp, Porphyromonas spp, and Clostridium spp. Agar plate diffusion was the method used for the bacterial cultures, which included a chlorhexidine control. All four glass-ionomer cements were found to inhibit bacterial growth, though with noteworthy differences in their spheres of action. Vitremer was the cement determined to have the greatest antibacterial effects, whereas Ketac-Silver presented the least inhibitory action.

Atomic Force Microscope Investigations of Bacterial Biofilms Treated with Gas Discharge Plasmas

NASA Astrophysics Data System (ADS)

Vandervoort, Kurt; Zelaya, Anna; Brelles-Marino, Graciela

2012-02-01

We present investigations of bacterial biofilms before and after treatment with gas discharge plasmas. Gas discharge plasmas represent a way to inactivate bacteria under conditions where conventional disinfection methods are often ineffective. These conditions involve biofilm communities, where bacteria grow embedded in an exopolysaccharide matrix, and cooperative interactions between cells make organisms less susceptible to standard inactivation methods. In this study, biofilms formed by the opportunistic bacterium Pseudomonas aeruginosa were imaged before and after plasma treatment using an atomic force microscope (AFM). Through AFM images and micromechanical measurements we observed bacterial morphological damage and reduced AFM tip-sample surface adhesion following plasma treatment.

Automatic identification of bacterial types using statistical imaging methods

NASA Astrophysics Data System (ADS)

Trattner, Sigal; Greenspan, Hayit; Tepper, Gapi; Abboud, Shimon

2003-05-01

The objective of the current study is to develop an automatic tool to identify bacterial types using computer-vision and statistical modeling techniques. Bacteriophage (phage)-typing methods are used to identify and extract representative profiles of bacterial types, such as the Staphylococcus Aureus. Current systems rely on the subjective reading of plaque profiles by human expert. This process is time-consuming and prone to errors, especially as technology is enabling the increase in the number of phages used for typing. The statistical methodology presented in this work, provides for an automated, objective and robust analysis of visual data, along with the ability to cope with increasing data volumes.

Vaginal ecosystem modeling of growth patterns of anaerobic bacteria in microaerophilic conditions.

PubMed

Medina-Colorado, Audrie A; Vincent, Kathleen L; Miller, Aaron L; Maxwell, Carrie A; Dawson, Lauren N; Olive, Trevelyn; Kozlova, Elena V; Baum, Marc M; Pyles, Richard B

2017-06-01

The human vagina constitutes a complex ecosystem created through relationships established between host mucosa and bacterial communities. In this ecosystem, classically defined bacterial aerobes and anaerobes thrive as communities in the microaerophilic environment. Levels of CO 2 and O 2 present in the vaginal lumen are impacted by both the ecosystem's physiology and the behavior and health of the human host. Study of such complex relationships requires controlled and reproducible causational approaches that are not possible in the human host that, until recently, was the only place these bacterial communities thrived. To address this need we have utilized our ex vivo human vaginal mucosa culture system to support controlled, reproducible colonization by vaginal bacterial communities (VBC) collected from healthy, asymptomatic donors. Parallel vaginal epithelial cells (VEC)-VBC co-cultures were exposed to two different atmospheric conditions to study the impact of CO 2 concentrations upon the anaerobic bacteria associated with dysbiosis and inflammation. Our data suggest that in the context of transplanted VBC, increased CO 2 favored specific lactobacilli species defined as microaerophiles when grown as monocultures. In preliminary studies, the observed community changes also led to shifts in host VEC phenotypes with significant changes in the host transcriptome, including altered expression of select molecular transporter genes. These findings support the need for additional study of the environmental changes associated with behavior and health upon the symbiotic and adversarial relationships that are formed in microbial communities present in the human vaginal ecosystem. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diversity of Cervical Microbiota in Asymptomatic Chlamydia trachomatis Genital Infection: A Pilot Study.

PubMed

Filardo, Simone; Di Pietro, Marisa; Porpora, Maria G; Recine, Nadia; Farcomeni, Alessio; Latino, Maria A; Sessa, Rosa

2017-01-01

Chlamydia trachomatis genital infection continues to be an important public health problem worldwide due to its increasing incidence. C. trachomatis infection can lead to severe sequelae, such as pelvic inflammatory disease, obstructive infertility, and preterm birth. Recently, it has been suggested that the cervico-vaginal microbiota may be an important defense factor toward C. trachomatis infection as well as the development of chronic sequelae. Therefore, the investigation of microbial profiles associated to chlamydial infection is of the utmost importance. Here we present a pilot study aiming to characterize, through the metagenomic analysis of sequenced 16s rRNA gene amplicons, the cervical microbiota from reproductive age women positive to C. trachomatis infection. The main finding of our study showed a marked increase in bacterial diversity in asymptomatic C. trachomatis positive women as compared to healthy controls in terms of Shannon's diversity and Shannon's evenness ( P = 0.031 and P = 0.026, respectively). More importantly, the cervical microbiota from C. trachomatis positive women and from healthy controls significantly separated into two clusters in the weighted UniFrac analysis ( P = 0.0027), suggesting that differences between the two groups depended entirely on the relative abundance of bacterial taxa rather than on the types of bacterial taxa present. Furthermore, C. trachomatis positive women showed an overall decrease in Lactobacillus spp. and an increase in anaerobes. These findings are part of an ongoing larger epidemiological study that will evaluate the potential role of distinct bacterial communities of the cervical microbiota in C. trachomatis infection.

Retrospective study of bacterial infective arthritis in 31 dogs.

PubMed

Clements, D N; Owen, M R; Mosley, J R; Carmichael, S; Taylor, D J; Bennett, D

2005-04-01

To characterise the presenting signs and pathological changes of canine bacterial infective arthritis in 31 dogs, and to document the response to different treatment regimens. Risk factors that may predispose joints to bacterial infective arthritis and influence the success of treatment were also investigated. A retrospective review of cases of bacterial infective arthritis that were presented to three university veterinary referral hospitals over a five-year period (January 1997 to January 2002) was performed. The elbow joint (38 per cent) and stifle joint (44 per cent) were most commonly affected. Radiographic changes consistent with pre-existing osteoarthritis were identified in 14 joints, which had no history of previous surgery (articular or periarticular) or penetrating wound. No significant difference (P = 0.78) was identified between the outcome of combined surgical and medical management, and medical management alone. There were trends for poorer outcomes with increased bodyweight of the dog, longer duration of lameness and a higher nucleated cell count of the affected joint fluid at presentation. The overall infection rate for articular surgical procedures at one institution was 1-3 per cent. Medical and/or surgical management were usually successful in resolving infection (94 per cent). However, they were frequently unsuccessful in restoring full joint function; this may in part have been due to the nature of the underlying joint

Amplification and sequence analysis of partial bacterial 16S ribosomal RNA gene in gallbladder bile from patients with primary biliary cirrhosis.

PubMed

Hiramatsu, K; Harada, K; Tsuneyama, K; Sasaki, M; Fujita, S; Hashimoto, T; Kaneko, S; Kobayashi, K; Nakanuma, Y

2000-07-01

The etiopathogenesis of bile duct lesion in primary biliary cirrhosis is unknown, though the participation of bacteria and/or their components and products is suspected. In this study, we tried to detect and identify bacteria in the bile of patients with primary biliary cirrhosis by polymerase chain reaction using universal bacterial primers of the 16S ribosomal RNA gene. Gallbladder bile samples from 15 patients with primary biliary cirrhosis, 5 with primary sclerosing cholangitis, 5 with hepatitis C virus-related liver cirrhosis, 11 with cholecystolithiasis, and from 12 normal adult gallbladders were used. In addition to the culture study, partial bacterial 16S ribosomal RNA gene was amplified by polymerase chain reaction (PCR) taking advantage of universal primers that can amplify the gene of almost all bacterial species, and the amplicons were cloned and sequenced. Sequence homology with specific bacterial species was analyzed by database research. Bacterial contamination at every step of the bile sampling, DNA extraction and PCR study was avoided. Furthermore, to confirm whether bacterial DNA is detectable in liver explants, the same analysis was performed using 10 liver explants of patients with primary biliary cirrhosis. In primary biliary cirrhosis, 75% (p<0.0001) of 100 clones were identified as so-called gram-positive cocci while these cocci were positive in only 5% in cholecystolithiasis (p<0.0001). In cholecystolithiasis gram-negative rods were predominant instead. One bacterial species detected in a normal adult was not related to those detected in primary biliary cirrhosis and cholecystolithiasis patients. No bacterial DNA was detected by PCR amplification in 10 liver explants of patients with primary biliary cirrhosis. The present results raise several possible roles of gram-positive bacteria in bile in the etiopathogenesis of primary biliary cirrhosis. However, these results could also reflect an epiphenomenon due to decreased bile flow in the patients with primary biliary cirrhosis at an advanced stage.

Fluoroquinolone Treatment and Susceptibility of Isolates From Bacterial Keratitis

PubMed Central

Ray, Kathryn J.; Prajna, Lalitha; Srinivasan, Muthiah; Geetha, Manoharan; Karpagam, Rajarathinam; Glidden, David; Oldenburg, Catherine E.; Sun, Catherine Q.; McLeod, Stephen D.; Acharya, Nisha R.; Lietman, Thomas M.

2013-01-01

Objective To analyze the relationship between fluoroquinolone use at presentation and minimum inhibitory concentration in bacterial keratitis. Methods The Steroids for Corneal Ulcers Trial was a randomized, double-masked, placebo-controlled trial assessing the effect of adjunctive topical corticosteroid treatment on outcomes in bacterial keratitis. After presentation, all patients were treated with moxifloxacin hydrochloride, 0.5%. We compare antibiotic use at presentation with minimum inhibitory concentration against moxifloxacin for all isolates. Separate analyses accounted for organism species and fluoroquinolone generation. Results Topical fluoroquinolone use at presentation was reported in 92 of 480 cases (19.2%). Causative organisms in the 480 cases included Streptococcus pneumoniae (247 cases [51.5%]), Pseudomonas aeruginosa (109 cases [22.7%]), and Nocardia species (55 cases [11.5%]). Isolates from patients who reported fluoroquinolone use at presentation had a 2.01-fold–higher minimum inhibitory concentration (95% CI, 1.39-fold to 2.91-fold; P <.001). Fourth-generation fluoroquinolones were associated with a 3.48-fold–higher minimum inhibitory concentration than those isolates that were not exposed to pretreatment at enrollment (95% CI, 1.99-fold to 6.06-fold; P <.001). Conclusion This study provides evidence that prior use of fluoroquinolones is associated with antibiotic resistance. PMID:23307105

Fluoroquinolone treatment and susceptibility of isolates from bacterial keratitis.

PubMed

Ray, Kathryn J; Prajna, Lalitha; Srinivasan, Muthiah; Geetha, Manoharan; Karpagam, Rajarathinam; Glidden, David; Oldenburg, Catherine E; Sun, Catherine Q; McLeod, Stephen D; Acharya, Nisha R; Lietman, Thomas M

2013-03-01

To analyze the relationship between fluoroquinolone use at presentation and minimum inhibitory concentration in bacterial keratitis. The Steroids for Corneal Ulcers Trial was a randomized, double-masked, placebo-controlled trial assessing the effect of adjunctive topical corticosteroid treatment on outcomes in bacterial keratitis. After presentation, all patients were treated with moxifloxacin hydrochloride, 0.5%. We compare antibiotic use at presentation with minimum inhibitory concentration against moxifloxacin for all isolates. Separate analyses accounted for organism species and fluoroquinolone generation. Topical fluoroquinolone use at presentation was reported in 92 of 480 cases (19.2%). Causative organisms in the 480 cases included Streptococcus pneumoniae (247 cases [51.5%]), Pseudomonas aeruginosa (109 cases [22.7%]), and Nocardia species (55 cases [11.5%]). Isolates from patients who reported fluoroquinolone use at presentation had a 2.01-fold-higher minimum inhibitory concentration (95% CI, 1.39-fold to 2.91-fold; P < .001). Fourth-generation fluoroquinolones were associated with a 3.48-fold-higher minimum inhibitory concentration than those isolates that were not exposed to pretreatment at enrollment (95% CI, 1.99-fold to 6.06-fold; P < .001). This study provides evidence that prior use of fluoroquinolones is associated with antibiotic resistance. clinicaltrials.gov Identifier: NCT00324168.

Intestinal Epithelial Cells Modulate Antigen-Presenting Cell Responses to Bacterial DNA

PubMed Central

Campeau, J. L.; Salim, S. Y.; Albert, E. J.; Hotte, N.

2012-01-01

Intestinal epithelial cells and antigen-presenting cells orchestrate mucosal innate immunity. This study investigated the role of bacterial DNA in modulating epithelial and bone marrow-derived antigen-presenting cells (BM-APCs) and subsequent T-lymphocyte responses. Murine MODE-K epithelial cells and BM-APCs were treated with DNA from either Bifidobacterium breve or Salmonella enterica serovar Dublin directly and under coculture conditions with CD4+ T cells. Apical stimulation of MODE-K cells with S. Dublin DNA enhanced secretion of cytokines from underlying BM-APCs and induced interleukin-17 (IL-17) and gamma interferon (IFN-γ) secretion from CD4+ T cells. Bacterial DNA isolated from either strain induced maturation and increased cytokine secretion from BM-APCs. Conditioned medium from S. Dublin-treated MODE-K cells elicited an increase in cytokine secretion similar to that seen for S. Dublin DNA. Treatment of conditioned medium from MODE-K cells with RNase and protease prevented the S. Dublin-induced increased cytokine secretion. Oral feeding of mice with B. breve DNA resulted in enhanced levels of colonic IL-10 and transforming growth factor β (TGFβ) compared with what was seen for mice treated with S. Dublin DNA. In contrast, feeding mice with S. Dublin DNA increased levels of colonic IL-17 and IL-12p70. T cells from S. Dublin DNA-treated mice secreted high levels of IL-12 and IFN-γ compared to controls and B. breve DNA-treated mice. These results demonstrate that intestinal epithelial cells are able to modulate subsequent antigen-presenting and T-cell responses to bacterial DNA with pathogenic but not commensal bacterial DNA inducing effector CD4+ T lymphocytes. PMID:22615241

Comparison of the test characteristics of procalcitonin to C-reactive protein and leukocytosis for the detection of serious bacterial infections in children presenting with fever without source: a systematic review and meta-analysis.

PubMed

Yo, Chia-Hung; Hsieh, Pei-Shan; Lee, Si-Huei; Wu, Jiunn-Yih; Chang, Shy-Shin; Tasi, Kuang-Chau; Lee, Chien-Chang

2012-11-01

We determine the usefulness of the procalcitonin for early identification of young children at risk for severe bacterial infection among those presenting with fever without source. The design was a systematic review and meta-analysis of diagnostic studies. Data sources were searches of MEDLINE and EMBASE in April 2011. Included were diagnostic studies that evaluated the diagnostic value of procalcitonin alone or compared with other laboratory markers, such as C-reactive protein or leukocyte count, to detect severe bacterial infection in children with fever without source who were aged between 7 days and 36 months. Eight studies were included (1,883 patients) for procalcitonin analysis, 6 (1,265 patients) for C-reactive protein analysis, and 7 (1,649 patients) for leukocyte analysis. The markers differed in their ability to predict serious bacterial infection: procalcitonin (odds ratio [OR] 10.6; 95% confidence interval [CI] 6.9 to 16.0), C-reactive protein (OR 9.83; 95% CI 7.05 to 13.7), and leukocytosis (OR 4.26; 95% CI 3.22 to 5.63). The random-effect model was used for procalcitonin analysis because heterogeneity across studies existed. Overall sensitivity was 0.83 (95% CI 0.70 to 0.91) for procalcitonin, 0.74 (95% CI 0.65 to 0.82) for C-reactive protein, and 0.58 (95% CI 0.49 to 0.67) for leukocyte count. Overall specificity was 0.69 (95% CI 0.59 to 0.85) for procalcitonin, 0.76 (95% CI 0.70 to 0.81) for C-reactive protein, and 0.73 (95% CI 0.67 to 0.77) for leukocyte count. Procalcitonin performs better than leukocyte count and C-reactive protein for detecting serious bacterial infection among children with fever without source. Considering the poor pooled positive likelihood ratio and acceptable pooled negative likelihood ratio, procalcitonin is better for ruling out serious bacterial infection than for ruling it in. Existing studies do not define how best to combine procalcitonin with other clinical information. Copyright © 2012. Published by Mosby, Inc.

Bacterial uptake of antibiotics in model unsaturated systems

NASA Astrophysics Data System (ADS)

Zhang, W.; Chen, Z.; Zhang, Y.; Zhao, Z.; Wang, G.; Gao, Y.; Boyd, S. A.; Zhu, D.; Li, H.

2016-12-01

Anthropogenic antibiotics are ubiquitously present in the environment due to large uses in human medicine and animal agriculture, and are causing unintended consequence to human and ecosystem health. Bacterial uptake of antibiotics could exert selection pressure on antibiotic resistance development among bacteria population. Therefore, understanding environmental factors controlling bioavailability of antibiotics to bacteria is critical to better assessing exposure risks and developing mitigation strategies. Nonetheless, conventional bioavailability assays are often performed in water-saturated systems that do not represent unsaturated soils where most bacteria live, therefore neglecting soil water as a controlling factor in determining the extent of antibiotic bacterial uptake. Therefore, we propose to study bacterial uptake of antibiotics in model unsaturated systems using GFP-tagged Escherichia coli bioreporter for tetracyclines. Our preliminary studies demonstrated the important role of water content (or water matric potential) in determining the bioavailability of antibiotics, and complex interactions of water potential, tetracycline diffusion, and E. coli growth. Therefore, unsaturated processes are important for understanding antibiotic resistance development and developing mitigation strategies.

Phytochemical, toxicological and antimicrobial evaluation of Lawsonia inermis extracts against clinical isolates of pathogenic bacteria.

PubMed

Gull, Iram; Sohail, Maria; Aslam, Muhammad Shahbaz; Amin Athar, Muhammad

2013-12-01

The emerging resistance of pathogen against the currently available antimicrobial agents demands the search of new antimicrobial agents. The use of medicinal plants as natural substitute is the paramount area of research to overwhelm the drug resistance of infectious agents. Scientists have not made enough effort on the evaluation of safety of medicinal plant yet. In the present study antimicrobial activity of Lawsonia inermis is investigated against clinical isolates of seven bacteria including four Gram negative (Escherichia coli, Salmonella typhi, Klebsiella spp., Shigella sonnei) and three Gram positive (Bacillus subtilis, Staphylococcus aureus, Staphylococcus epidermidis) using disc diffusion method. Four types of Lawsonia inermis extracts were prepared using methanol, chloroform, acetone and water as extraction solvents, while DMSO (Dimethyl sulfoxide) and water as dissolution solvents. The rate and extent of bacterial killing was estimated by time-kill kinetic assay at 1× MIC of each bacterial isolate. The overall safety of Lawsonia inermis extracts was assessed in mice. Lawsonia inermis displayed noteworthy antimicrobial activity against both gram positive and gram negative bacterial strains used in the study. The minimum value of MIC for different bacterial strains ranged from 2.31 mg/ml to 9.27 mg/ml. At 1x MIC of each bacterial isolate, 3log10 decrease in CFU was recorded after 6 hours of drug exposure and no growth was observed in almost all tested bacteria after 24 hours of exposure. No sign of toxidrome were observed during in vivo toxicity evaluation in mice at 300 mg/kg concentration. In conclusion, the present study provides the scientific rational for medicinal use of Lawsonia inermis. The use of Lawsonia inermis extracts is of great significance as substitute antimicrobial agent in therapeutics.

Phytochemical, toxicological and antimicrobial evaluation of lawsonia inermis extracts against clinical isolates of pathogenic bacteria

PubMed Central

2013-01-01

Background The emerging resistance of pathogen against the currently available antimicrobial agents demands the search of new antimicrobial agents. The use of medicinal plants as natural substitute is the paramount area of research to overwhelm the drug resistance of infectious agents. Scientists have not made enough effort on the evaluation of safety of medicinal plant yet. Methods In the present study antimicrobial activity of Lawsonia inermis is investigated against clinical isolates of seven bacteria including four Gram negative (Escherichia coli, Salmonella typhi, Klebsiella spp., Shigella sonnei) and three Gram positive (Bacillus subtilis, Staphylococcus aureus, Staphylococcus epidermidis) using disc diffusion method. Four types of Lawsonia inermis extracts were prepared using methanol, chloroform, acetone and water as extraction solvents, while DMSO (Dimethyl sulfoxide) and water as dissolution solvents. The rate and extent of bacterial killing was estimated by time-kill kinetic assay at 1× MIC of each bacterial isolate. The overall safety of Lawsonia inermis extracts was assessed in mice. Results Lawsonia inermis displayed noteworthy antimicrobial activity against both gram positive and gram negative bacterial strains used in the study. The minimum value of MIC for different bacterial strains ranged from 2.31 mg/ml to 9.27 mg/ml. At 1x MIC of each bacterial isolate, 3log10 decrease in CFU was recorded after 6 hours of drug exposure and no growth was observed in almost all tested bacteria after 24 hours of exposure. No sign of toxidrome were observed during in vivo toxicity evaluation in mice at 300 mg/kg concentration. Conclusion In conclusion, the present study provides the scientific rational for medicinal use of Lawsonia inermis. The use of Lawsonia inermis extracts is of great significance as substitute antimicrobial agent in therapeutics. PMID:24289297

Incidence and Predictors of Bacterial infection in Febrile Children with Sickle Cell Disease.

PubMed

Morrissey, Benita J; Bycroft, Thomas P; Almossawi, Ofran; Wilkey, Olufunke B; Daniels, Justin G

2015-01-01

Children with sickle cell disease are at increased risk of developing bacteremia and other serious bacterial infections. Fever is a common symptom in sickle cell disease and can also occur with sickle cell crises and viral infections. We aimed to evaluate the incidence and predictors of bacteremia and bacterial infection in children with sickle cell disease presenting with fever to a district hospital and sickle cell center in London. A retrospective analysis was performed on all attendances of children (aged under 16 years) with sickle cell disease presenting with a fever of 38.5 °C or higher over a 1-year period. Confirmed bacterial infection was defined as bacteremia, bacterial meningitis, urinary tract infection (UTI), pneumonia, osteomyelitis or other bacterial infection with positive identification of organism. Children were defined as having a suspected bacterial infection if a bacterial infection was suspected clinically, but no organism was identified. Over a 1-year period there were 88 episodes analyzed in 59 children. Bacteremia occurred in 3.4% of episodes and confirmed bacterial infection in 7.0%. Suspected bacterial infection occurred in 33.0%. One death occurred from Salmonella typhirium septicemia. C-reactive protein (CRP) level and white blood cell (WBC) count were both significantly associated with bacterial infection (p = 0.004 and 0.02, respectively.) In conclusion, bacterial infections continue to be a significant problem in children with sickle cell disease. C-reactive protein was significantly associated with bacterial infections, and could be included in clinical risk criteria for febrile children with sickle cell disease.

A proteomics approach to study synergistic and antagonistic interactions of the fungal-bacterial consortium Fusarium oxysporum wild-type MSA 35.

PubMed

Moretti, Marino; Grunau, Alexander; Minerdi, Daniela; Gehrig, Peter; Roschitzki, Bernd; Eberl, Leo; Garibaldi, Angelo; Gullino, Maria Lodovica; Riedel, Kathrin

2010-09-01

Fusarium oxysporum is an important plant pathogen that causes severe damage of many economically important crop species. Various microorganisms have been shown to inhibit this soil-borne plant pathogen, including non-pathogenic F. oxysporum strains. In this study, F. oxysporum wild-type (WT) MSA 35, a biocontrol multispecies consortium that consists of a fungus and numerous rhizobacteria mainly belonging to gamma-proteobacteria, was analyzed by two complementary metaproteomic approaches (2-DE combined with MALDI-Tof/Tof MS and 1-D PAGE combined with LC-ESI-MS/MS) to identify fungal or bacterial factors potentially involved in antagonistic or synergistic interactions between the consortium members. Moreover, the proteome profiles of F. oxysporum WT MSA 35 and its cured counter-part CU MSA 35 (WT treated with antibiotics) were compared with unravel the bacterial impact on consortium functioning. Our study presents the first proteome mapping of an antagonistic F. oxysporum strain and proposes candidate proteins that might play an important role for the biocontrol activity and the close interrelationship between the fungus and its bacterial partners.

Bacterial computing: a form of natural computing and its applications.

PubMed

Lahoz-Beltra, Rafael; Navarro, Jorge; Marijuán, Pedro C

2014-01-01

The capability to establish adaptive relationships with the environment is an essential characteristic of living cells. Both bacterial computing and bacterial intelligence are two general traits manifested along adaptive behaviors that respond to surrounding environmental conditions. These two traits have generated a variety of theoretical and applied approaches. Since the different systems of bacterial signaling and the different ways of genetic change are better known and more carefully explored, the whole adaptive possibilities of bacteria may be studied under new angles. For instance, there appear instances of molecular "learning" along the mechanisms of evolution. More in concrete, and looking specifically at the time dimension, the bacterial mechanisms of learning and evolution appear as two different and related mechanisms for adaptation to the environment; in somatic time the former and in evolutionary time the latter. In the present chapter it will be reviewed the possible application of both kinds of mechanisms to prokaryotic molecular computing schemes as well as to the solution of real world problems.

L-arginine mediated renaturation enhances yield of human, α6 type IV collagen non-collagenous domain from bacterial inclusion bodies

PubMed Central

Gunda, Venugopal; Boosani, Chandra Shekhar; Verma, Raj Kumar; Guda, Chittibabu; Akul Sudhakar, Yakkanti

2012-01-01

The anti-angiogenic, carboxy terminal non-collagenous domain (NC1) derived from human Collagen type IV alpha 6 chain, [α6(IV)NC1] or hexastatin, was earlier obtained using different recombinant methods of expression in bacterial systems. However, the effect of L-arginine mediated renaturation in enhancing the relative yields of this protein from bacterial inclusion bodies has not been evaluated. In the present study, direct stirring and on-column renaturation methods using L-arginine and different size exclusion chromatography matrices were applied for enhancing the solubility in purifying the recombinant α6(IV)NC1 from bacterial inclusion bodies. This methodology enabled purification of higher quantities of soluble protein from inclusion bodies, which inhibited endothelial cell proliferation, migration and tube formation. Thus, the scope for L-arginine mediated renaturation in obtaining higher yields of soluble, biologically active NC1 domain from bacterial inclusion bodies was evaluated. PMID:22512648

L-arginine mediated renaturation enhances yield of human, α6 Type IV collagen non-collagenous domain from bacterial inclusion bodies.

PubMed

Gunda, Venugopal; Boosani, Chandra Shekhar; Verma, Raj Kumar; Guda, Chittibabu; Sudhakar, Yakkanti Akul

2012-10-01

The anti-angiogenic, carboxy terminal non-collagenous domain (NC1) derived from human Collagen type IV alpha 6 chain, [α6(IV)NC1] or hexastatin, was earlier obtained using different recombinant methods of expression in bacterial systems. However, the effect of L-arginine mediated renaturation in enhancing the relative yields of this protein from bacterial inclusion bodies has not been evaluated. In the present study, direct stirring and on-column renaturation methods using L-arginine and different size exclusion chromatography matrices were applied for enhancing the solubility in purifying the recombinant α6(IV)NC1 from bacterial inclusion bodies. This methodology enabled purification of higher quantities of soluble protein from inclusion bodies, which inhibited endothelial cell proliferation, migration and tube formation. Thus, the scope for L-arginine mediated renaturation in obtaining higher yields of soluble, biologically active NC1 domain from bacterial inclusion bodies was evaluated.

Carbohydrate hydrogels with stabilized phage particles for bacterial biosensing: bacterium diffusion studies.

PubMed

Balcão, Victor M; Barreira, Sérgio V P; Nunes, Thiago M; Chaud, Marco V; Tubino, Matthieu; Vila, Marta M D C

2014-02-01

Bacteriophage particles have been reported as potentially useful in the development of diagnosis tools for pathogenic bacteria as they specifically recognize and lyse bacterial isolates thus confirming the presence of viable cells. One of the most representative microorganisms associated with health care services is the bacterium Pseudomonas aeruginosa, which alone is responsible for nearly 15% of all nosocomial infections. In this context, structural and functional stabilization of phage particles within biopolymeric hydrogels, aiming at producing cheap (chromogenic) bacterial biosensing devices, has been the goal of a previous research effort. For this, a detailed knowledge of the bacterial diffusion profile into the hydrogel core, where the phage particles lie, is of utmost importance. In the present research effort, the bacterial diffusion process into the biopolymeric hydrogel core was mathematically described and the theoretical simulations duly compared with experimental results, allowing determination of the effective diffusion coefficients of P. aeruginosa in the agar and calcium alginate hydrogels tested.

Bacterial computing: a form of natural computing and its applications

PubMed Central

Lahoz-Beltra, Rafael; Navarro, Jorge; Marijuán, Pedro C.

2014-01-01

The capability to establish adaptive relationships with the environment is an essential characteristic of living cells. Both bacterial computing and bacterial intelligence are two general traits manifested along adaptive behaviors that respond to surrounding environmental conditions. These two traits have generated a variety of theoretical and applied approaches. Since the different systems of bacterial signaling and the different ways of genetic change are better known and more carefully explored, the whole adaptive possibilities of bacteria may be studied under new angles. For instance, there appear instances of molecular “learning” along the mechanisms of evolution. More in concrete, and looking specifically at the time dimension, the bacterial mechanisms of learning and evolution appear as two different and related mechanisms for adaptation to the environment; in somatic time the former and in evolutionary time the latter. In the present chapter it will be reviewed the possible application of both kinds of mechanisms to prokaryotic molecular computing schemes as well as to the solution of real world problems. PMID:24723912

Sink or link? The bacterial role in benthic carbon cycling in the Arabian Sea's oxygen minimum zone

NASA Astrophysics Data System (ADS)

Pozzato, L.; Van Oevelen, D.; Moodley, L.; Soetaert, K.; Middelburg, J. J.

2013-11-01

The bacterial loop, the consumption of dissolved organic matter (DOM) by bacteria and subsequent transfer of bacterial carbon to higher trophic levels, plays a prominent role in pelagic food webs. However, its role in sedimentary ecosystems is not well documented. Here we present the results of isotope tracer experiments performed under in situ oxygen conditions in sediments from inside and outside the Arabian Sea's oxygen minimum zone (OMZ) to study the importance of the microbial loop in this setting. Particulate organic matter, added as phytodetritus, was processed by bacteria, protozoa and metazoans, while dissolved organic matter was processed only by bacteria and there was very little, if any, transfer to higher trophic levels within the 7 day experimental period. This lack of significant transfer of bacterial-derived carbon to metazoan consumers indicates that the bacterial loop is rather inefficient, in sediments both inside and outside the OMZ. Moreover, metazoans directly consumed labile particulate organic matter resources and thus competed with bacteria for phytodetritus.

Sink or link? The bacterial role in benthic carbon cycling in the Arabian sea oxygen minimum zone

NASA Astrophysics Data System (ADS)

Pozzato, L.; Van Oevelen, D.; Moodley, L.; Soetaert, K.; Middelburg, J. J.

2013-06-01

The bacterial loop, the consumption of dissolved organic matter (DOM) by bacteria and subsequent transfer of bacterial carbon to higher trophic levels, plays a prominent role in pelagic aquatic food webs. However, its role in sedimentary ecosystems is not well documented. Here we present the results of isotope tracer experiments performed under in situ oxygen conditions in sediments from inside and outside the Arabian Sea Oxygen Minimum Zone (OMZ) to study the importance of the microbial loop in this setting. Particulate organic matter, added as phytodetritus, was processed by bacteria, protozoa and metazoans, while dissolved organic matter was processed only by bacteria and there was very little, if any, transfer to higher trophic levels within the experimental period. This lack of significant transfer of bacterial-derived carbon to metazoan consumers indicates that the bacterial loop is rather inefficient in these sediments. Moreover, metazoans directly consume labile particulate organic matter resources and thus compete with bacteria for phytodetritus.

On the usage of classical nucleation theory in quantification of the impact of bacterial INP on weather and climate

NASA Astrophysics Data System (ADS)

Sahyoun, Maher; Wex, Heike; Gosewinkel, Ulrich; Šantl-Temkiv, Tina; Nielsen, Niels W.; Finster, Kai; Sørensen, Jens H.; Stratmann, Frank; Korsholm, Ulrik S.

2016-08-01

Bacterial ice-nucleating particles (INP) are present in the atmosphere and efficient in heterogeneous ice-nucleation at temperatures up to -2 °C in mixed-phase clouds. However, due to their low emission rates, their climatic impact was considered insignificant in previous modeling studies. In view of uncertainties about the actual atmospheric emission rates and concentrations of bacterial INP, it is important to re-investigate the threshold fraction of cloud droplets containing bacterial INP for a pronounced effect on ice-nucleation, by using a suitable parameterization that describes the ice-nucleation process by bacterial INP properly. Therefore, we compared two heterogeneous ice-nucleation rate parameterizations, denoted CH08 and HOO10 herein, both of which are based on classical-nucleation-theory and measurements, and use similar equations, but different parameters, to an empirical parameterization, denoted HAR13 herein, which considers implicitly the number of bacterial INP. All parameterizations were used to calculate the ice-nucleation probability offline. HAR13 and HOO10 were implemented and tested in a one-dimensional version of a weather-forecast-model in two meteorological cases. Ice-nucleation-probabilities based on HAR13 and CH08 were similar, in spite of their different derivation, and were higher than those based on HOO10. This study shows the importance of the method of parameterization and of the input variable, number of bacterial INP, for accurately assessing their role in meteorological and climatic processes.

The Drosophila melanogaster host model.

PubMed

Igboin, Christina O; Griffen, Ann L; Leys, Eugene J

2012-01-01

The deleterious and sometimes fatal outcomes of bacterial infectious diseases are the net result of the interactions between the pathogen and the host, and the genetically tractable fruit fly, Drosophila melanogaster, has emerged as a valuable tool for modeling the pathogen-host interactions of a wide variety of bacteria. These studies have revealed that there is a remarkable conservation of bacterial pathogenesis and host defence mechanisms between higher host organisms and Drosophila. This review presents an in-depth discussion of the Drosophila immune response, the Drosophila killing model, and the use of the model to examine bacterial-host interactions. The recent introduction of the Drosophila model into the oral microbiology field is discussed, specifically the use of the model to examine Porphyromonas gingivalis-host interactions, and finally the potential uses of this powerful model system to further elucidate oral bacterial-host interactions are addressed.

A Primer on Infectious Disease Bacterial Genomics

PubMed Central

Petkau, Aaron; Knox, Natalie; Graham, Morag; Van Domselaar, Gary

2016-01-01

SUMMARY The number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects. PMID:28590251

You Are What You Eat: A Genomic Analysis of the Gut Microbiome of Captive and Wild Octopus vulgaris Paralarvae and Their Zooplankton Prey

PubMed Central

Roura, Álvaro; Doyle, Stephen R.; Nande, Manuel; Strugnell, Jan M.

2017-01-01

The common octopus (Octopus vulgaris) is an attractive species for aquaculture, however, several challenges inhibit sustainable commercial production. Little is known about the early paralarval stages in the wild, including diet and intestinal microbiota, which likely play a significant role in development and vitality of this important life stage. High throughput sequencing was used to characterize the gastrointestinal microbiome of wild O. vulgaris paralarvae collected from two different upwelling regions off the coast of North West Spain (n = 41) and Morocco (n = 35). These were compared to that of paralarvae reared with Artemia for up to 25 days in captivity (n = 29). In addition, the gastrointestinal microbiome of zooplankton prey (crabs, copepod and krill) was also analyzed to determine if the microbial communities present in wild paralarvae are derived from their diet. Paralarvae reared in captivity with Artemia showed a depletion of bacterial diversity, particularly after day 5, when almost half the bacterial species present on day 0 were lost and two bacterial families (Mycoplasmataceae and Vibrionaceae) dominated the microbial community. In contrast, bacterial diversity increased in wild paralarvae as they developed in the oceanic realm of both upwelling systems, likely due to the exposure of new bacterial communities via ingestion of a wide diversity of prey. Remarkably, the bacterial diversity of recently hatched paralarvae in captivity was similar to that of wild paralarvae and zooplankton, thus suggesting a marked effect of the diet in both the microbial community species diversity and evenness. This study provides a comprehensive overview of the bacterial communities inhabiting the gastrointestinal tract of O. vulgaris paralarvae, and reveals new research lines to challenge the current bottlenecks preventing sustainable octopus aquaculture. PMID:28620315

You Are What You Eat: A Genomic Analysis of the Gut Microbiome of Captive and Wild Octopus vulgaris Paralarvae and Their Zooplankton Prey.

PubMed

Roura, Álvaro; Doyle, Stephen R; Nande, Manuel; Strugnell, Jan M

2017-01-01

The common octopus ( Octopus vulgaris ) is an attractive species for aquaculture, however, several challenges inhibit sustainable commercial production. Little is known about the early paralarval stages in the wild, including diet and intestinal microbiota, which likely play a significant role in development and vitality of this important life stage. High throughput sequencing was used to characterize the gastrointestinal microbiome of wild O. vulgaris paralarvae collected from two different upwelling regions off the coast of North West Spain ( n = 41) and Morocco ( n = 35). These were compared to that of paralarvae reared with Artemia for up to 25 days in captivity ( n = 29). In addition, the gastrointestinal microbiome of zooplankton prey (crabs, copepod and krill) was also analyzed to determine if the microbial communities present in wild paralarvae are derived from their diet. Paralarvae reared in captivity with Artemia showed a depletion of bacterial diversity, particularly after day 5, when almost half the bacterial species present on day 0 were lost and two bacterial families (Mycoplasmataceae and Vibrionaceae) dominated the microbial community. In contrast, bacterial diversity increased in wild paralarvae as they developed in the oceanic realm of both upwelling systems, likely due to the exposure of new bacterial communities via ingestion of a wide diversity of prey. Remarkably, the bacterial diversity of recently hatched paralarvae in captivity was similar to that of wild paralarvae and zooplankton, thus suggesting a marked effect of the diet in both the microbial community species diversity and evenness. This study provides a comprehensive overview of the bacterial communities inhabiting the gastrointestinal tract of O. vulgaris paralarvae, and reveals new research lines to challenge the current bottlenecks preventing sustainable octopus aquaculture.

Bacterial gene transfer by natural genetic transformation in the environment.

PubMed Central

Lorenz, M G; Wackernagel, W

1994-01-01

Natural genetic transformation is the active uptake of free DNA by bacterial cells and the heritable incorporation of its genetic information. Since the famous discovery of transformation in Streptococcus pneumoniae by Griffith in 1928 and the demonstration of DNA as the transforming principle by Avery and coworkers in 1944, cellular processes involved in transformation have been studied extensively by in vitro experimentation with a few transformable species. Only more recently has it been considered that transformation may be a powerful mechanism of horizontal gene transfer in natural bacterial populations. In this review the current understanding of the biology of transformation is summarized to provide the platform on which aspects of bacterial transformation in water, soil, and sediments and the habitat of pathogens are discussed. Direct and indirect evidence for gene transfer routes by transformation within species and between different species will be presented, along with data suggesting that plasmids as well as chromosomal DNA are subject to genetic exchange via transformation. Experiments exploring the prerequisites for transformation in the environment, including the production and persistence of free DNA and factors important for the uptake of DNA by cells, will be compiled, as well as possible natural barriers to transformation. The efficiency of gene transfer by transformation in bacterial habitats is possibly genetically adjusted to submaximal levels. The fact that natural transformation has been detected among bacteria from all trophic and taxonomic groups including archaebacteria suggests that transformability evolved early in phylogeny. Probable functions of DNA uptake other than gene acquisition will be discussed. The body of information presently available suggests that transformation has a great impact on bacterial population dynamics as well as on bacterial evolution and speciation. PMID:7968924

Distinctive bacterial communities in the rhizoplane of four tropical tree species.

PubMed

Oh, Yoon Myung; Kim, Mincheol; Lee-Cruz, Larisa; Lai-Hoe, Ang; Go, Rusea; Ainuddin, N; Rahim, Raha Abdul; Shukor, Noraini; Adams, Jonathan M

2012-11-01

It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0-10 cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both tropical forestry and conservation.

Direct Growth of Bacteria in Headspace Vials Allows for Screening of Volatiles by Gas Chromatography Mass Spectrometry.

PubMed

Timm, Collin M; Lloyd, Evan P; Egan, Amanda; Mariner, Ray; Karig, David

2018-01-01

Bacterially produced volatile organic compounds (VOCs) can modify growth patterns of eukaryotic hosts and competing/cohabiting microbes. These compounds have been implicated in skin disorders and attraction of biting pests. Current methods to detect and characterize VOCs from microbial cultures can be laborious and low-throughput, making it difficult to understand the behavior of microbial populations. In this work we present an efficient method employing gas chromatography/mass spectrometry with autosampling to characterize VOC profiles from solid-phase bacterial cultures. We compare this method to complementary plate-based assays and measure the effects of growth media and incubation temperature on the VOC profiles from a well-studied Pseudomonas aeruginosa PAO1 system. We observe that P. aeruginosa produces longer chain VOCs, such as 2-undecanone and 2-undecanol in higher amounts at 37°C than 30°C. We demonstrate the throughput of this method by studying VOC profiles from a representative collection of skin bacterial isolates under three parallel growth conditions. We observe differential production of various aldehydes and ketones depending on bacterial strain. This generalizable method will support screening of bacterial populations in a variety of research areas.

Evaluation of bacterial flora during the ripening of Kedong sufu, a typical Chinese traditional bacteria-fermented soybean product.

PubMed

Feng, Zhen; Gao, Wei; Ren, Dan; Chen, Xi; Li, Juan-juan

2013-04-01

Kedong sufu is a typical bacteria-fermented sufu in China. Isolation and identification of the autochthonous bacteria involved would allow the design of specific starters for this speciality. The purpose of the present study was to evaluate the bacterial flora during the ripening of Kedong sufu using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and culturing. In terms of bacterial diversity, 22 strains were isolated and identified and 27 strains were detected by DGGE. Regarding bacterial dynamics, the results of culturing and PCR-DGGE exhibited a similar trend towards dominant strains. Throughout the fermentation of sufu, Enterococcus avium, Enterococcus faecalis and Staphylococcus carnosus were the dominant microflora, while the secondary microflora comprised Leuconostoc mesenteroides, Staphylococcus saprophyticus, Streptococcus lutetiensis, Kocuria rosea, Kocuria kristinae, Bacillus pumilus, Bacillus cereus and Bacillus subtilis. This study is the first to reveal the bacterial flora during the ripening of Kedong sufu using both culture-dependent and culture-independent methods. This information will help in the design of autochthonous starter cultures for the production of Kedong sufu with desirable characteristic sensory profiles and shorter ripening times. © 2012 Society of Chemical Industry.

From source to filter: changes in bacterial community composition during potable water treatment.

PubMed

Zanacic, Enisa; McMartin, Dena W; Stavrinides, John

2017-06-01

Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNA-based profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of 2 rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria, with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of transects of a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although Mycobacterium was of high abundance and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.

Direct Growth of Bacteria in Headspace Vials Allows for Screening of Volatiles by Gas Chromatography Mass Spectrometry

PubMed Central

Timm, Collin M.; Lloyd, Evan P.; Egan, Amanda; Mariner, Ray; Karig, David

2018-01-01

Bacterially produced volatile organic compounds (VOCs) can modify growth patterns of eukaryotic hosts and competing/cohabiting microbes. These compounds have been implicated in skin disorders and attraction of biting pests. Current methods to detect and characterize VOCs from microbial cultures can be laborious and low-throughput, making it difficult to understand the behavior of microbial populations. In this work we present an efficient method employing gas chromatography/mass spectrometry with autosampling to characterize VOC profiles from solid-phase bacterial cultures. We compare this method to complementary plate-based assays and measure the effects of growth media and incubation temperature on the VOC profiles from a well-studied Pseudomonas aeruginosa PAO1 system. We observe that P. aeruginosa produces longer chain VOCs, such as 2-undecanone and 2-undecanol in higher amounts at 37°C than 30°C. We demonstrate the throughput of this method by studying VOC profiles from a representative collection of skin bacterial isolates under three parallel growth conditions. We observe differential production of various aldehydes and ketones depending on bacterial strain. This generalizable method will support screening of bacterial populations in a variety of research areas. PMID:29662472

Evaluation of the bacterial diversity in the rumen and feces of cattle fed different diets containing levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

USDA-ARS?s Scientific Manuscript database

Dietary components and changes cause shifts in the intestinal ecology of the gut, which can play a role in animal health and productivity. However, most information about the microbial populations in the gut of livestock species has not been quantitative. In the present study, we utilized a new m...

Role of berberine in anti-bacterial as a high-affinity LPS antagonist binding to TLR4/MD-2 receptor

PubMed Central

2014-01-01

Background Berberine is an isoquinoline alkaloid mainly extracted from Rhizoma Coptidis and has been shown to possess a potent inhibitory activity against bacterial. However, the role of berberine in anti-bacterial action has not been extensively studied. Methods The animal model was established to investigate the effects of berberine on bacterial and LPS infection. Docking analysis, Molecular dynamics simulations and Real-time RT-PCR analysis was adopted to investigate the molecular mechanism. Results Treatment with 40 mg/kg berberine significantly increased the survival rate of mice challenged with Salmonella typhimurium (LT2), but berberine show no effects in bacteriostasis. Further study indicated that treatment with 0.20 g/kg berberine markedly increased the survival rate of mice challenged with 2 EU/ml bacterial endotoxin (LPS) and postpone the death time of the dead mice. Moreover, pretreatment with 0.05 g/kg berberine significantly lower the increasing temperature of rabbits challenged with LPS. The studies of molecular mechanism demonstrated that Berberine was able to bind to the TLR4/MD-2 receptor, and presented higher affinity in comparison with LPS. Furthermore, berberine could significantly suppressed the increasing expression of NF-κB, IL-6, TNFα, and IFNβ in the RAW264.7 challenged with LPS. Conclusion Berberine can act as a LPS antagonist and block the LPS/TLR4 signaling from the sourse, resulting in the anti-bacterial action. PMID:24602493

Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis

PubMed Central

Tian, Ren-Mao; Lee, On On; Wang, Yong; Cai, Lin; Bougouffa, Salim; Chiu, Jill Man Ying; Wu, Rudolf Shiu Sun; Qian, Pei-Yuan

2014-01-01

Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2′,4,4′-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge. PMID:25642227

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado.

PubMed

de Araujo, Ademir Sergio Ferreira; Bezerra, Walderly Melgaço; Dos Santos, Vilma Maria; Rocha, Sandra Mara Barbosa; Carvalho, Nilza da Silva; de Lyra, Maria do Carmo Catanho Pereira; Figueiredo, Marcia do Vale Barreto; de Almeida Lopes, Ângela Celis; Melo, Vania Maria Maciel

2017-04-01

The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene. The bacterial operational taxonomic units (OTUs) were assigned to 37 different phyla, 96 classes, and 83 genera. At the phylum level, a core comprised by Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Verrucomicrobia and Planctomycetes, was detected in all areas of Cerrado. 'Cerrado stricto sensu' and 'Cerradao' share more similarities between edaphic properties and vegetation and also present more similar bacterial communities, while 'Floresta decidual' and 'Campo graminoide' show the largest environmental differences and also more distinct bacterial communities. Proteobacteria (26%), Acidobacteria (21%) and Actinobacteria (21%) were the most abundant phyla within the four areas. All the samples present similar bacteria richness (alpha diversity) and the observed differences among them (beta diversity) were more related to the abundance of specific taxon OTUs compared to their presence or absence. Total organic C, N and P are the main abiotic factors structuring the bacterial communities. In summary, our findings show the bacterial community structure was clearly different across the Cerrado gradient, but that these environments share a bacterial phylum-core comprising Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes with other Brazilian savannas.

Molecular identification and antibiotic resistant bacteria isolated from primary dentition infections.

PubMed

Loyola-Rodriguez, J P; Garcia-Cortes, J O; Martinez-Martinez, R E; Patiño-Marin, N; Martinez-Castañon, G A; Zavala-Alonso, N V; Amano, A

2014-12-01

Bacterial resistance to antibiotics is a health problem in many parts of the world. The aim of this study was to identify bacteria from dental infections and determine bacterial resistance to antibiotics used in dental care in the primary dentition. This cross-sectional study comprised 60 children who presented for dental treatment for active dental infections in the primary dentition. Samples from dental infections were collected and bacteria were identified by polymerase chain reaction (PCR) assay. Bacterial resistance to antibiotics was determined by colony forming units on agar plates containing amoxicillin, clindamycin and amoxillicin-clavulanic acid (A-CA) tested at 8 μg/ml or 16 μg/ml. Clindamycin in both concentrations tested (8 μg/ml and 16 μg/ml) showed the highest bacterial resistance (85.9%), followed by amoxicillin (43.7%) and A-CA (12.0%). All comparisons among the three antibiotics used in the study exhibited statistical significance (p = <0.05) in both concentrations tested (8 μg/ml and 16 μg/ml), and under aerobic and anaerobic conditions. The most prevalent resistant species identified by PCR in primary dentition infections were: Streptococcus oralis and Prevotella intermedia (75.0%); Treponema denticola and Porphyromonas gingivalis (48.3%); Streptococcus mutans (45.0%); Campylobacter rectus; and Streptococcus salivarius (40%). This study demonstrated that A-CA exhibited the lowest bacterial resistance for clinical isolates in primary dentition infections. © 2014 Australian Dental Association.

Investigation of pituitary functions in patients with acute meningitis: a pilot study.

PubMed

Tanriverdi, F; Alp, E; Demiraslan, H; Dokmetas, H S; Unluhizarci, K; Doganay, M; Casanueva, F F; Kelestimur, F

2008-06-01

Although long-term pituitary consequences of tuberculous meningitis are well documented in the literature, there have been few case reports of pituitary dysfunction after acute bacterial or viral meningitis. In this preliminary study, we have assessed the pituitary functions in adult patients who had acute bacterial or viral meningitis. Fourteen patients (8 men, 6 women; mean age 35.3+/-13.3) were included in the study. The diagnosis of bacterial and viral meningitis was proven by clinical findings, cerebrospinal fluid (CSF) examination, gram staining, and blood and CSF cultures. Pituitary functions were evaluated ranging from 6 to 48 months (mean 20 months) after acute meningitis. GH deficiency was investigated by the GHRH+arginine stimulation test. Four of 14 patients (28.6%) had isolated GH deficiency. In GH-deficient patients, the earliest duration was 6 months and the latest duration was 48 months after the diagnosis of acute meningitis. Three of the GH-deficient patients had acute bacterial meningitis and 1 patient had acute viral meningitis. Pituitary magnetic resonance imaging revealed normal pituitary gland in the patients with GH deficiency. This is the first systematic study evaluating the anterior pituitary function long term after the diagnosis of acute meningitis. Based on the present study, it is tempting to speculate that pituitary dysfunction is a more common sequel of acute bacterial or viral meningitis than hitherto reported. Studies with high numbers of patients are warranted to ascertain the prevalence of meningitis-induced hypopituitarism.

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial.

PubMed

Holscher, Hannah D; Caporaso, J Gregory; Hooda, Seema; Brulc, Jennifer M; Fahey, George C; Swanson, Kelly S

2015-01-01

In our published randomized, double-blind, placebo-controlled, 3-period crossover trial, healthy adult men (n = 21) consumed bars containing no supplemental fiber (placebo; NFC), polydextrose (21 g/d), and soluble corn fiber (SCF; 21 g/d) for 21 d each. Fecal specimens were collected between days 16 and 21 for fermentative end-product analysis and 16S ribosomal RNA bacterial gene amplification for bacterial taxa identification. Fiber supplementation decreased fecal putrefaction compounds and shifted abundances of several bacterial taxa. The objective was to perform whole-genome shotgun 454 pyrosequencing on the same fecal specimens collected in that clinical trial to obtain comprehensive fecal bacterial genome sequencing coverage and explore the full range of bacterial genetic information in the fecal microbiome, thereby using a systematic approach to study the impact of dietary fiber supplementation on fecal metabolites, bacterial taxa, and bacterial metagenomes. Fecal samples were subjected to whole-genome shotgun 454 pyrosequencing to identify both fecal bacterial populations present and their functional genetic capacity. Whole-genome shotgun sequencing results revealed that fiber consumption shifted the Bacteroidetes:Firmicutes ratio, increasing the relative abundance of Bacteroidetes 12 ± 2% and 13 ± 2% with polydextrose and SCF, respectively, compared with NFC. Bivariate correlations showed a positive correlation between the Bacteroidetes:Firmicutes ratio and total dietary fiber intake but not body mass index. Principal coordinates analysis of Bray-Curtis distances indicated that bacterial gene composition was more similar in participants consuming fibers (polydextrose and SCF combined) in comparison with NFC. Shifts in bacterial gene abundances after polydextrose and SCF supplementation included genes associated with carbohydrate, amino acid, and lipid metabolism, as well as metabolism of cofactors and vitamins. This study conveys novel information about the impact of dietary fiber supplementation on the phylogenetic structure and functional capacity of the fecal microbiome of healthy adults. © 2015 American Society for Nutrition.

Pyrosequencing analysis of bacterial diversity in dental unit waterlines.

PubMed

Costa, Damien; Mercier, Anne; Gravouil, Kevin; Lesobre, Jérôme; Delafont, Vincent; Bousseau, Anne; Verdon, Julien; Imbert, Christine

2015-09-15

Some infections cases due to exposure to output water from dental unit waterlines (DUWL) have been reported in the literature. However, this type of healthcare-associated risk has remained unclear and up until now the overall bacterial composition of DUWL has been poorly documented. In this study, 454 high-throughput pyrosequencing was used to investigate the bacterial community in seven dental offices (N = 7) and to identify potential bacterial pathogenic sequences. Dental unit waters (DUW) were collected from the tap water supplying units (Incoming Water; IW) to the output exposure point of the turbine handpiece (Output water; OW) following a stagnation period (OWS), and immediately after the last patient of the sampling day (OWA). A high bacterial diversity was revealed in DUW with 394 operational taxonomic units detected at the genus level. In addition to the inter-unit variability observed, results showed increased total bacterial cell concentration and shifts in bacterial community composition and abundance at the genus level, mainly within the Gamma- and Alpha-Proteobacteria class, as water circulated in the dental unit (DU). Results showed that 96.7%, 96.8% and 97.4% of the total sequences from IW, OWS and OWA respectively were common to the 3 defined water groups, thereby highlighting a common core microbiome. Results also suggested that stagnation and DU maintenance practices were critical to composition of the bacterial community. The presence of potentially pathogenic genera was detected, including Pseudomonas and Legionella spp. Emerging and opportunistic pathogenic genera such as Mycobacterium, Propionibacterium and Stenotrophomonas were likewise recovered in DUW. For the first time, an exhaustive evaluation of the bacterial communities present in DUW was performed taking into account the circulation of water within the DU. This study highlights an ignored diversity of the DUWL bacterial community. Our findings also contribute to a better appreciation of the potential infectious risk associated with dental care and suggest the importance of better managing microbial quality in DUW. Copyright © 2015 Elsevier Ltd. All rights reserved.

ELMO1 Regulates Autophagy Induction and Bacterial Clearance During Enteric Infection.

PubMed

Sarkar, Arup; Tindle, Courtney; Pranadinata, Rama F; Reed, Sharon; Eckmann, Lars; Stappenbeck, Thaddeus S; Ernst, Peter B; Das, Soumita

2017-12-19

Macrophages are specialized phagocytic cells involved in clearing invading pathogens. Previously we reported that engulfment and cell motility protein 1 (ELMO1) in macrophages mediates bacterial internalization and intestinal inflammation. Here we studied the role of ELMO1 in the fate of internalized targets. ELMO1 is present in the intracellular vesicles and enhances accumulation of the protein LC3B following engulfment of Salmonella or treatment with autophagy-inducing rapamycin. The protein ATG5 and the kinase ULK1 are involved in classical autophagy, while LC3-associated phagocytosis is ULK1 independent. ATG5 but not ULK1 cooperated with ELMO1 in LC3 accumulation after infection, suggesting the ELMO1 preferentially regulated LC3-associated phagocytosis. Because LC3-associated phagocytosis delivers cargo for degradation, the contribution of ELMO1 to the lysosome degradation pathways was evaluated by studying pH and cathepsin B activity. ELMO1-depleted macrophages showed a time-dependent increase in pH and a decrease in cathepsin B activity associated with bacterial survival. Together, ELMO1 regulates LC3B accumulation and antimicrobial responses involved in the clearance of enteric pathogens. This paper investigated how innate immune pathways involving ELMO1 work in a coordinated fashion to eliminate bacterial threats. ELMO1 is present in the phagosome and enhances bacterial clearance by differential regulation of lysosomal acidification and enzymatic activity. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Bacterial community composition in the water column of a lake formed by a former uranium open pit mine.

PubMed

Edberg, Frida; Andersson, Anders F; Holmström, Sara J M

2012-11-01

Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.

Bacteria in the apical root canals of teeth with apical periodontitis.

PubMed

Lee, Li-Wan; Lee, Ya-Ling; Hsiao, Sheng-Huang; Lin, Hung-Pin

2017-06-01

Bacteria in the tooth root canal may cause apical periodontitis. This study examined the bacterial species present in the apical root canal of teeth with apical periodontitis. Antibiotic sensitivity tests were performed to evaluate whether these identified bacterial species were susceptible to specific kinds of antibiotics. Selective media plating and biochemical tests were used first to detect the bacterial species in samples taken from the apical portion of root canals of 62 teeth with apical periodontitis. The isolated bacterial species were further confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry. We found concomitant presence of two (32 teeth) or three species (18 teeth) of bacteria in 50 (80.6%) out of 62 tested teeth. However, only 34 bacterial species were identified. Of a total of 118 bacterial isolates (83 anaerobes and 35 aerobes), Prophyromonas endodontalis was detected in 10; Bacteroides, Dialister invisus or Fusobacterium nucleatum in 9; Treponema denticola or Enterococcus faecalis in 8; Peptostreptococcus or Olsenella uli in 6; and Veillonella in 5 teeth. The other 25 bacterial species were detected in fewer than five teeth. Approximately 80-95% of bacterial isolates of anaerobes were sensitive to ampicillin/sulbactam (Unasyn), amoxicillin/clavulanate (Augmentin), cefoxitin, and clindamycin. For E. faecalis, 85-90% of bacterial isolates were sensitive to gentamicin and linezolid. Root canal infections are usually caused by a mixture of two or three species of bacteria. Specific kinds of antibiotic can be selected to control these bacterial infections after antibiotic sensitivity testing. Copyright © 2016. Published by Elsevier B.V.

A Persistent and Diverse Airway Microbiota Present during Chronic Obstructive Pulmonary Disease Exacerbations

PubMed Central

Huang, Yvonne J.; Kim, Eugenia; Cox, Michael J.; Brodie, Eoin L.; Brown, Ron; Wiener-Kronish, Jeanine P.

2010-01-01

Abstract Acute exacerbations of chronic obstructive pulmonary disease (COPD) are a major source of morbidity and contribute significantly to healthcare costs. Although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in COPD airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. The aim of this study was to comprehensively profile airway bacterial communities using a culture-independent microarray, the 16S rRNA PhyloChip, of a cohort of COPD patients requiring ventilatory support and antibiotic therapy for exacerbation-related respiratory failure. PhyloChip analysis revealed the presence of over 1,200 bacterial taxa representing 140 distinct families, many previously undetected in airway diseases; bacterial community composition was strongly influenced by the duration of intubation. A core community of 75 taxa was detected in all patients, many of which are known pathogens. Bacterial community diversity in COPD airways is substantially greater than previously recognized and includes a number of potential pathogens detected in the setting of antibiotic exposure. Comprehensive assessment of the COPD airway microbiota using high-throughput, culture-independent methods may prove key to understanding the relationships between airway bacterial colonization, acute exacerbation, and clinical outcomes in this and other chronic inflammatory airway diseases. PMID:20141328

Early symptomatic and late seizures in Kosovar children with bacterial meningitis.

PubMed

Namani, Sadie A; Kuchar, Ernest; Koci, Remzie; Mehmeti, Murat; Dedushi, Kreshnike

2011-11-01

Despite the dramatic decrease of mortality rate among children with bacterial meningitis in recent decades, some patients are left with neurologic sequelae. The purpose of this study was to analyze the occurrence of seizures as predictors for meningitis-related deaths or neurological sequelae including late seizures. This study uses a retrospective chart review of 277 children (aged 0-16 years, median 2 years, 162 boys) treated for bacterial meningitis in University Clinical Centre in Prishtina (Kosovo). Of the 277 children treated for bacterial meningitis, 60 children (22%) manifested seizures prior to admission, 57 children (21%) had seizures after admission, and late seizures were diagnosed in 24 children (9%). The risk for adverse outcome was significantly higher in patients who had seizures prior to admission (52/60) and in patients who manifested seizures later than 24 h (41/41; RR 8.17 and 6.78 respectively, p < 0.0001). All children who manifested late seizures were diagnosed with meningitis-related acute neurologic complications: subdural effusion (18), hydrocephalus (6), intracranial bleeding (1), and subdural empyema (2). Of the 60 children who presented seizures prior to admission, only 11 manifested late seizures. Seizures prior to admission were predictors of high risk of adverse outcome in bacterial meningitis in children. The risk of secondary epilepsy (9%) occurred only in children with evident structural neurologic complications during the acute phase of bacterial meningitis.

Vitamin D was not associated with survival or cerebrospinal fluid cathelicidin levels in children with bacterial meningitis.

PubMed

Savonius, Okko; Pelkonen, Tuula; Roine, Irmeli; Viljakainen, Heli; Andersson, Sture; Fernandez, Josefina; Peltola, Heikki; Helve, Otto

2018-05-11

Vitamin D deficiency impairs the immunological system and has been associated with worse outcomes of infectious diseases, but its role in bacterial meningitis remains unknown. We investigated whether serum 25-hydroxyvitamin D concentrations related to disease outcomes and to cerebrospinal fluid cathelicidin concentrations in childhood bacterial meningitis. All consecutively enrolled patients in a clinical trial on childhood bacterial meningitis in Latin America in 1996-2003 were considered and 142 children, with a median age of seven months who had a confirmed bacterial aetiology and frozen serum available for further analyses, were included in the present study. Serum 25-hydroxyvitamin D concentrations were determined with a chemiluminescence immunoassay analyser, while cerebrospinal fluid cathelicidin was measured by enzyme-linked immunosorbent assay. The median serum 25-hydroxyvitamin D concentration was 96 (range 19-251) nmol/L. No relationship was found with patient survival, but children with any neurological sequelae had lower serum 25-hydroxyvitamin D levels than children without sequelae. Serum 25-hydroxyvitamin D was unrelated to cathelicidin concentrations in cerebrospinal fluid. Although serum 25-hydroxyvitamin D in children with bacterial meningitis was not associated with survival or cerebrospinal fluid cathelicidin concentrations, its relationship with more detailed disease outcomes warrants further study. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Effect of Lactobacillus johnsonii La1 and antioxidants on intestinal flora and bacterial translocation in rats with experimental cirrhosis.

PubMed

Chiva, Maite; Soriano, Germán; Rochat, Isabelle; Peralta, Carmen; Rochat, Florence; Llovet, Teresa; Mirelis, Beatriz; Schiffrin, Eduardo J; Guarner, Carlos; Balanzó, Joaquim

2002-10-01

Probiotics and antioxidants could be alternatives to antibiotics in the prevention of bacterial infections in cirrhosis. The aim of the present study was to determine the effect of Lactobacillus johnsonii La1 and antioxidants on intestinal flora, endotoxemia, and bacterial translocation in cirrhotic rats. Twenty-nine Sprague-Dawley rats with cirrhosis induced by CCl(4) and ascites received Lactobacillus johnsonii La1 10(9)cfu/day in vehicle (antioxidants: vitamin C+glutamate) (n=10), vehicle alone (n=11), or water (n=8) by gavage. Another eight non-cirrhotic rats formed the control group. After 10 days of treatment, a laparotomy was performed to determine microbiological study of ileal and cecal feces, bacterial translocation, endotoxemia, and intestinal malondialdehyde (MDA) levels as index of intestinal oxidative damage. Intestinal enterobacteria and enterococci, bacterial translocation (0/11 and 0/10 vs. 5/8, P<0.01), and ileal MDA levels (P<0.01) were lower in cirrhotic rats treated with antioxidants alone or in combination with Lactobacillus johnsonii La1 compared to cirrhotic rats receiving water. Only rats treated with antioxidants and Lactobacillus johnsonii La1 showed a decrease in endotoxemia with respect to cirrhotic rats receiving water (P<0.05). Antioxidants alone or in combination with Lactobacillus johnsonii La1 can be useful in preventing bacterial translocation in cirrhosis.

Prevalence and prognostic influence of bacterial pyuria in elderly patients with pneumonia: A retrospective study.

PubMed

Oka, Hiroaki; Komiya, Kosaku; Ohama, Minoru; Kawano, Yoshiyuki; Uchida, Masahiro; Miyajima, Hajime; Iwashita, Tomohiko; Okabe, Eiji; Kawamura, Tadao; Yasuda, Kazuhiro; Matsumoto, Taisuke; Kadota, Jun-Ichi

2017-07-01

The number of elderly patients with pneumonia is significantly increasing as the populations in many countries age. Although elderly patients with pneumonia are at risk of developing urinary tract infections, no studies have examined the prevalence or the prognostic impact of this complication. The aim of the present study was to investigate the prevalence of comorbid bacterial pyuria and the impact on the prognosis of elderly patients with pneumonia. We retrospectively evaluated 132 patients aged >65 years who were hospitalized for pneumonia and who underwent a urinary sediment test on admission. The background characteristics, laboratory results and treatment regimens were documented, and the risk factors for the complication of bacterial pyuria and its association with 90-day mortality in pneumonia patients were elucidated. A total of 37 (28%) of 132 patients were complicated by bacterial pyuria. The patients with bacterial pyuria were more often women, showed a poorer performance status, were more frequently fed by percutaneous endoscopic gastrostomy, and more frequently used diapers and/or a bladder catheter. Regarding first-line drugs, 82.6% of the patients received beta-lactamase inhibitors and extended-spectrum penicillins. The use of a bladder catheter and a poor performance status were associated with bacterial pyuria. A multivariate analysis showed that a poor performance status was the only factor associated with 90-day mortality. Bacterial pyuria did not affect the prognosis of patients who were treated with penicillin-based regimens. Thus, broad-spectrum antibiotics are not necessarily required for elderly patients with pneumonia complicated by urinary tract infection. Geriatr Gerontol Int 2017; 17: 1076-1080. © 2016 Japan Geriatrics Society.

Development of bacterial colony phenotyping instrument using reflected scatter light

NASA Astrophysics Data System (ADS)

Doh, Iyll-Joon

Bacterial rapid detection using optical scattering technology (BARDOT) involves in differentiating elastic scattering pattern of bacterial colony. This elastic light scatter technology has shown promising label-free classification rate. However, there is limited success in certain circumstances where either a growth media or a colony has higher opacity. This situation is due to the physical principles of the current BARDOT which mainly relies on optical patterns generated by transmitted signals. Incoming light is obstructed and cannot be transmitted through the dense bacterial colonies, such as Lactobacillus, Yeast, mold and soil bacteria. Moreover, a blood agar, widely used in clinical field, is an example of an opaque media that does not allow light to be transmitted through. Therefore, in this research, a newly designed reflection type scatterometer is presented. The reflection type scatterometer measures the elastic scattering pattern generated by reflected signal. A theoretical model to study the optical pattern characteristic with respect to bacterial colony morphology is presented. Both theoretical and experiment results show good agreement that the size of backward scattering pattern has positive correlation to colony aspect ratio, a colony elevation to diameter ratio. Four pathogenic bacteria on blood agar, Escherichia coli K12, Listeria innocua, Salmonella Typhimurium, and Staphylococcus aureus, are tested and measured with proposed instrument. The measured patterns are analyzed with a classification software, and high classification rate can be achieved.

Precise, High-throughput Analysis of Bacterial Growth.

PubMed

Kurokawa, Masaomi; Ying, Bei-Wen

2017-09-19

Bacterial growth is a central concept in the development of modern microbial physiology, as well as in the investigation of cellular dynamics at the systems level. Recent studies have reported correlations between bacterial growth and genome-wide events, such as genome reduction and transcriptome reorganization. Correctly analyzing bacterial growth is crucial for understanding the growth-dependent coordination of gene functions and cellular components. Accordingly, the precise quantitative evaluation of bacterial growth in a high-throughput manner is required. Emerging technological developments offer new experimental tools that allow updates of the methods used for studying bacterial growth. The protocol introduced here employs a microplate reader with a highly optimized experimental procedure for the reproducible and precise evaluation of bacterial growth. This protocol was used to evaluate the growth of several previously described Escherichia coli strains. The main steps of the protocol are as follows: the preparation of a large number of cell stocks in small vials for repeated tests with reproducible results, the use of 96-well plates for high-throughput growth evaluation, and the manual calculation of two major parameters (i.e., maximal growth rate and population density) representing the growth dynamics. In comparison to the traditional colony-forming unit (CFU) assay, which counts the cells that are cultured in glass tubes over time on agar plates, the present method is more efficient and provides more detailed temporal records of growth changes, but has a stricter detection limit at low population densities. In summary, the described method is advantageous for the precise and reproducible high-throughput analysis of bacterial growth, which can be used to draw conceptual conclusions or to make theoretical observations.

A comparative study of the effects of Escherichia coli and Clostridium perfringens upon boar semen preserved in liquid storage.

PubMed

Pinart, Elisabeth; Domènech, Esther; Bussalleu, Eva; Yeste, Marc; Bonet, Sergi

2017-02-01

The present study compares the sperm quality of boar seminal doses artificially inoculated with Escherichia coli and Clostridium perfringens, and maintained in liquid storage at 15°C for a 9-day period. Seminal doses from 10 sexually mature Piétrain boars were diluted in a Beltsville Thawing Solution (BTS)-based extender and infected either with E. coli or C. perfringens, with bacterial loads ranging from 10 1 to 10 7 cfumL -1 . During storage, the changes in sperm quality were determined by assessing pH, sperm viability, sperm motiliy, sperm morphology, sperm agglutination degree, and sperm-bacteria interaction. The infection of seminal doses led to an alkalinization of the medium, which was of higher extend in doses infected with C. perfringens. The effect of contamination on sperm viability and motility relied on bacterial type and load. Therefore, while E. coli was more harmful than C. perfringens in bacterial loads ranging from 10 1 to 10 6 cfumL -1 , the detrimental impact of C. perfringens was more apparent than that of E. coli at a bacterial load of 10 7 cfumL -1 . Despite sperm morphology not being affected by either bacterial type or load, sperm agglutination and sperm-bacteria interaction were characteristic of doses infected with E. coli, and increased concomintantly with bacterial load and along storage period. In conclusion, the effects of infection by E. coli on sperm quality were dependent of both bacterial load and storage period, whereas the effects of C. perfringens were mainly dependent on the bacterial load, with a threshold at 10 7 cfumL -1 from which the sperm quality of seminal doses was greatly impaired. Copyright © 2016 Elsevier B.V. All rights reserved.

Taking Root: Enduring Effect of Rhizosphere Bacterial Colonization in Mangroves

PubMed Central

Pinto, Fernando N.; Egas, Conceição; Almeida, Adelaide; Cunha, Angela; Mendonça-Hagler, Leda C. S.; Smalla, Kornelia

2010-01-01

Background Mangrove forests are of global ecological and economic importance, but are also one of the world's most threatened ecosystems. Here we present a case study examining the influence of the rhizosphere on the structural composition and diversity of mangrove bacterial communities and the implications for mangrove reforestation approaches using nursery-raised plants. Methodology/Principal Findings A barcoded pyrosequencing approach was used to assess bacterial diversity in the rhizosphere of plants in a nursery setting, nursery-raised transplants and native (non-transplanted) plants in the same mangrove habitat. In addition to this, we also assessed bacterial composition in the bulk sediment in order to ascertain if the roots of mangrove plants affect sediment bacterial composition. We found that mangrove roots appear to influence bacterial abundance and composition in the rhizosphere. Due to the sheer abundance of roots in mangrove habitat, such an effect can have an important impact on the maintenance of bacterial guilds involved in nutrient cycling and other key ecosystem functions. Surprisingly, we also noted a marked impact of initial nursery conditions on the rhizosphere bacterial composition of replanted mangrove trees. This result is intriguing because mangroves are periodically inundated with seawater and represent a highly dynamic environment compared to the more controlled nursery environment. Conclusions/Significance In as far as microbial diversity and composition influences plant growth and health, this study indicates that nursery conditions and early microbial colonization patterns of the replants are key factors that should be considered during reforestation projects. In addition to this, our results provide information on the role of the mangrove rhizosphere as a habitat for bacteria from estuarine sediments. PMID:21124923

Detection of carboxylesterase and esterase activity in culturable gut bacterial flora isolated from diamondback moth, Plutella xylostella (Linnaeus), from India and its possible role in indoxacarb degradation.

PubMed

Ramya, Shanivarsanthe Leelesh; Venkatesan, Thiruvengadam; Srinivasa Murthy, Kottilingam; Jalali, Sushil Kumar; Verghese, Abraham

2016-01-01

Diamondback moth (DBM), Plutella xylostella (Linnaeus), is a notorious pest of brassica crops worldwide and is resistant to all groups of insecticides. The insect system harbors diverse groups of microbiota, which in turn helps in enzymatic degradation of xenobiotic-like insecticides. The present study aimed to determine the diversity of gut microflora in DBM, quantify esterase activity and elucidate their possible role in degradation of indoxacarb. We screened 11 geographic populations of DBM in India and analyzed them for bacterial diversity. The culturable gut bacterial flora underwent molecular characterization with 16S rRNA. We obtained 25 bacterial isolates from larvae (n=13) and adults (n=12) of DBM. In larval gut isolates, gammaproteobacteria was the most abundant (76%), followed by bacilli (15.4%). Molecular characterization placed adult gut bacterial strains into three major classes based on abundance: gammaproteobacteria (66%), bacilli (16.7%) and flavobacteria (16.7%). Esterase activity from 19 gut bacterial isolates ranged from 0.072 to 2.32μmol/min/mg protein. Esterase bands were observed in 15 bacterial strains and the banding pattern differed in Bacillus cereus - KC985225 and Pantoea agglomerans - KC985229. The bands were characterized as carboxylesterase with profenofos used as an inhibitor. Minimal media study showed that B. cereus degraded indoxacarb up to 20%, so it could use indoxacarb for metabolism and growth. Furthermore, esterase activity was greater with minimal media than control media: 1.87 versus 0.26μmol/min/mg protein. Apart from the insect esterases, bacterial carboxylesterase may aid in the degradation of insecticides in DBM. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Temporal trends in paediatric bacterial meningitis in a tropical Australian region: 1992-2014.

PubMed

White, Stephanie; Katf, Hala; Baird, Rob; Francis, Joshua

2018-05-13

The epidemiology of community-acquired bacterial meningitis has changed following the introduction of routine immunisation against common causative organisms. Indigenous children living in the Northern Territory, Australia, have high rates of bacterial infections. This study describes changes in the epidemiology of childhood bacterial meningitis and the distribution of the burden of disease in the Top End. A retrospective review of cases derived from hospital medical records and laboratory data was performed. Inclusion criteria were children aged 3 months to 14 years of age, admitted to Royal Darwin Hospital between 1992 and 2014 and diagnosed with bacterial meningitis. Annual incidence of bacterial meningitis and the distribution of causative pathogens are described. Demographic data, investigations, treatment and outcomes were compared between Indigenous and non-Indigenous children. There were 137 cases of childhood bacterial meningitis identified over the 23-year period. The incidence reduced from 21 per 100 000 children per year for 1992-2002 to 11 per 100 000 per year for 2003-2014 (P = 0.0025). Haemophilus influenzae type b, Streptococcus pneumoniae and Neisseria meningitidis were the most common causative organisms, with a reduction in cases for each pathogen observed across the study period. Indigenous children were over-represented (104/137, 76%). Case fatality rate was 8% (11/137); 91% of fatal cases presented to a remote facility. The incidence of childhood bacterial meningitis has declined in the Northern Territory of Australia, but Indigenous children are disproportionately affected. Routine immunisation is beneficial for all, although further efforts to 'Close the Gap' between health outcomes in Indigenous and non-Indigenous Australians is required. © 2018 Paediatrics and Child Health Division (The Royal Australasian College of Physicians).

BACTERIAL GROWTH AND MULTIPLICATION AS DISCLOSED BY MICRO MOTION PICTURES

PubMed Central

Wyckoff, Ralph W. G.

1934-01-01

Using a micro motion picture technique for making records, studies covering several thousand hours of observation have been made of the growth of a number of bacteria. On the basis of these experiments a discussion is offered of bacterial division and its influence on gross colony appearance, of different kinds of pleomorphism that have been observed, and of the nature of the internal structure that is seen in some bacteria. Several of the microorganisms chosen for examination are ones that have been thought to give evidence of life cycle phenomena. The present pictures, however, contain no evidence of a bacterial cycle in the commonly accepted meaning of the term. PMID:19870252

Diagnostic test accuracy of a 2-transcript host RNA signature for discriminating bacterial vs viral infection in febrile children

PubMed Central

Shailes, Hannah; Eleftherohorinou, Hariklia; Hoggart, Clive J; Cebey-Lopez, Miriam; Carter, Michael J; Janes, Victoria A; Gormley, Stuart; Shimizu, Chisato; Tremoulet, Adriana H; Barendregt, Anouk M; Salas, Antonio; Kanegaye, John; Pollard, Andrew J; Faust, Saul N; Patel, Sanjay; Kuijpers, Taco; Martinon-Torres, Federico; Burns, Jane C; Coin, Lachlan JM; Levin, Michael

2018-01-01

Importance As clinical features do not reliably distinguish bacterial from viral infection, many children worldwide receive unnecessary antibiotic treatment whilst bacterial infection is missed in others. Objective To identify a blood RNA expression signature that distinguishes bacterial from viral infection in febrile children. Design Febrile children presenting to participating hospitals in UK, Spain, Netherlands and USA between 2009-2013 were prospectively recruited, comprising a discovery group and validation group. Each group was classified after microbiological investigation into definite bacterial, definite viral infection or indeterminate infection. RNA expression signatures distinguishing definite bacterial from viral infection were identified in the discovery group and diagnostic performance assessed in the validation group. Additional validation was undertaken in separate studies of children with meningococcal disease (n=24) inflammatory diseases (n=48), and on published gene expression datasets. Exposures A 2-transcript RNA expression signature distinguishing bacterial infection from viral infection was evaluated against clinical and microbiological diagnosis. Main Outcomes Definite Bacterial and viral infection was confirmed by culture or molecular detection of the pathogens. Performance of the RNA signature was evaluated in the definite bacterial and viral group, and the indeterminate group. Results The discovery cohort of 240 children (median age 19 months, 62% males) included 52 with definite bacterial infection of whom 36 (69%) required intensive care; and 92 with definite viral infection of whom 32 (35%) required intensive care. 96 children had indeterminate infection. Bioinformatic analysis of RNA expression data identified a 38-transcript signature distinguishing bacterial from viral infection. A smaller (2-transcript) signature (FAM89A and IFI44L) was identified by removing highly correlated transcripts. When this 2-transcript signature was implemented as a Disease Risk Score in the validation group (130 children, including 23 bacterial, 28 viral, 79 indeterminate; median age 17 months, 57% males), bacterial infection was identified in all 23 microbiologically-confirmed definite bacterial patients, with a sensitivity of 100% (95% confidence interval [CI], 100 - 100), and in 1 of 28 definite viral patients, with specificity of 96.4% (95% CI, 89.3 – 100). When applied to additional validation datasets from patients with meningococcal and inflammatory diseases, bacterial infection was identified with a sensitivity of 91.7% (79.2-100) and 90.0% (70.0-100) respectively, and with specificity of 96.0% (88.0-100) and 95.8% (89.6-100). A minority of children in the indeterminate group were classified as having bacterial infection (63 of 136, 46.3%), although most received antibiotic treatment (129 of 136, 94.9%). Conclusions and Relevance This study provides preliminary data regarding test accuracy of a 2-transcript host RNA signature discriminating bacterial from viral infection in febrile children. Further studies are needed in diverse groups of patients to assess accuracy and clinical utility of this test in different clinical settings. PMID:27552617

Jellyfish as vectors of bacterial disease for farmed salmon (Salmo salar).

PubMed

Ferguson, Hugh W; Delannoy, Christian M J; Hay, Stephen; Nicolson, James; Sutherland, David; Crumlish, Margaret

2010-05-01

Swarms or blooms of jellyfish are increasingly problematic and can result in high mortality rates of farmed fish. Small species of jellyfish, such as Phialella quadrata (13 mm in diameter), are capable of passing through the mesh of sea cages and being sucked into the mouth of fish during respiration. Results of the current study show that the initial damage to gills of farmed Atlantic salmon, likely produced by nematocyst-derived toxins from the jellyfish, was compounded by secondary bacterial infection with Tenacibaculum maritimum. Results also demonstrate that these filamentous bacteria were present on the mouth of the jellyfish and that their DNA sequences were almost identical to those of bacteria present on the salmon gills. This suggests that the bacterial lesions were not the result of an opportunistic infection of damaged tissue, as previously thought. Instead, P. quadrata is probably acting as a vector for this particular bacterial pathogen, and it is the first time that evidence to support such a link has been presented. No prior literature describing the presence of bacteria associated with jellyfish, except studies about their decay, could be found. It is not known if all jellyfish of this and other species carry similar bacteria or the relationship to each other. Their source, the role they play under other circumstances, and indeed whether the jellyfish were themselves diseased are also not known. The high proteolytic capabilities of T. maritimum mean that partially digested gill tissues were readily available to the jellyfish, which rely heavily on intracellular digestion for their nutrition.

Comparative study of the clinical presentation of Legionella pneumonia and other community-acquired pneumonias.

PubMed

Sopena, N; Sabrià-Leal, M; Pedro-Botet, M L; Padilla, E; Dominguez, J; Morera, J; Tudela, P

1998-05-01

The aim of this study was to compare the clinical, biological, and radiologic features of presentation in the emergency ward of community-acquired pneumonia (CAP) by Legionella pneumophila (LP) and other community-acquired bacterial pneumonias to help in early diagnosis of CAP by LP. Three hundred ninety-two patients with CAP were studied prospectively in the emergency department of a 600-bed university hospital. Univariate and multivariate analyses were performed to compare epidemiologic and demographic data and clinical, analytical, and radiologic features of presentation in 48 patients with CAP by LP and 125 patients with CAP by other bacterial etiology (68 by Streptococcus pneumoniae, 41 by Chlamydia pneumoniae, 5 by Mycoplasma pneumoniae, 4 by Coxiella burnetii, 3 by Pseudomonas aeruginosa, 2 by Haemophilus influenzae, and 2 by Nocardia species. Univariate analysis showed that CAP by LP was more frequent in middle-aged, male healthy (but alcohol drinking) patients than CAP by other etiology. Moreover, the lack of response to previous beta-lactamic drugs, headache, diarrhea, severe hyponatremia, and elevation in serum creatine kinase (CK) levels on presentation were more frequent in CAP by LP, while cough, expectoration, and thoracic pain were more frequent in CAP by other bacterial etiology. However, multivariate analysis only confirmed these differences with respect to lack of underlying disease, diarrhea, and elevation in the CK level. We conclude that detailed analysis of features of presentation of CAP allows suspicion of Legionnaire's disease in the emergency department. The initiation of antibiotic treatment, including a macrolide, and the performance of rapid diagnostic techniques are mandatory in these cases.

Combined effect of temperature and copper pollution on soil bacterial community: climate change and regional variation aspects.

PubMed

Henriques, Isabel; Araújo, Susana; Pereira, Anabela; Menezes-Oliveira, Vanessa B; Correia, António; Soares, Amadeu M V M; Scott-Fordsmand, Janeck J; Amorim, Mónica J B

2015-01-01

The aim of this study was to assess the combined effects of temperature and copper (Cu) contamination in the structure of soil bacterial community. For this, contaminated or spiked and control soils from two different geographic origins (PT-Portugal and DK-Denmark) were used. The DK soil was from a historically contaminated study field, representing a long-term exposure to Cu while the PT soil was from a clean site and freshly spiked with Cu. Soil bacterial communities were exposed in mesocosms during 84 days to 3 different temperatures based on values typically found in each geographic region and temperature conditions that simulated a warming scenario. Obtained results indicate that Cu stress alters the structure of bacterial community and that this effect is, to some extent, temperature-dependent. Effects on bacterial diversity for both soils were also observed. Differences in the DK and PT communities' response were apparent, with the community from the historically contaminated soil being more resilient to temperature fluctuations. This study presents evidence to support the hypothesis that temperature alters the effect of metals on soils. Further, our results suggest that the definition of soils quality criteria must be based on studies performed under temperatures selected for the specific geographic region. Studies taking into account temperature changes are needed to model and predict risks, this is important to e.g. future adjustments of the maximum permissible levels for soil metal contamination. Copyright © 2014 Elsevier Inc. All rights reserved.

Characterization of Batrachochytrium dendrobatidis Inhibiting Bacteria from Amphibian Populations in Costa Rica

PubMed Central

Madison, Joseph D.; Berg, Elizabeth A.; Abarca, Juan G.; Whitfield, Steven M.; Gorbatenko, Oxana; Pinto, Adrian; Kerby, Jacob L.

2017-01-01

Global amphibian declines and extinction events are occurring at an unprecedented rate. While several factors are responsible for declines and extinction, the fungal pathogen Batrachochytrium dendrobatidis (Bd) has been cited as a major constituent in these events. While the effects of this chytrid fungus have been shown to cause broad scale population declines and extinctions, certain individuals and relict populations have shown resistance. This resistance has been attributed in part to the cutaneous bacterial microbiome. Here, we present the first study characterizing anti-Bd bacterial isolates from amphibian populations in Costa Rica, including the characterization of two strains of Serratia marcescens presenting strong anti-Bd activity. Transcriptome sequencing was utilized for delineation of shifts in gene expression of the two previously uncharacterized strains of S. marcescens grown in three different treatments comprising Bd, heat-killed Bd, and a no Bd control. These results revealed up- and down-regulation of key genes associated with different metabolic and regulatory pathways. This information will be valuable in continued efforts to develop a bacterial-based approach for amphibian protection as well as providing direction for continued mechanistic inquiries of the bacterial anti-Bd response. PMID:28293222

Self-Test Kit: Rapid Diagnosis of Urogenital Infections in Military Women

DTIC Science & Technology

1999-09-01

in women with other infections and it was not clear whether they had symptomatic urinary tract infections or asymptomatic bacteriuria and symptoms from...CA), and bacterial vaginosis (BV) by PCR or standard methods. A asymptomatic pregnant women (n=1 57) were also screened for TV and bacterial...were less likely to respond to the survey.6 In another study of 476 asymptomatic active duty army women presenting for routine pap smears, 39(8.2

Anti-Pseudomonas aeruginosa IgY Antibodies Induce Specific Bacterial Aggregation and Internalization in Human Polymorphonuclear Neutrophils

PubMed Central

Thomsen, K.; Christophersen, L.; Bjarnsholt, T.; Jensen, P. Ø.; Moser, C.

2015-01-01

Polymorphonuclear neutrophils (PMNs) are essential cellular constituents in the innate host response, and their recruitment to the lungs and subsequent ubiquitous phagocytosis controls primary respiratory infection. Cystic fibrosis pulmonary disease is characterized by progressive pulmonary decline governed by a persistent, exaggerated inflammatory response dominated by PMNs. The principal contributor is chronic Pseudomonas aeruginosa biofilm infection, which attracts and activates PMNs and thereby is responsible for the continuing inflammation. Strategies to prevent initial airway colonization with P. aeruginosa by augmenting the phagocytic competence of PMNs may postpone the deteriorating chronic biofilm infection. Anti-P. aeruginosa IgY antibodies significantly increase the PMN-mediated respiratory burst and subsequent bacterial killing of P. aeruginosa in vitro. The mode of action is attributed to IgY-facilitated formation of immobilized bacteria in aggregates, as visualized by fluorescence microscopy and the induction of increased bacterial hydrophobicity. Thus, the present study demonstrates that avian egg yolk immunoglobulins (IgY) targeting P. aeruginosa modify bacterial fitness, which enhances bacterial killing by PMN-mediated phagocytosis and thereby may facilitate a rapid bacterial clearance in airways of people with cystic fibrosis. PMID:25895968

A comparative study of sequence- and structure-based features of small RNAs and other RNAs of bacteria.

PubMed

Barik, Amita; Das, Santasabuj

2018-01-02

Small RNAs (sRNAs) in bacteria have emerged as key players in transcriptional and post-transcriptional regulation of gene expression. Here, we present a statistical analysis of different sequence- and structure-related features of bacterial sRNAs to identify the descriptors that could discriminate sRNAs from other bacterial RNAs. We investigated a comprehensive and heterogeneous collection of 816 sRNAs, identified by northern blotting across 33 bacterial species and compared their various features with other classes of bacterial RNAs, such as tRNAs, rRNAs and mRNAs. We observed that sRNAs differed significantly from the rest with respect to G+C composition, normalized minimum free energy of folding, motif frequency and several RNA-folding parameters like base-pairing propensity, Shannon entropy and base-pair distance. Based on the selected features, we developed a predictive model using Random Forests (RF) method to classify the above four classes of RNAs. Our model displayed an overall predictive accuracy of 89.5%. These findings would help to differentiate bacterial sRNAs from other RNAs and further promote prediction of novel sRNAs in different bacterial species.

Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms.

PubMed

Gat, Daniella; Mazar, Yinon; Cytryn, Eddie; Rudich, Yinon

2017-06-20

Microorganisms carried by dust storms are transported through the atmosphere and may affect human health and the functionality of microbial communities in various environments. Characterizing the dust-borne microbiome in dust storms of different origins or that followed different trajectories provides valuable data to improve our understanding of global health and environmental impacts. We present a comparative study on the diversity of dust-borne bacterial communities in dust storms from three distinct origins (North Africa, Syria and Saudi Arabia) and compare them with local bacterial communities sampled on clear days, all collected at a single location: Rehovot, Israel. Storms from different dust origins exhibited distinct bacterial communities, with signature bacterial taxa. Dust storms were characterized by a lower abundance of selected antibiotic resistance genes (ARGs) compared with ambient dust, asserting that the origin of these genes is local and possibly anthropogenic. With the progression of the storm, the storm-borne bacterial community showed increasing resemblance to ambient dust, suggesting mixing with local dust. These results show, for the first time, that dust storms from different sources display distinct bacterial communities, suggesting possible diverse effects on the environment and public health.

Tiny cells meet big questions: a closer look at bacterial cell biology.

PubMed

Goley, Erin D

2013-04-01

While studying actin assembly as a graduate student with Matt Welch at the University of California at Berkeley, my interest was piqued by reports of surprising observations in bacteria: the identification of numerous cytoskeletal proteins, actin homologues fulfilling spindle-like functions, and even the presence of membrane-bound organelles. Curiosity about these phenomena drew me to Lucy Shapiro's lab at Stanford University for my postdoctoral research. In the Shapiro lab, and now in my lab at Johns Hopkins, I have focused on investigating the mechanisms of bacterial cytokinesis. Spending time as both a eukaryotic cell biologist and a bacterial cell biologist has convinced me that bacterial cells present the same questions as eukaryotic cells: How are chromosomes organized and accurately segregated? How is force generated for cytokinesis? How is polarity established? How are signals transduced within and between cells? These problems are conceptually similar between eukaryotes and bacteria, although their solutions can differ significantly in specifics. In this Perspective, I provide a broad view of cell biological phenomena in bacteria, the technical challenges facing those of us who peer into bacterial cells, and areas of common ground as research in eukaryotic and bacterial cell biology moves forward.

Molecular bacterial community analysis of clean rooms where spacecraft are assembled.

PubMed

Moissl, Christine; Osman, Shariff; La Duc, Myron T; Dekas, Anne; Brodie, Eoin; DeSantis, Todd; Desantis, Tadd; Venkateswaran, Kasthuri

2007-09-01

Molecular bacterial community composition was characterized from three geographically distinct spacecraft-associated clean rooms to determine whether such populations are influenced by the surrounding environment or the maintenance of the clean rooms. Samples were collected from facilities at the Jet Propulsion Laboratory (JPL), Kennedy Space Flight Center (KSC), and Johnson Space Center (JSC). Nine clone libraries representing different surfaces within the spacecraft facilities and three libraries from the surrounding air were created. Despite the highly desiccated, nutrient-bare conditions within these clean rooms, a broad diversity of bacteria was detected, covering all the main bacterial phyla. Furthermore, the bacterial communities were significantly different from each other, revealing only a small subset of microorganisms common to all locations (e.g. Sphingomonas, Staphylococcus). Samples from JSC assembly room surfaces showed the greatest diversity of bacteria, particularly within the Alpha- and Gammaproteobacteria and Actinobacteria. The bacterial community structure of KSC assembly surfaces revealed a high presence of proteobacterial groups, whereas the surface samples collected from the JPL assembly facility showed a predominance of Firmicutes. Our study presents the first extended molecular survey and comparison of NASA spacecraft assembly facilities, and provides new insights into the bacterial diversity of clean room environments .

Effect of different mixing methods on the bacterial microleakage of calcium-enriched mixture cement.

PubMed

Shahi, Shahriar; Jeddi Khajeh, Soniya; Rahimi, Saeed; Yavari, Hamid R; Jafari, Farnaz; Samiei, Mohammad; Ghasemi, Negin; Milani, Amin S

2016-10-01

Calcium-enriched mixture (CEM) cement is used in the field of endodontics. It is similar to mineral trioxide aggregate in its main ingredients. The present study investigated the effect of different mixing methods on the bacterial microleakage of CEM cement. A total of 55 human single-rooted human permanent teeth were decoronated so that 14-mm-long samples were obtained and obturated with AH26 sealer and gutta-percha using lateral condensation technique. Three millimeters of the root end were cut off and randomly divided into 3 groups of 15 each (3 mixing methods of amalgamator, ultrasonic and conventional) and 2 negative and positive control groups (each containing 5 samples). BHI (brain-heart infusion agar) suspension containing Enterococcus faecalis was used for bacterial leakage assessment. Statistical analysis was carried out using descriptive statistics, Kaplan-Meier survival analysis with censored data and log rank test. Statistical significance was set at P<0.05. The survival means for conventional, amalgamator and ultrasonic methods were 62.13±12.44, 68.87±12.79 and 77.53±12.52 days, respectively. The log rank test showed no significant differences between the groups. Based on the results of the present study it can be concluded that different mixing methods had no significant effect on the bacterial microleakage of CEM cement.

Characterisation of Arctic Bacterial Communities in the Air above Svalbard

PubMed Central

Cuthbertson, Lewis; Amores-Arrocha, Herminia; Malard, Lucie A.; Els, Nora; Sattler, Birgit; Pearce, David A.

2017-01-01

Atmospheric dispersal of bacteria is increasingly acknowledged as an important factor influencing bacterial community biodiversity, biogeography and bacteria–human interactions, including those linked to human health. However, knowledge about patterns in microbial aerobiology is still relatively scarce, and this can be attributed, in part, to a lack of consensus on appropriate sampling and analytical methodology. In this study, three different methods were used to investigate aerial biodiversity over Svalbard: impaction, membrane filtration and drop plates. Sites around Svalbard were selected due to their relatively remote location, low human population, geographical location with respect to air movement and the tradition and history of scientific investigation on the archipelago, ensuring the presence of existing research infrastructure. The aerial bacterial biodiversity found was similar to that described in other aerobiological studies from both polar and non-polar environments, with Proteobacteria, Actinobacteria, and Firmicutes being the predominant groups. Twelve different phyla were detected in the air collected above Svalbard, although the diversity was considerably lower than in urban environments elsewhere. However, only 58 of 196 bacterial genera detected were consistently present, suggesting potentially higher levels of heterogeneity. Viable bacteria were present at all sampling locations, showing that living bacteria are ubiquitous in the air around Svalbard. Sampling location influenced the results obtained, as did sampling method. Specifically, impaction with a Sartorius MD8 produced a significantly higher number of viable colony forming units (CFUs) than drop plates alone. PMID:28481257

Phylogenetic diversity of bacteria associated with Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma).

PubMed

Schabereiter-Gurtner, Claudia; Saiz-Jimenez, Cesareo; Piñar, Guadalupe; Lubitz, Werner; Rölleke, Sabine

2004-02-01

Bacterial diversity in caves is still rarely investigated using culture-independent techniques. In the present study, bacterial communities on Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma) were analyzed, using 16S rDNA-based denaturing gradient gel electrophoresis community fingerprinting and phylogenetic analyses without prior cultivation. Results revealed complex bacterial communities consisting of a high number of novel 16S rDNA sequence types and indicated a high biodiversity of lithotrophic and heterotrophic bacteria. Identified bacteria were related to already cultured bacteria (39 clones) and to environmental 16S rDNA clones (46 clones). The nearest phylogenetic relatives were members of the Proteobacteria (41.1%), of the Acidobacterium division (16.5%), Actinobacteria (20%), Firmicutes (10.6%), of the Cytophaga/Flexibacter/Bacteroides division (5.9%), Nitrospira group (3.5%), green non-sulfur bacteria (1.2%), and candidate WS3 division (1.2%). Thirteen of these clones were most closely related to those obtained from the previous studies on Tito Bustillo Cave. The comparison of the present data with the data obtained previously from Altamira and Tito Bustillo Caves revealed similarities in the bacterial community components, especially in the high abundance of the Acidobacteria and Rhizobiaceae, and in the presence of bacteria related to ammonia and sulfur oxidizers.

Role of Sulfhydryl Sites on Bacterial Cell Walls in the Biosorption, Mobility and Bioavailability of Mercury and Uranium

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

Myneni, Satish C.; Mishra, Bhoopesh; Fein, Jeremy

2009-04-01

The goal of this exploratory study is to provide a quantitative and mechanistic understanding of the impact of bacterial sulfhydryl groups on the bacterial uptake, speciation, methylation and bioavailability of Hg and redox changes of uranium. The relative concentration and reactivity of different functional groups present on bacterial surfaces will be determined, enabling quantitative predictions of the role of biosorption of Hg under the physicochemical conditions found at contaminated DOE sites.The hypotheses we propose to test in this investigation are as follows- 1) Sulfhydryl groups on bacterial cell surfaces modify Hg speciation and solubility, and play an important role, specificallymore » in the sub-micromolar concentration ranges of metals in the natural and contaminated systems. 2) Sulfhydryl binding of Hg on bacterial surfaces significantly influences Hg transport into the cell and the methylation rates by the bacteria. 3) Sulfhydryls on cell membranes can interact with hexavalent uranium and convert to insoluble tetravalent species. 4) Bacterial sulfhydryl surface groups are inducible by the presence of metals during cell growth. Our studies focused on the first hypothesis, and we examined the nature of sulfhydryl sites on three representative bacterial species: Bacillus subtilis, a common gram-positive aerobic soil species; Shewanella oneidensis, a facultative gram-negative surface water species; and Geobacter sulfurreducens, an anaerobic iron-reducing gram-negative species that is capable of Hg methylation; and at a range of Hg concentration (and Hg:bacterial concentration ratio) in which these sites become important. A summary of our findings is as follows- Hg adsorbs more extensively to bacteria than other metals. Hg adsorption also varies strongly with pH and chloride concentration, with maximum adsorption occurring under circumneutral pH conditions for both Cl-bearing and Cl-free systems. Under these conditions, all bacterial species tested exhibit almost complete removal of Hg from the experimental solutions at relatively low bacterial concentrations. Synchrotron based X-ray spectroscopic studies of these samples indicate that the structure and the coordination environment of Hg surface complexes on bacterial cell walls change dramatically- with sulfhydryls as the dominant Hg-binding groups in the micromolar and submicromolar range, and carboxyls and phosphoryls dominating at high micromolar concentrations. Hg interactions change from a trigonal or T-shaped HgS{sub 3} complex to HgS or HgS{sub 2} type complexes as the Hg concentration increases in the submicromolar range. Although all bacterial species studied exhibited the same types of coordination environments for Hg, the relative concentrations of the complexes change as a function of Hg concentration.« less

Distinct molecular features facilitating ice-binding mechanisms in hyperactive antifreeze proteins closely related to an Antarctic sea ice bacterium.

PubMed

Banerjee, Rachana; Chakraborti, Pratim; Bhowmick, Rupa; Mukhopadhyay, Subhasish

2015-01-01

Antifreeze proteins or ice-binding proteins (IBPs) facilitate the survival of certain cellular organisms in freezing environment by inhibiting the growth of ice crystals in solution. Present study identifies orthologs of the IBP of Colwellia sp. SLW05, which were obtained from a wide range of taxa. Phylogenetic analysis on the basis of conserved regions (predicted as the 'ice-binding domain' [IBD]) present in all the orthologs, separates the bacterial and archaeal orthologs from that of the eukaryotes'. Correspondence analysis pointed out that the bacterial and archaeal IBDs have relatively higher average hydrophobicity than the eukaryotic members. IBDs belonging to bacterial as well as archaeal AFPs contain comparatively more strands, and therefore are revealed to be under higher evolutionary selection pressure. Molecular docking studies prove that the ice crystals form more stable complex with the bacterial as well as archaeal proteins than the eukaryotic orthologs. Analysis of the docked structures have traced out the ice-binding sites (IBSs) in all the orthologs which continue to facilitate ice-binding activity even after getting mutated with respect to the well-studied IBSs of Typhula ishikariensis and notably, all these mutations performing ice-binding using 'anchored clathrate mechanism' have been found to prefer polar and hydrophilic amino acids. Horizontal gene transfer studies point toward a strong selection pressure favoring independent evolution of the IBPs in some polar organisms including prokaryotes as well as eukaryotes because these proteins facilitate the polar organisms to acclimatize to the adversities in their niche, thus safeguarding their existence.

Diversity of Cervical Microbiota in Asymptomatic Chlamydia trachomatis Genital Infection: A Pilot Study

PubMed Central

Filardo, Simone; Di Pietro, Marisa; Porpora, Maria G.; Recine, Nadia; Farcomeni, Alessio; Latino, Maria A.; Sessa, Rosa

2017-01-01

Chlamydia trachomatis genital infection continues to be an important public health problem worldwide due to its increasing incidence. C. trachomatis infection can lead to severe sequelae, such as pelvic inflammatory disease, obstructive infertility, and preterm birth. Recently, it has been suggested that the cervico-vaginal microbiota may be an important defense factor toward C. trachomatis infection as well as the development of chronic sequelae. Therefore, the investigation of microbial profiles associated to chlamydial infection is of the utmost importance. Here we present a pilot study aiming to characterize, through the metagenomic analysis of sequenced 16s rRNA gene amplicons, the cervical microbiota from reproductive age women positive to C. trachomatis infection. The main finding of our study showed a marked increase in bacterial diversity in asymptomatic C. trachomatis positive women as compared to healthy controls in terms of Shannon's diversity and Shannon's evenness (P = 0.031 and P = 0.026, respectively). More importantly, the cervical microbiota from C. trachomatis positive women and from healthy controls significantly separated into two clusters in the weighted UniFrac analysis (P = 0.0027), suggesting that differences between the two groups depended entirely on the relative abundance of bacterial taxa rather than on the types of bacterial taxa present. Furthermore, C. trachomatis positive women showed an overall decrease in Lactobacillus spp. and an increase in anaerobes. These findings are part of an ongoing larger epidemiological study that will evaluate the potential role of distinct bacterial communities of the cervical microbiota in C. trachomatis infection. PMID:28770172

Comparison of pharyngocutaneous fistula closure with and without bacterial cellulose in a rat model.

PubMed

Demir, Berat; Sarı, Murat; Binnetoglu, Adem; Yumusakhuylu, Ali Cemal; Filinte, Deniz; Tekin, İshak Özel; Bağlam, Tekin; Batman, Abdullah Çağlar

2018-04-01

The present study aimed to compare the effects of bacterial cellulose used for closure of pharyngocutaneous fistulae, a complication of total laryngectomy, with those of primary sutures in a rat model. Thirty female Sprague-Dawley underwent experimental pharyngoesophagotomy and were grouped depending on the material used for pharyngocutaneous fistula closure: group I, which received primary sutures alone, group II, which received bacterial cellulose alone; and group III, which received both. After 7 days, the rats were sacrificed. Pharyngocutaneous fistula development was assessed, the gross wound was inspected, and histological examination was conducted. Pharyngocutaneous fistulae developed in 12 rats (41%) in all: 6 from group I (21%), 4 from group II (14%) and 2 from group III (7%). Fibroblast density and inflammatory cell infiltration were significantly greater in group III than group I. We concluded that bacterial cellulose may be useful for pharyngocutaneous fistula closure. Copyright © 2017 Elsevier B.V. All rights reserved.

MICROBIAL VOLATILE ORGANIC COMPOUND EMISSION RATES AND EXPOSURE MODEL

EPA Science Inventory

This paper presents the results from a study that examined microbial volatile organic compound (MVOC) emissions from six fungi and one bacterial species (Streptomyces spp.) commonly found in indoor environments. Data are presented on peak emission rates from inoculated agar plate...

Beneficial effect of Cu on Ti-Nb-Ta-Zr sputtered uniform/adhesive gum films accelerating bacterial inactivation under indoor visible light.

PubMed

Alhussein, Akram; Achache, Sofiane; Deturche, Regis; Sanchette, Frederic; Pulgarin, Cesar; Kiwi, John; Rtimi, Sami

2017-04-01

This article presents the evidence for the significant effect of copper accelerating the bacterial inactivation on Ti-Nb-Ta-Zr (TNTZ) sputtered films on glass up to a Cu content of 8.3 at.%. These films were deposited by dc magnetron co-sputtering of an alloy target Ti-23Nb-0.7Ta-2Zr (at.%) and a Cu target. The fastest bacterial inactivation of E. coli on this later TNTZ-Cu surface proceeded within ∼75min. The films deposited by magnetron sputtering are chemically homogenous. The film roughness evaluated by atomic force spectroscopy (AFM) on the TNTZ-Cu 8.3 at.% Cu sample presented an RMS-value of 20.1nm being the highest RMS of any Cu-sputtered TNTZ sample. The implication of the RMS value found for this sample leading to the fastest interfacial bacterial inactivation kinetics is also discussed. Values for the Young's modulus and hardness are reported for the TNTZ films in the presence of various Cu-contents. Evaluation of the bacterial inactivation kinetics of E. coli under low intensity actinic hospital light and in the dark was carried out. The stable repetitive bacterial inactivation was consistent with the extremely low Cu-ion release from the samples of 0.4 ppb. Evidence is presented by the bacterial inactivation dependence on the applied light intensity for the intervention of Cu as semiconductor CuO during the bacterial inactivation at the TNTZ-Cu interface. The mechanism of CuO-intervention under light is suggested based on the pH/and potential changes registered during bacterial disinfection. Copyright © 2017 Elsevier B.V. All rights reserved.

Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use.

PubMed

Abia, Akebe Luther King; Alisoltani, Arghavan; Keshri, Jitendra; Ubomba-Jaswa, Eunice

2018-03-01

Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations. Samples were collected on river stretches influenced by an informal, a peri-urban and a rural settlement. Genomic DNA was extracted from water and sediment samples and sequenced on an Illumina® MiSeq platform targeting the 16S rRNA gene variable region V3-V4 from the genomic DNA. Metagenomic data analysis revealed that there was a great diversity in the microbial populations associated with the different land uses, with the informal settlement having the most considerable influence on the bacterial diversity in the water and sediments of the Apies River. The Proteobacteria (69.8%), Cyanobacteria (4.3%), Bacteroidetes (2.7%), and Actinobacteria (2.7%) were the most abundant phyla; the Alphaproteobacteria, Betaproteobacteria and Anaerolineae were the most recorded classes. Also, the sediments had a greater diversity and abundance in bacterial population than the water column. The functional profiles of the bacterial populations revealed an association with many human diseases including cancer pathways. Further studies that would isolate these potentially pathogenic organisms in the aquatic environment are therefore needed as this would help in protecting the lives of communities using such rivers, especially against emerging bacterial pathogens. Copyright © 2017 Elsevier B.V. All rights reserved.

Modeling Transfer of Vibrio Parahaemolyticus During Peeling of Raw Shrimp.

PubMed

Xiao, Xingning; Pang, Haiying; Wang, Wen; Fang, Weihuan; Fu, Yingchun; Li, Yanbin

2018-03-01

This study aimed to qualify the transfer of Vibrio parahaemolyticus during the shrimp peeling process via gloves under 3 different scenarios. The 1st 2 scenarios provided quantitative information for the probability distribution of bacterial transfer rates from (i) contaminated shrimp (6 log CFU/g) to non-contaminated gloves (Scenario 1) and (ii) contaminated gloves (6 log CFU/per pair) to non-contaminated shrimp (Scenario 2). In Scenario 3, bacterial transfer from contaminated shrimp to non-contaminated shrimp in the shrimp peeling process via gloves was investigated to develop a predictive model for describing the successive bacterial transfer. The range of bacterial transfer rate (%) in Scenarios 1 and 2 was 7% to 91.95% and 0.04% to 12.87%, respectively, indicating that the bacteria can be transferred from shrimp to gloves much easier than that from gloves to shrimp. A Logistic (1.59, 0.14) and Triangle distribution (-1.61, 0.12, 1.32) could be used to describe the bacterial transfer rate in Scenarios 1 and 2, respectively. In Scenario 3, a continuously decay patterning with fluctuations as the peeling progressed has been observed at all inoculation levels of the 1st shrimp (5, 6, and 7 log CFU/g). The bacteria could be transferred easier at 1st few peels, and the decreasing bacterial transfer was found in later phase. Two models (exponential and Weibull) could describe the successive bacterial transfer satisfactorily (pseudo-R 2 > 0.84, RMSE < 1.23, SEP < 10.37). The result of this study can provide information regarding cross-contamination events in the seafood factory. This study presented that Vibrio parahaemolyticus cross-contamination could be caused by gloves during the shrimp peeling process. The bacterial transfer rate distribution and predictive model derived from this work could be used in risk assessment of V. parahaemolyticus to ensure peeled shrimp safety. © 2018 Institute of Food Technologists®.

Characterization of Epiphytic Bacterial Communities from Grapes, Leaves, Bark and Soil of Grapevine Plants Grown, and Their Relations

PubMed Central

Martins, Guilherme; Lauga, Béatrice; Miot-Sertier, Cécile; Mercier, Anne; Lonvaud, Aline; Soulas, Marie-Louise; Soulas, Guy; Masneuf-Pomarède, Isabelle

2013-01-01

Despite its importance in plant health and crop quality, the diversity of epiphytic bacteria on grape berries and other plant parts, like leaves and bark, remains poorly described, as does the role of telluric bacteria in plant colonization. In this study, we compare the bacterial community size and structure in vineyard soils, as well as on grapevine bark, leaves and berries. Analyses of culturable bacteria revealed differences in the size and structure of the populations in each ecosystem. The highest bacteria population counts and the greatest diversity of genera were found in soil samples, followed by bark, grapes and leaves. The identification of isolates revealed that some genera – Pseudomonas, Curtobacterium, and Bacillus – were present in all ecosystems, but in different amounts, while others were ecosystem-specific. About 50% of the genera were common to soil and bark, but absent from leaves and grapes. The opposite was also observed: grape and leaf samples presented 50% of genera in common that were absent from trunk and soil. The bacterial community structure analyzed by T-RFLP indicated similarities between the profiles of leaves and grapes, on the one hand, and bark and soil, on the other, reflecting the number of shared T-RFs. The results suggest an interaction between telluric bacterial communities and the epiphytic bacteria present on the different grapevine parts. PMID:24023666

New insights on the baker's yeast-mediated hydration of oleic acid: the bacterial contaminants of yeast are responsible for the stereoselective formation of (R)-10-hydroxystearic acid.

PubMed

Serra, S; De Simeis, D

2018-03-01

The preparation of the high-value flavour γ-dodecalactone is based on the biotransformation of natural 10-HSA, which is in turn obtained by microbial hydration of oleic acid. We want to establish a reliable baker's yeast-mediated procedure for 10-HSA preparation. The previously reported yeast-mediated hydration procedures are unreliable because bacteria-free baker's yeast is not able to hydrate oleic acid. The actual responsible for performing this reaction are the bacterial contaminants present in baker's yeast. Moreover, we demonstrated that the enantioselectivity in the production of (R)-10-HSA is affected mainly by the temperature used in the biotransformation. We demonstrated that Saccharomyces cerevisiae is not able to hydrate oleic acid, whereas different bacterial strains present in baker's yeast transform oleic acid into (R)-10-HSA. We reported a general procedure for the preparation of (R)-10-HSA starting from oleic acid and using commercially available baker's yeast. This study holds both scientific and industrial interest. It unambiguously establishes that the eukaryote micro-organisms present in baker's yeast are not able to hydrate oleic acid. The isolation of oleic acid hydrating bacterial strains from commercial baker's yeast points to their prospective use for the industrial synthesis of 10-HSA. © 2017 The Society for Applied Microbiology.

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

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

Wright, Justin; Kirchner, Veronica; Bernard, William

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. Here, we investigate the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L.more » Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. And across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.« less

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

DOE PAGES

Wright, Justin; Kirchner, Veronica; Bernard, William; ...

2017-11-22

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. Here, we investigate the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L.more » Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. And across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.« less

Advances in Bacterial Methionine Aminopeptidase Inhibition

PubMed Central

Helgren, Travis R.; Wangtrakuldee, Phumvadee; Staker, Bart L.; Hagen, Timothy J.

2016-01-01

Methionine aminopeptidases (MetAPs) are metalloenzymes that cleave the N-terminal methionine from newly synthesized peptides and proteins. These MetAP enzymes are present in bacteria, and knockout experiments have shown that MetAP activity is essential for cell life, suggesting that MetAPs are good antibacterial drug targets. MetAP enzymes are also present in the human host and selectivity is essential. There have been significant structural biology efforts and over 65 protein crystal structures of bacterial MetAPs are deposited into the PDB. This review highlights the available crystallographic data for bacterial MetAPs. Structural comparison of bacterial MetAPs with human MetAPs highlights differences that can lead to selectivity. In addition, this review includes the chemical diversity of molecules that bind and inhibit the bacterial MetAP enzymes. Analysis of the structural biology and chemical space of known bacterial MetAP inhibitors leads to a greater understanding of this antibacterial target and the likely development of potential antibacterial agents. PMID:26268344

Demonstration of bacterial biofilms in culture-negative silicone stent and jones tube.

PubMed

Parsa, Kami; Schaudinn, Christoph; Gorur, Amita; Sedghizadeh, Parish P; Johnson, Thomas; Tse, David T; Costerton, John W

2010-01-01

To demonstrate the presence of bacterial biofilms on a dacryocystorhinostomy silicone stent and a Jones tube. One dacryocystorhinostomy silicone stent and one Jones tube were removed from 2 patients who presented with an infection of their respective nasolacrimal system. Cultures were obtained, and the implants were processed for scanning electron microscopy and confocal laser scanning microscopy, advanced microscopic methods that are applicable for detection of uncultivable biofilm organisms. Routine bacterial cultures revealed no growth, but bacterial biofilms on outer and inner surfaces of both implants were confirmed by advanced microscopic techniques. To the authors' knowledge, this is the first article that documents the presence of biofilms on a Crawford stent or a Jones tube on patients who presented with infections involving the nasolacrimal system. Although initial cultures revealed absence of any bacterial growth, confocal laser scanning microscopy and scanning electron microscopy documented bacterial colonization. Clinicians should consider the role of biofilms and the limitation of our standard culturing techniques while treating patients with device- or implant-related infections.

Health Threats from Contamination of Spices Commercialized in Romania: Risks of Fungal and Bacterial Infections.

PubMed

Man, Adrian; Mare, Anca; Toma, Felicia; Curticăpean, Augustin; Santacroce, Luigi

2016-01-01

The study of fungal contamination in food and mycotoxicoses is a priority today, both internationally and nationally. The purpose of this study is to have a general view over the quality of the most common spices that are sold in Romanian markets, by assessing the degree of fungal, bacterial and mycotoxin contamination in pepper and chili powders. We tested four types of spices: white pepper, black pepper, sweet and hot chili powders from 12 different distributing companies, summing a total of 35 sample types. The fungal and bacterial load was assessed by Standard Plate Count, while the mycotoxin content by High-performance liquid chromatography. Environmental conditions (humidity, pH) and the selling price for each product were also followed. Fungi were observed in 72.7% of black pepper samples, 33.3% in white pepper, 30% in sweet chili and 25% in hot chili products. The most common isolated fungus was Aspergillus spp., while Rhizopus, Mucor, Fusarium, Penicillium, Absidia species were found, in smaller percentage. Four producers (44.4%) presented fungal contamination of over 10^3 CFU/g and two producers (22.2%) presented no fungal contamination in their products. Bacterial contamination was found in 85.7% of the tested products, consisting mostly in Bacillus spp. Aflatoxin B1 was present in all the tested products, mostly in black pepper (mean value 126.3 ng/g); Ochratoxin A was present in sweet chili (mean value 328 ng/g) and Zearalenone in hot chili (mean value 604 ng/g) and sweet chili (mean value 382 ng/g). All spices presented either fungal contamination, mycotoxin contamination, or both. The high humidity and the high pH of spices represent favorable conditions for fungal growth. The selling price was partly related to the physic-chemical conditions and microbiological quality of the spices. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Bacterial community structure in the drinking water microbiome is governed by filtration processes.

PubMed

Pinto, Ameet J; Xi, Chuanwu; Raskin, Lutgarde

2012-08-21

The bacterial community structure of a drinking water microbiome was characterized over three seasons using 16S rRNA gene based pyrosequencing of samples obtained from source water (a mix of a groundwater and a surface water), different points in a drinking water plant operated to treat this source water, and in the associated drinking water distribution system. Even though the source water was shown to seed the drinking water microbiome, treatment process operations limit the source water's influence on the distribution system bacterial community. Rather, in this plant, filtration by dual media rapid sand filters played a primary role in shaping the distribution system bacterial community over seasonal time scales as the filters harbored a stable bacterial community that seeded the water treatment processes past filtration. Bacterial taxa that colonized the filter and sloughed off in the filter effluent were able to persist in the distribution system despite disinfection of finished water by chloramination and filter backwashing with chloraminated backwash water. Thus, filter colonization presents a possible ecological survival strategy for bacterial communities in drinking water systems, which presents an opportunity to control the drinking water microbiome by manipulating the filter microbial community. Grouping bacterial taxa based on their association with the filter helped to elucidate relationships between the abundance of bacterial groups and water quality parameters and showed that pH was the strongest regulator of the bacterial community in the sampled drinking water system.

A Lactobacillus-Deficient Vaginal Microbiota Dominates Postpartum Women in Rural Malawi

PubMed Central

2018-01-01

ABSTRACT The bacterial community found in the vagina is an important determinant of a woman's health and disease status. A healthy vaginal microbiota is associated with low species richness and a high proportion of one of a number of different Lactobacillus spp. When disrupted, the resulting abnormal vaginal microbiota is associated with a number of disease states and poor pregnancy outcomes. Studies up until now have concentrated on relatively small numbers of American and European populations that may not capture the full complexity of the community or adequately predict what constitutes a healthy microbiota in all populations. In this study, we sampled and characterized the vaginal microbiota found on vaginal swabs taken postpartum from a cohort of 1,107 women in rural Malawi. We found a population dominated by Gardnerella vaginalis and devoid of the most common vaginal Lactobacillus species, even if the vagina was sampled over a year postpartum. This Lactobacillus-deficient anaerobic community, commonly labeled community state type (CST) 4, could be subdivided into four further communities. A Lactobacillus iners-dominated vaginal microbiota became more common the longer after delivery the vagina was sampled, but G. vaginalis remained the dominant organism. These results outline the difficulty in all-encompassing definitions of what a healthy or abnormal postpartum vaginal microbiota is. Previous identification of community state types and associations among bacterial species, bacterial vaginosis, and adverse birth outcomes may not represent the complex heterogeneity of the microbiota present. (This study has been registered at ClinicalTrials.gov as NCT01239693.) IMPORTANCE A bacterial community in the vaginal tract is dominated by a small number of Lactobacillus species, and when not present there is an increased incidence of inflammatory conditions and adverse birth outcomes. A switch to a vaginal bacterial community lacking in Lactobacillus species is common after pregnancy. In this study, we characterized the postpartum vaginal bacterial community of a large group of women from a resource-poor, undersampled population in rural Malawi. The majority of women were found to have a Lactobacillus-deficient community, and even when sampled a year after delivery the majority of women still did not have Lactobacillus present in their vaginal microbiota. The effect of becoming pregnant again for those who do not revert to a Lactobacillus-dominant community is unknown, and this could suggest that not all Lactobacillus-deficient community structures are adverse. A better understanding of this complex community state type is needed. PMID:29305501

Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing.

PubMed

Païssé, Sandrine; Valle, Carine; Servant, Florence; Courtney, Michael; Burcelin, Rémy; Amar, Jacques; Lelouvier, Benjamin

2016-05-01

Recent studies have revealed that the blood of healthy humans is not as sterile as previously supposed. The objective of this study was to provide a comprehensive description of the microbiome present in different fractions of the blood of healthy individuals. The study was conducted in 30 healthy blood donors to the French national blood collection center (Établissement Français du Sang). We have set up a 16S rDNA quantitative polymerase chain reaction assay as well as a 16S targeted metagenomics sequencing pipeline specifically designed to analyze the blood microbiome, which we have used on whole blood as well as on different blood fractions (buffy coat [BC], red blood cells [RBCs], and plasma). Most of the blood bacterial DNA is located in the BC (93.74%), and RBCs contain more bacterial DNA (6.23%) than the plasma (0.03%). The distribution of 16S DNA is different for each fraction and spreads over a relatively broad range among donors. At the phylum level, blood fractions contain bacterial DNA mostly from the Proteobacteria phylum (more than 80%) but also from Actinobacteria, Firmicutes, and Bacteroidetes. At deeper taxonomic levels, there are striking differences between the bacterial profiles of the different blood fractions. We demonstrate that a diversified microbiome exists in healthy blood. This microbiome has most likely an important physiologic role and could be implicated in certain transfusion-transmitted bacterial infections. In this regard, the amount of 16S bacterial DNA or the microbiome profile could be monitored to improve the safety of the blood supply. © 2016 AABB.

Structure and dynamics of the gut bacterial microbiota of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) across their life stages

PubMed Central

2017-01-01

Bark beetles play an important role as agents of natural renovation and regeneration in coniferous forests. Several studies have documented the metabolic capacity of bacteria associated with the gut, body surface, and oral secretions of these insects; however, little is known about how the bacterial community structure changes during the life cycle of the beetles. This study represents the first comprehensive analysis of the bacterial community of the gut of the bark beetle D. rhizophagus during the insect’s life cycle using 454 pyrosequencing. A total of 4 bacterial phyla, 7 classes, 15 families and 23 genera were identified. The α-diversity was low, as demonstrated in previous studies. The dominant bacterial taxa belonged to the Enterobacteriaceae and Pseudomonadaceae families. This low α-diversity can be attributed to the presence of defensive chemical compounds in conifers or due to different morpho-physiological factors in the gut of these insects acting as strong selective factors. Members of the genera Rahnella, Serratia, Pseudomonas and Propionibacterium were found at all life stages, and the first three genera, particularly Rahnella, were predominant suggesting the presence of a core microbiome in the gut. Significant differences in β-diversity were observed, mainly due to bacterial taxa present at low frequencies and only in certain life stages. The predictive functional profiling indicated metabolic pathways related to metabolism of amino acids and carbohydrates, and membrane transport as the most significant in the community. These differences in the community structure might be due to several selective factors, such as gut compartmentalization, physicochemical conditions, and microbial interactions. PMID:28406998

Bacterial community structure in two permafrost wetlands on the Tibetan Plateau and Sanjiang Plain, China.

PubMed

Yun, Juanli; Ju, Yiwen; Deng, Yongcui; Zhang, Hongxun

2014-08-01

Permafrost wetlands are important methane emission sources and fragile ecosystems sensitive to climate change. Presently, there remains a lack of knowledge regarding bacterial communities, especially methanotrophs in vast areas of permafrost on the Tibetan Plateau in Northwest China and the Sanjiang Plain (SJ) in Northeast China. In this study, 16S rRNA-based quantitative PCR (qPCR) and 454 pyrosequencing were used to identify bacterial communities in soils sampled from a littoral wetland of Lake Namco on the Tibetan Plateau (NMC) and an alluvial wetland on the SJ. Additionally, methanotroph-specific primers targeting particulate methane monooxygenase subunit A gene (pmoA) were used for qPCR and pyrosequencing analysis of methanotrophic community structure in NMC soils. qPCR analysis revealed the presence of 10(10) 16S rRNA gene copies per gram of wet soil in both wetlands, with 10(8) pmoA copies per gram of wet soil in NMC. The two permafrost wetlands showed similar bacterial community compositions, which differed from those reported in other cold environments. Proteobacteria, Actinobacteria , and Chloroflexi were the most abundant phyla in both wetlands, whereas Acidobacteria was prevalent in the acidic wetland SJ only. These four phyla constituted more than 80 % of total bacterial community diversity in permafrost wetland soils, and Methylobacter of type I methanotrophs was overwhelmingly dominant in NMC soils. This study is the first major bacterial sequencing effort of permafrost in the NMC and SJ wetlands, which provides fundamental data for further studies of microbial function in extreme ecosystems under climate change scenarios.

Bacterial agents causing meningitis during 2013-2014 in Turkey: A multi-center hospital-based prospective surveillance study.

PubMed

Ceyhan, Mehmet; Ozsurekci, Yasemin; Gürler, Nezahat; Karadag Oncel, Eda; Camcioglu, Yıldız; Salman, Nuran; Celik, Melda; Emiroglu, Melike Keser; Akin, Fatih; Tezer, Hasan; Parlakay, Aslinur Ozkaya; Tuygun, Nilden; Tamburaci, Diyar; Dinleyici, Ener Cagri; Karbuz, Adem; Uluca, Ünal; Alhan, Emre; Çay, Ümmühan; Kurugol, Zafer; Hatipoğlu, Nevin; Şiraneci, Rengin; İnce, Tolga; Sensoy, Gülnar; Belet, Nursen; Coskun, Enes; Yilmaz, Fatih; Hacimustafaoglu, Mustafa; Celebi, Solmaz; Celik, Ümit; Ozen, Metehan; Akaslan, Aybüke; Devrim, İlker; Kuyucu, Necdet; Öz, Fatmanur; Bozdemir, Sefika Elmas; Kara, Ahu

2016-11-01

This is an observational epidemiological study to describe causes of bacterial meningitis among persons between 1 month and 18 y of age who are hospitalized with suspected bacterial meningitis in 7 Turkish regions. covering 32% of the entire population of Turkey. We present here the results from 2013 and 2014. A clinical case with meningitis was defined according to followings: any sign of meningitis including fever, vomiting, headache, and meningeal irritation in children above one year of age and fever without any documented source, impaired consciousness, prostration and seizures in those < 1 y of age. Single tube multiplex PCR assay was performed for the simultaneous identification of bacterial agents. The specific gene targets were ctrA, bex, and ply for N. meningitidis, Hib, and S. pneumoniae, respectively. PCR positive samples were recorded as laboratory-confirmed acute bacterial meningitis. A total of 665 children were hospitalized for suspected acute meningitis. The annual incidences of acute laboratory-confirmed bacterial meningitis were 0.3 cases / 100,000 population in 2013 and 0.9 cases/100,000 in 2014. Of the 94 diagnosed cases of bacterial meningitis by PCR, 85 (90.4%) were meningococcal and 9 (9.6%) were pneumococcal. Hib was not detected in any of the patients. Among meningococcal meningitis, cases of serogroup Y, A, B and W-135 were 2.4% (n = 2), 3.5% (n = 3), 32.9% (n = 28), and 42.4% (n = 36). No serogroup C was detected among meningococcal cases. Successful vaccination policies for protection from bacterial meningitis are dependent on accurate determination of the etiology of bacterial meningitis. Additionally, the epidemiology of meningococcal disease is dynamic and close monitoring of serogroup distribution is comprehensively needed to assess the benefit of adding meningococcal vaccines to the routine immunization program.

Inhibitor design strategy based on an enzyme structural flexibility: a case of bacterial MurD ligase.

PubMed

Perdih, Andrej; Hrast, Martina; Barreteau, Hélène; Gobec, Stanislav; Wolber, Gerhard; Solmajer, Tom

2014-05-27

Increasing bacterial resistance to available antibiotics stimulated the discovery of novel efficacious antibacterial agents. The biosynthesis of the bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of the UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design. In our previous computational studies, the C-terminal domain motion of the MurD ligase was investigated using Targeted Molecular Dynamic (TMD) simulation and the Off-Path Simulation (OPS) technique. In this study, we present a drug design strategy using multiple protein structures for the identification of novel MurD ligase inhibitors. Our main focus was the ATP-binding site of the MurD enzyme. In the first stage, three MurD protein conformations were selected based on the obtained OPS/TMD data as the initial criterion. Subsequently, a two-stage virtual screening approach was utilized combining derived structure-based pharmacophores with molecular docking calculations. Selected compounds were then assayed in the established enzyme binding assays, and compound 3 from the aminothiazole class was discovered to act as a dual MurC/MurD inhibitor in the micomolar range. A steady-state kinetic study was performed on the MurD enzyme to provide further information about the mechanistic aspects of its inhibition. In the final stage, all used conformations of the MurD enzyme with compound 3 were simulated in classical molecular dynamics (MD) simulations providing atomistic insights of the experimental results. Overall, the study depicts several challenges that need to be addressed when trying to hit a flexible moving target such as the presently studied bacterial MurD enzyme and show the possibilities of how computational tools can be proficiently used at all stages of the drug discovery process.

In vitro evaluation of the sealing ability of three newly developed root canal sealers: A bacterial microleakage study

PubMed Central

Sobhani, Ehsan; Samadi-Kafil, Hossein; Pirzadeh, Ahmad; Jafari, Sanaz

2016-01-01

Background The purpose of this study was to compare the sealing ability of MTA Fillapex, Apatite Root Canal Sealer and AH26 sealers. Material and Methods The present in vitro study was carried out on 142 extracted single-rooted human mature teeth. The teeth were randomly divided into three experimental groups (n=44) and two control groups (n=5). Three root canal sealers were MTA Fillapex, Apatite Root Canal Sealer and AH26. The teeth in the control groups were either filled with no sealer or made completely impermeable. The root canals were prepared and obturated with gutta-percha and one of the sealers. The teeth were sterilized with ethylene oxide gas prior to the bacterial leakage assessment using Enterococcus faecalis. Leakage was evaluated every 24 hours for 90 days. Data were analyzed with descriptive statistical methods and chi-squared test. If the data were significant, a proper post hoc test was used. Statistical significance was set at P<0.05. Results The positive control specimens exhibited total bacterial penetration whilst the negative control specimens showed no evidence of bacterial penetration. At the end of the study, the analysis of microleakage with chi-squared test showed no significant differences between the experimental groups (P<0.05). The results of chi-squared test analyzing the pair-wise differences between the groups considering the numerical values for leakage day indicated the lowest leakage with AH26 and the highest with Apatite root sealer. Conclusions According to the results of the present study, sealing ability of AH26 was significantly higher than that of MTA Fillapex and Apatite Root Canal Sealer. Key words:Mineral Trioxide aggregate, root canal obturation, dental seal. PMID:27957271

Comparison of Removal Behavior of Two Biotrickling Filters under Transient Condition and Effect of pH on the Bacterial Communities

PubMed Central

Tu, Xiang; Li, Jianjun; Feng, Rongfang; Sun, Guoping; Guo, Jun

2016-01-01

Although biotrickling filters (BTFs) applied under acidic condition to remove H2S from waste gases have been reported, the removal behavior of the acidic BTF under transient condition which was normal in most industry processes, and corresponding bacterial community have not been thoroughly studied. In the present study, two BTFs were run under neutral (BTFn) and acidic (BTFa) conditions, respectively. The results revealed that the removal performance of BTFa under transient condition was superior to that of BTFn; the maximum H2S eliminating capacities (ECs) achieved by BTFa and BTFn were 489.9 g/m3 h and 443.6 g/m3 h, respectively. High-throughput sequencing suggested that pH was the critical factor and several other factors including nutrient and the inlet loadings also had roles in shaping bacterial community structure. Acidithiobacillus was the most abundant bacterial group. The results indicated that BTF acclimation under acidic condition may facilitate generating microbial community with high H2S-degrading capability. PMID:27196300

Cyclic Dinucleotides in Oral Bacteria and in Oral Biofilms.

PubMed

Gürsoy, Ulvi K; Gürsoy, Mervi; Könönen, Eija; Sintim, Herman O

2017-01-01

Oral cavity acts as a reservoir of bacterial pathogens for systemic infections and several oral microorganisms have been linked to systemic diseases. Quorum sensing and cyclic dinucleotides, two "decision-making" signaling systems, communicate to regulate physiological process in bacteria. Discovery of cyclic dinucleotides has a long history, but the progress in our understanding of how cyclic dinucleotides regulate bacterial lifestyle is relatively new. Oral microorganisms form some of the most intricate biofilms, yet c-di-GMP, and c-di-AMP signaling have been rarely studied in oral biofilms. Recent studies demonstrated that, with the aid of bacterial messenger molecules and their analogs, it is possible to activate host innate and adaptive immune responses and epithelial integrity with a dose that is relevant to inhibit bacterial virulence mechanisms, such as fimbriae and exopolysaccharide production, biofilm formation, and host cell invasion. The aim of this perspective article is to present available information on cyclic dinucleotides in oral bacteria and in oral biofilms. Moreover, technologies that can be used to detect cyclic dinucleotides in oral biofilms are described. Finally, directions for future research are highlighted.

Culture-Independent Identification of Periodontitis-Associated Porphyromonas and Tannerella Populations by Targeted Molecular Analysis

PubMed Central

de Lillo, A.; Booth, V.; Kyriacou, L.; Weightman, A. J.; Wade, W. G.

2004-01-01

Periodontitis is the commonest bacterial disease of humans and is the major cause of adult tooth loss. About half of the oral microflora is unculturable; and 16S rRNA PCR, cloning, and sequencing techniques have demonstrated the high level of species richness of the oral microflora. In the present study, a PCR primer set specific for the genera Porphyromonas and Tannerella was designed and used to analyze the bacterial populations in subgingival plaque samples from inflamed shallow and deep sites in subjects with periodontitis and shallow sites in age- and sex-matched controls. A total of 308 clones were sequenced and found to belong to one of six Porphyromonas or Tannerella species or phylotypes, one of which, Porphyromonas P3, was novel. Tannerella forsythensis was found in significantly higher proportions in patients than in controls. Porphyromonas catoniae and Tannerella phylotype BU063 appeared to be associated with shallow sites. Targeted culture-independent molecular ecology studies have a valuable role to play in the identification of bacterial targets for further investigations of the pathogenesis of bacterial infections. PMID:15583276

Efficacy of rifaximin vaginal tablets in treatment of bacterial vaginosis: a molecular characterization of the vaginal microbiota.

PubMed

Cruciani, Federica; Brigidi, Patrizia; Calanni, Fiorella; Lauro, Vittoria; Tacchi, Raffaella; Donders, Gilbert; Peters, Klaus; Guaschino, Secondo; Vitali, Beatrice

2012-08-01

Bacterial vaginosis (BV) is a common vaginal disorder characterized by an alteration of the vaginal bacterial morphotypes, associated with sexually transmitted infections and adverse pregnancy outcomes. The purpose of the present study was to evaluate the impact of different doses of rifaximin vaginal tablets (100 mg/day for 5 days, 25 mg/day for 5 days, and 100 mg/day for 2 days) on the vaginal microbiota of 102 European patients with BV enrolled in a multicenter, double-blind, randomized, placebo-controlled study. An integrated molecular approach based on quantitative PCR (qPCR) and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the effects of vaginal tablets containing the antibiotic. An increase in members of the genus Lactobacillus and a decrease in the BV-related bacterial groups after the antibiotic treatment were demonstrated by qPCR. PCR-DGGE profiles confirmed the capability of rifaximin to modulate the composition of the vaginal microbial communities and to reduce their complexity. This molecular analysis supported the clinical observation that rifaximin at 25 mg/day for 5 days represents an effective treatment to be used in future pivotal studies for the treatment of BV.

Efficacy of Rifaximin Vaginal Tablets in Treatment of Bacterial Vaginosis: a Molecular Characterization of the Vaginal Microbiota

PubMed Central

Cruciani, Federica; Brigidi, Patrizia; Calanni, Fiorella; Lauro, Vittoria; Tacchi, Raffaella; Donders, Gilbert; Peters, Klaus; Guaschino, Secondo

2012-01-01

Bacterial vaginosis (BV) is a common vaginal disorder characterized by an alteration of the vaginal bacterial morphotypes, associated with sexually transmitted infections and adverse pregnancy outcomes. The purpose of the present study was to evaluate the impact of different doses of rifaximin vaginal tablets (100 mg/day for 5 days, 25 mg/day for 5 days, and 100 mg/day for 2 days) on the vaginal microbiota of 102 European patients with BV enrolled in a multicenter, double-blind, randomized, placebo-controlled study. An integrated molecular approach based on quantitative PCR (qPCR) and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the effects of vaginal tablets containing the antibiotic. An increase in members of the genus Lactobacillus and a decrease in the BV-related bacterial groups after the antibiotic treatment were demonstrated by qPCR. PCR-DGGE profiles confirmed the capability of rifaximin to modulate the composition of the vaginal microbial communities and to reduce their complexity. This molecular analysis supported the clinical observation that rifaximin at 25 mg/day for 5 days represents an effective treatment to be used in future pivotal studies for the treatment of BV. PMID:22585228

Analysis of the bacterial strains using Biolog plates in the contaminated soil from Riyadh community.

PubMed

Al-Dhabaan, Fahad Abdullah M; Bakhali, Ali Hassan

2017-05-01

Routine manufacture, detonation and disposal of explosives in land and groundwater have resulted in complete pollution. Explosives are xenobiotic compounds, being toxic to biological systems, and their recalcitrance leads to persistence in the environment. The methods currently used for the remediation of explosive contaminated sites are expensive and can result in the formation of toxic products. The present study aimed to investigate the bacterial strains using the Biolog plates in the soil from the Riyadh community. The microbial strains were isolated using the spread plate technique and were identified using the Biolog method. In this study we have analyzed from bacterial families of soil samples, obtained from the different sites in 5 regions at Explosive Institute. Our results conclude that Biolog MicroPlates were developed for the rapid identification of bacterial isolates by sole-carbon source utilization and can be used for the identification of bacteria. Out of five communities, only four families of bacteria indicate that the microbial community lacks significant diversity in region one from the Riyadh community in Saudi Arabia. More studies are needed to be carried out in different regions to validate our results.

Biodiversity of Bacterial Ecosystems in Traditional Egyptian Domiati Cheese▿

PubMed Central

El-Baradei, Gaber; Delacroix-Buchet, Agnès; Ogier, Jean-Claude

2007-01-01

Bacterial biodiversity occurring in traditional Egyptian soft Domiati cheese was studied by PCR-temporal temperature gel electrophoresis (TTGE) and PCR-denaturing gradient gel electrophoresis (DGGE). Bands were identified using a reference species database (J.-C. Ogier et al., Appl. Environ. Microbiol. 70:5628-5643, 2004); de novo bands having nonidentified migration patterns were identified by DNA sequencing. Results reveal a novel bacterial profile and extensive bacterial biodiversity in Domiati cheeses, as reflected by the numerous bands present in TTGE and DGGE patterns. The dominant lactic acid bacteria (LAB) identified were as follows: Leuconostoc mesenteroides, Lactococcus garvieae, Aerococcus viridans, Lactobacillus versmoldensis, Pediococcus inopinatus, and Lactococcus lactis. Frequent non-LAB species included numerous coagulase-negative staphylococci, Vibrio spp., Kocuria rhizophila, Kocuria kristinae, Kocuria halotolerans, Arthrobacter spp./Brachybacterium tyrofermentans. This is the first time that the majority of these species has been identified in Domiati cheese. Nearly all the dominant and frequent bacterial species are salt tolerant, and several correspond to known marine bacteria. As Domiati cheese contains 5.4 to 9.5% NaCl, we suggest that these bacteria are likely to have an important role in the ripening process. This first systematic study of the microbial composition of Domiati cheeses reveals great biodiversity and evokes a role for marine bacteria in determining cheese type. PMID:17189434

Biodiversity of bacterial ecosystems in traditional Egyptian Domiati cheese.

PubMed

El-Baradei, Gaber; Delacroix-Buchet, Agnès; Ogier, Jean-Claude

2007-02-01

Bacterial biodiversity occurring in traditional Egyptian soft Domiati cheese was studied by PCR-temporal temperature gel electrophoresis (TTGE) and PCR-denaturing gradient gel electrophoresis (DGGE). Bands were identified using a reference species database (J.-C. Ogier et al., Appl. Environ. Microbiol. 70:5628-5643, 2004); de novo bands having nonidentified migration patterns were identified by DNA sequencing. Results reveal a novel bacterial profile and extensive bacterial biodiversity in Domiati cheeses, as reflected by the numerous bands present in TTGE and DGGE patterns. The dominant lactic acid bacteria (LAB) identified were as follows: Leuconostoc mesenteroides, Lactococcus garvieae, Aerococcus viridans, Lactobacillus versmoldensis, Pediococcus inopinatus, and Lactococcus lactis. Frequent non-LAB species included numerous coagulase-negative staphylococci, Vibrio spp., Kocuria rhizophila, Kocuria kristinae, Kocuria halotolerans, Arthrobacter spp./Brachybacterium tyrofermentans. This is the first time that the majority of these species has been identified in Domiati cheese. Nearly all the dominant and frequent bacterial species are salt tolerant, and several correspond to known marine bacteria. As Domiati cheese contains 5.4 to 9.5% NaCl, we suggest that these bacteria are likely to have an important role in the ripening process. This first systematic study of the microbial composition of Domiati cheeses reveals great biodiversity and evokes a role for marine bacteria in determining cheese type.

Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing.

PubMed

Naveed, Muhammad; Mubeen, Samavia; Khan, SamiUllah; Ahmed, Iftikhar; Khalid, Nauman; Suleria, Hafiz Ansar Rasul; Bano, Asghari; Mumtaz, Abdul Samad

2014-01-01

In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

Rice root-associated bacteria – insights in community structures across ten cultivars

PubMed Central

Hardoim, Pablo Rodrigo; Andreote, Fernando Dini; Reinhold-Hurek, Barbara; Sessitsch, Angela; van Overbeek, Leonard Simon; van Elsas, Jan Dirk

2015-01-01

In this study, the effect of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Beta-proteobacteria, Pseudomonas and Actinobacteria were studied using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined to a large extent the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa subspecies indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of ‘improved’ and ‘traditional’ plants was noted for all communities analysed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed amongst rice replicates. The data suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants. PMID:21426364

Femtosecond laser induced surface modification for prevention of bacterial adhesion on 45S5 bioactive glass

NASA Astrophysics Data System (ADS)

Shaikh, Shazia; Singh, Deepti; Subramanian, Mahesh; Kedia, Sunita; Singh, Anil Kumar; Singh, Kulwant; Gupta, Nidhi; Sinha, Sucharita

2018-02-01

Bacterial attachment and biofilm formation on implant surface has been a major concern in hospital and industrial environment. Prevention of bacterial infections of implant surface through surface treatment could be a potential solution and hence this has become a key area of research. In the present study, the antibacterial and biocompatible properties of femtosecond laser surface treated 45S5 bioactive glass (BG) have been investigated. Adhesion and sustainability of both gram positive S. aureus and gram negative P.aeruginosa and E. coli nosocomial bacteria on untreated and laser treated BG samples has been explored. An imprint method has been used to visualize the growth of bacteria on the sample surface. We observed complete bacterial rejection potentially reducing risk of biofilm formation on laser treated surface. This was correlated with surface roughness, wettability and change in surface chemical composition of the samples before and after laser treatment. Biocompatibility of the laser treated BG was demonstrated by studying the anchoring and growth of human cervix cell line INT407. Our results demonstrate that, laser surface modification of BG enables enhanced bacterial rejection without affecting its biocompatibility towards growth of human cells on it. These results open a significantly potential approach towards use of laser in successfully imparting desirable characteristics to BG based bio-implants and devices.

Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

PubMed Central

Naveed, Muhammad; Mubeen, Samavia; khan, SamiUllah; Ahmed, Iftikhar; Khalid, Nauman; Suleria, Hafiz Ansar Rasul; Bano, Asghari; Mumtaz, Abdul Samad

2014-01-01

In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization. PMID:25477935

Diagnostic accuracy of history and physical examination in bacterial acute rhinosinusitis.

PubMed

Autio, Timo J; Koskenkorva, Timo; Närkiö, Mervi; Leino, Tuomo K; Koivunen, Petri; Alho, Olli-Pekka

2015-07-01

To evaluate the diagnostic accuracy of symptoms, the symptom progression pattern, and clinical signs in identifying bacterial acute rhinosinusitis (ARS). We conducted an inception cohort study among 50 military recruits with ARS. We collected symptoms daily from the onset of symptoms to approximately 10 days. At 9 to 10 days, standardized data on symptoms and physical findings were gathered. A positive culture of maxillary sinus aspirate was considered to be the reference standard for bacterial ARS. At 9 to 10 days, the presence or deterioration after 5 days of any of the symptoms could not be used to diagnose bacterial ARS. Toothache had an adequate positive likelihood ratio (positive likelihood ratio [LR+] 4.4) but was too rare to be used for screening. In contrast, several physical findings at 9 to 10 days were of more diagnostic use and frequent enough for screening. Moderate or profuse (vs. none/minimal) amount of secretion in nasal passage seen in anterior rhinoscopy satisfactorily either ruled in, if present (LR+ 3.2), or ruled out, if absent (negative likelihood ratio 0.2), bacterial ARS. If any secretion was seen in the posterior pharynx or middle meatus, the probability of bacterial ARS increased markedly (LR+ 5.3 and LR+ 11.0, respectively). We found symptoms or their change to be of little use in identifying bacterial ARS. In contrast, we observed several clinical findings after 9 to 10 days of symptoms to predict bacterial ARS quite accurately. © 2015 The American Laryngological, Rhinological and Otological Society, Inc.

Indoor microbiota in severely moisture damaged homes and the impact of interventions.

PubMed

Jayaprakash, Balamuralikrishna; Adams, Rachel I; Kirjavainen, Pirkka; Karvonen, Anne; Vepsäläinen, Asko; Valkonen, Maria; Järvi, Kati; Sulyok, Michael; Pekkanen, Juha; Hyvärinen, Anne; Täubel, Martin

2017-10-13

The limited understanding of microbial characteristics in moisture-damaged buildings impedes efforts to clarify which adverse health effects in the occupants are associated with the damage and to develop effective building intervention strategies. The objectives of this current study were (i) to characterize fungal and bacterial microbiota in house dust of severely moisture-damaged residences, (ii) to identify microbial taxa associated with moisture damage renovations, and (iii) to test whether the associations between the identified taxa and moisture damage are replicable in another cohort of homes. We applied bacterial 16S rRNA gene and fungal ITS amplicon sequencing complemented with quantitative PCR and chemical-analytical approaches to samples of house dust, and also performed traditional cultivation of bacteria and fungi from building material samples. Active microbial growth on building materials had significant though small influence on the house dust bacterial and fungal communities. Moisture damage interventions-including actual renovation of damaged homes and cases where families moved to another home-had only a subtle effect on bacterial community structure, seen as shifts in abundance weighted bacterial profiles after intervention. While bacterial and fungal species richness were reduced in homes that were renovated, they were not reduced for families that moved houses. Using different discriminant analysis tools, we were able identify taxa that were significantly reduced in relative abundance during renovation of moisture damage. For bacteria, the majority of candidates belonged to different families within the Actinomycetales order. Results for fungi were overall less consistent. A replication study in approximately 400 homes highlighted some of the identified taxa, confirming associations with observations of moisture damage and mold. The present study is one of the first studies to analyze changes in microbiota due to moisture damage interventions using high-throughput sequencing. Our results suggest that effects of moisture damage and moisture damage interventions may appear as changes in the abundance of individual, less common, and especially bacterial taxa, rather than in overall community structure.

Microbiological evaluation of different strategies for management of snakes in captivity.

PubMed

Campagner, M V; Bosco, S M G; Bagagli, E; Cunha, M L R S; Jeronimo, B C; Saad, E; Biscola, N P; Ferreira, R S; Barraviera, B

2012-01-01

Keeping snakes in captivity to produce venom for scientific research and production of inputs is now a worldwide practice. Maintaining snakes in captivity involves capture, infrastructure investments, management techniques, and appropriate qualified personnel. Further, the success of the project requires knowledge of habitat, nutrition, and reproduction, and control of opportunistic infections. This study evaluated the management of snakes in three types of captivity (quarantine, intensive, and semiextensive) and diagnosed bacterial and fungal contaminants. A bacteriological profile was obtained by swabbing the oral and cloacal cavities, scales, and venoms of healthy adult snakes from Bothrops jararaca (Bj) and Crotalus durissus terrificus (Cdt). There was predominance of Enterobacteriaceae, especially non-fermenting Gram-negative bacilli excluding Pseudomonas spp and Gram- positive bacteria. Statistically, intensive captivity resulted in the highest number of bacterial isolates, followed by recent capture (quarantine) and by semiextensive captivity. No statistical difference was found between Bj and Cdt bacterial frequency. In vitro bacterial susceptibility testing found the highest resistance against the semisynthetic penicillins (amoxicillin and ampicillin) and highest sensitivity to amicacin and tobramycin aminoglycosides. To evaluate mycological profile of snakes from intensive captivity, samples were obtained from two healthy Bj and one B. moojeni, one B. pauloensis, and one Cdt showing whitish lesions on the scales suggestive of ringworm. Using conventional methods and DNA-based molecular procedures, five samples of Trichosporon asahii were identified. Despite the traditional role of intense captivity in ophidian venom production, semiextensive captivity was more effective in the present study by virtue of presenting superior control of bacterial and fungal transmission, easier management, lowest cost, and decreased rate of mortality; therefore, it should be considered as a good alternative for tropical countries.

The diagnostic value of cerebrospinal fluid lactate for post-neurosurgical bacterial meningitis: a meta-analysis.

PubMed

Xiao, Xiong; Zhang, Yang; Zhang, Liwei; Kang, Peng; Ji, Nan

2016-09-13

Bacterial meningitis is not rare in post-neurosurgical patients. If patients are not treated promptly, the mortality rate can reach 20 to 50 %. The concentration of cerebrospinal fluid (CSF) lactate has been reported to be helpful in the diagnosis of bacterial meningitis; however, no systematic evaluations have investigated CSF from a postoperative perspective. In this study, we performed a systematic evaluation and meta-analysis of the efficacy of using CSF lactate concentrations in the diagnosis of post-neurosurgical bacterial meningitis. We retrieved studies that investigated the diagnostic value of CSF lactate for the diagnosis of post-neurosurgical bacterial meningitis by searching PubMed, EBSCO, the Cochrane Library and ClinicalTrials.gov. All these databases were searched from inception to November 2015. We used Quality Assessment of Diagnostic Accuracy Studies (QUADAS), a tool for the quality assessment of diagnostic accuracy, to evaluate the quality of the included studies. The Meta-DiSc 1.4 and Review Manager 5.3 software programs were used to analyze the included studies. Forest plots and summary receiver operating characteristics (SROC) curves were also drawn. Five studies, involving a total of 404 post-neurosurgical patients, were selected from 1,672 articles according to the inclusion criteria. The quality of the five included studies was assessed using QUADAS, and the related results are presented in tables. The meta-analysis revealed the following diagnostic values regarding CSF lactate for post-neurosurgical bacterial meningitis: a pooled sensitivity of 0.92 (95 % CI 0.85-0.96), a pooled specificity of 0.88 (95 % CI 0.84-0.92 with significant heterogeneity), a diagnostic odds ratio of 83.09 (95 % CI 36.83-187.46), an area under the curve (AUCSROC) of 0.9601, an SE(AUC) of 0.0122, a Q* of 0.9046 and an SE(Q*) of 0.0179. The meta-analysis indicated that the CSF lactate concentration has relatively high sensitivity and specificity for the diagnosis of post-neurosurgical bacterial meningitis and thus has relatively good efficacy.

Pathogen Presence in European Starlings Inhabiting Commercial Piggeries in South Australia.

PubMed

Pearson, Hayley E; Lapidge, Steven J; Hernández-Jover, Marta; Toribio, Jenny-Ann L M L

2016-06-01

The majority of bacterial diarrhea-causing illnesses in domestic pigs result from infection with Escherichia coli, Salmonella spp., or Campylobacter spp. These bacterial enteropathogens also correspond with the most-common bacteria isolated from wild birds. Additionally, viral pathogens such as avian influenza virus (AIV), West Nile virus (WNV, including Kunjin disease), and Newcastle disease virus (NDV) may also be carried and transmitted by birds in Australia. Introduced European starlings (Sturnus vulgarus) are one of the most-frequently reported birds on piggeries in Australia. The presence of the three bacterial pathogens, Salmonella spp., Campylobacter spp., and Escherichia coli , as well as the three viral pathogens AIV, WNV, and NDV, were evaluated in starlings captured on four commercial piggeries in South Australia. A total of 473 starlings were captured on the four piggeries in 2008 and 2009. A cloacal swab was taken from each bird and cultured for bacterial identification, with follow-up serotyping of any positives, whilst fifty samples were analyzed by PCR for the three target viral pathogens. There was no AIV, WNV, or NDV detected in the 50 starlings sampled. Escherichia coli was found to be present in the starling populations on all four piggeries whilst Salmonella spp. and Campylobacter jejuni were found to be present only in the starling population sampled on one piggery. Serotyping identified pig-pathogenic strains of the bacteria. The prevalence of these production-limiting bacterial pathogens in starlings, coupled with the large starling populations often found inside piggeries during daylight hours in the summer months, presents a disease transmission risk and jeopardizes piggery disease management. Removal of starlings from agricultural enterprises (as shown by international studies), or prevention of starling access to animal feed and water, could substantially reduce the risk of transmission of enterobacterial pathogens from starlings to livestock.

Microbial solubilization of coal

DOEpatents

Strandberg, G.W.; Lewis, S.N.

1988-01-21

The present invention relates to a cell-free preparation and process for the microbial solubilization of coal into solubilized coal products. More specifically, the present invention relates to bacterial solubilization of coal into solubilized coal products and a cell-free bacterial byproduct useful for solubilizing coal. 5 tabs.

Bacterial diversity in soil from geophagic mining sites in the Qwa-Qwa region of South Africa.

PubMed

de Smidt, Olga; Smit, Nellie Jacoba; Botes, Elsabe

2015-01-01

Geophagia is practised in many parts of the world and can be associated with medicinal treatments, ceremonial events and spiritual behaviours/practices. This is the first report on a systematic investigation and description of the bacterial diversity in soil regularly ingested by geophagic individuals using a culture-independent method. Diversity in 17 different mining sites was investigated using denaturing gradient gel electrophoresis. Genetic material from Pantoea, Stenotrophomonas, Listeria, Rhodococcus and Sphingomonads was present in most of the soil samples. Species from these genera are recognised, potential or immerging human pathogens, and are of special interest in immune-compromised individuals. Other genera able to produce a variety of bacteriocins and antimicrobial/antifungal substances inhibitory towards food borne pathogens (Dactylosporangium and Bacillus) and able to degrade a range of environmental pollutants and toxins (Duganella and Massilia) were also present. These essential insights provide the platform for adjusting culturing strategies to isolate specific bacteria, further phylogenetic studies and microbial mining prospect for bacterial species of possible economic importance.

Functional Genotyping of Sulfurospirillum spp. in Mixed Cultures Allowed the Identification of a New Tetrachloroethene Reductive Dehalogenase

PubMed Central

Buttet, Géraldine F.; Holliger, Christof

2013-01-01

Reductive dehalogenases are the key enzymes involved in the anaerobic respiration of organohalides such as the widespread groundwater pollutant tetrachloroethene. The increasing number of available bacterial genomes and metagenomes gives access to hundreds of new putative reductive dehalogenase genes that display a high level of sequence diversity and for which substrate prediction remains very challenging. In this study, we present the development of a functional genotyping method targeting the diverse reductive dehalogenases present in Sulfurospirillum spp., which allowed us to unambiguously identify a new reductive dehalogenase from our tetrachloroethene-dechlorinating SL2 bacterial consortia. The new enzyme, named PceATCE, shows 92% sequence identity with the well-characterized PceA enzyme of Sulfurospirillum multivorans, but in contrast to the latter, it is restricted to tetrachloroethene as a substrate. Its apparent higher dechlorinating activity with tetrachloroethene likely allowed its selection and maintenance in the bacterial consortia among other enzymes showing broader substrate ranges. The sequence-substrate relationships within tetrachloroethene reductive dehalogenases are also discussed. PMID:23995945

The effect of bacterial cellulose on the shape memory behavior of polyvinyl alcohol nanocomposite hydrogel

NASA Astrophysics Data System (ADS)

Pirahmadi, Pegah; Kokabi, Mehrdad

2018-01-01

Most research on shape memory polymers has been confined to neat polymers in their dry state, while, some hydrogel networks are known for their shape memory properties. Hydrogels have low glass transition temperatures which are below 100°C depend on the content of water. But they are usually weak and brittle, and not suitable for structural applications due to their low mechanical strengths because of these materials have large amount of water (>50%), so they could not remember original shape perfectly. Bacterial cellulose nanofibers with perfect properties such as high water holding capacity, high crystallinity, high tensile strength and good biocompatibility can dismiss all the drawbacks. In the present study, polyvinyl alcohol/bacterial cellulose nanocomposite hydrogel prepared by repetitive freezing-thawing method. The bacterial cellulose was used as reinforcement to improve the mechanical properties and stimuli response. Differential scanning calorimetry was employed to obtain the glass transition temperature. Nanocomposite morphology was characterized by field-emission scanning electron microscopy and mechanical properties were investigated by standard tensile test. Finally, the effect of bacterial cellulose nanofiber on shape memory behavior of polyvinyl alcohol/bacterial cellulose nanocomposite hydrogel was investigated. It is found that switching temperature of this system is the glass transition temperature of the nano domains formed within the system. The results also show increase of shape recovery, and shape recovery speed due to presence of bacterial cellulose.

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing.

PubMed

Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

2015-01-01

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system.

Bacterial Communities of Surface Mixed Layer in the Pacific Sector of the Western Arctic Ocean during Sea-Ice Melting

PubMed Central

Ha, Ho Kyung; Kim, Hyun Cheol; Kim, Ok-Sun; Lee, Bang Yong; Cho, Jang-Cheon; Hur, Hor-Gil; Lee, Yoo Kyung

2014-01-01

From July to August 2010, the IBRV ARAON journeyed to the Pacific sector of the Arctic Ocean to monitor bacterial variation in Arctic summer surface-waters, and temperature, salinity, fluorescence, and nutrient concentrations were determined during the ice-melting season. Among the measured physicochemical parameters, we observed a strong negative correlation between temperature and salinity, and consequently hypothesized that the melting ice decreased water salinity. The bacterial community compositions of 15 samples, includicng seawater, sea-ice, and melting pond water, were determined using a pyrosequencing approach and were categorized into three habitats: (1) surface seawater, (2) ice core, and (3) melting pond. Analysis of these samples indicated the presence of local bacterial communities; a deduction that was further corroborated by the discovery of seawater- and ice-specific bacterial phylotypes. In all samples, the Alphaproteobacteria, Flavobacteria, and Gammaproteobacteria taxa composed the majority of the bacterial communities. Among these, Alphaproteobacteria was the most abundant and present in all samples, and its variation differed among the habitats studied. Linear regression analysis suggested that changes in salinity could affect the relative proportion of Alphaproteobacteria in the surface water. In addition, the species-sorting model was applied to evaluate the population dynamics and environmental heterogeneity in the bacterial communities of surface mixed layer in the Arctic Ocean during sea-ice melting. PMID:24497990

Bacterial communities of surface mixed layer in the Pacific sector of the western Arctic Ocean during sea-ice melting.

PubMed

Han, Dukki; Kang, Ilnam; Ha, Ho Kyung; Kim, Hyun Cheol; Kim, Ok-Sun; Lee, Bang Yong; Cho, Jang-Cheon; Hur, Hor-Gil; Lee, Yoo Kyung

2014-01-01

From July to August 2010, the IBRV ARAON journeyed to the Pacific sector of the Arctic Ocean to monitor bacterial variation in Arctic summer surface-waters, and temperature, salinity, fluorescence, and nutrient concentrations were determined during the ice-melting season. Among the measured physicochemical parameters, we observed a strong negative correlation between temperature and salinity, and consequently hypothesized that the melting ice decreased water salinity. The bacterial community compositions of 15 samples, includicng seawater, sea-ice, and melting pond water, were determined using a pyrosequencing approach and were categorized into three habitats: (1) surface seawater, (2) ice core, and (3) melting pond. Analysis of these samples indicated the presence of local bacterial communities; a deduction that was further corroborated by the discovery of seawater- and ice-specific bacterial phylotypes. In all samples, the Alphaproteobacteria, Flavobacteria, and Gammaproteobacteria taxa composed the majority of the bacterial communities. Among these, Alphaproteobacteria was the most abundant and present in all samples, and its variation differed among the habitats studied. Linear regression analysis suggested that changes in salinity could affect the relative proportion of Alphaproteobacteria in the surface water. In addition, the species-sorting model was applied to evaluate the population dynamics and environmental heterogeneity in the bacterial communities of surface mixed layer in the Arctic Ocean during sea-ice melting.

Effect of bacterial antagonists on lettuce: active biocontrol of Rhizoctonia solani and negligible, short-term effects on nontarget microorganisms.

PubMed

Scherwinski, Katja; Grosch, Rita; Berg, Gabriele

2008-04-01

The aim of this study was to assess the biocontrol efficacy against Rhizoctonia solani of three bacterial antagonists introduced into naturally Rhizoctonia-infested lettuce fields and to analyse their impact on the indigenous plant-associated bacteria and fungi. Lettuce seedlings were inoculated with bacterial suspensions of two endophytic strains, Serratia plymuthica 3Re4-18 and Pseudomonas trivialis 3Re2-7, and with the rhizobacterium Pseudomonas fluorescens L13-6-12 7 days before and 5 days after planting in the field. Similar statistically significant biocontrol effects were observed for all applied bacterial antagonists compared with the uninoculated control. Single-strand conformation polymorphism analysis of 16S rRNA gene or ITS1 fragments revealed a highly diverse rhizosphere and a less diverse endophytic microbial community for lettuce. Representatives of several bacterial (Alpha-, Beta- and Gammaproteobacteria, Firmicutes, Bacteriodetes), fungal (Ascomycetes, Basidiomycetes) and protist (Oomycetes) groups were present inside or on lettuce plants. Surprisingly, given that lettuce is a vegetable that is eaten raw, species of genera such as Flavobacterium, Burkholderia, Staphylococcus, Cladosporium and Aspergillus, which contain potentially human pathogenic strains, were identified. Analysis of the indigenous bacterial and endophytic fungal populations revealed only negligible, short-term effects resulting from the bacterial treatments, and that they were more influenced by field site, plant growth stage and microenvironment.

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing

PubMed Central

Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

2015-01-01

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system. PMID:26317364

A uniform bacterial growth potential assay for different water types.

PubMed

Farhat, Nadia; Hammes, Frederik; Prest, Emmanuelle; Vrouwenvelder, Johannes

2018-06-06

The bacterial growth potential is important to understand and manage bacterial regrowth-related water quality concerns. Bacterial growth potential depends on growth promoting/limiting compounds, therefore, nutrient availability is the key factor governing bacterial growth potential. Selecting proper tools for bacterial growth measurement is essential for routine implementation of the growth potential measurement. This study proposes a growth potential assay that is universal and can be used for different water types and soil extract without restrictions of pure culture or cultivability of the bacterial strain. The proposed assay measures the sample bacterial growth potential by using the indigenous community as inocula. Flow cytometry (FCM) and adenosine tri-phosphate (ATP) were used to evaluate the growth potential of six different microbial communities indigenous to the sample being analyzed, with increasing carbon concentrations. Bottled mineral water, non-chlorinated tap water, seawater, river water, wastewater effluent and a soil organic carbon extract were analyzed. Results showed that indigenous bacterial communities followed normal batch growth kinetics when grown on naturally present organic carbon. Indigenous bacterial growth could detect spiked organic carbon concentrations as low as 10 μg/L. The indigenous community in all samples responded proportionally to the increase in acetate-carbon and proportional growth could be measured with both FCM and ATP. Bacterial growth was proportional to the carbon concentration but not the same proportion factor for the different water samples tested. The effect of inoculating the same water with different indigenous microbial communities on the growth potential was also examined. The FCM results showed that the highest increase in total bacterial cell concentration was obtained with bacteria indigenous to the water sample. The growth potential assay using indigenous bacterial community revealed consistent results of bacterial growth in all the different samples tested and therefore providing a fast, more stable, and accurate approach for monitoring the biological stability of waters compared to the previously developed assays. The growth potential assay can be used to aid in detecting growth limitations by compounds other than organic carbon. Copyright © 2018 Elsevier Ltd. All rights reserved.

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps

PubMed Central

Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E.; Adatte, Thierry; Guisan, Antoine; van der Meer, Jan Roelof

2016-01-01

ABSTRACT Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. IMPORTANCE This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700-km2 study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters. PMID:27542929

A universal surface complexation framework for modeling proton binding onto bacterial surfaces in geologic settings

USGS Publications Warehouse

Borrok, D.; Turner, B.F.; Fein, J.B.

2005-01-01

Adsorption onto bacterial cell walls can significantly affect the speciation and mobility of aqueous metal cations in many geologic settings. However, a unified thermodynamic framework for describing bacterial adsorption reactions does not exist. This problem originates from the numerous approaches that have been chosen for modeling bacterial surface protonation reactions. In this study, we compile all currently available potentiometric titration datasets for individual bacterial species, bacterial consortia, and bacterial cell wall components. Using a consistent, four discrete site, non-electrostatic surface complexation model, we determine total functional group site densities for all suitable datasets, and present an averaged set of 'universal' thermodynamic proton binding and site density parameters for modeling bacterial adsorption reactions in geologic systems. Modeling results demonstrate that the total concentrations of proton-active functional group sites for the 36 bacterial species and consortia tested are remarkably similar, averaging 3.2 ?? 1.0 (1??) ?? 10-4 moles/wet gram. Examination of the uncertainties involved in the development of proton-binding modeling parameters suggests that ignoring factors such as bacterial species, ionic strength, temperature, and growth conditions introduces relatively small error compared to the unavoidable uncertainty associated with the determination of cell abundances in realistic geologic systems. Hence, we propose that reasonable estimates of the extent of bacterial cell wall deprotonation can be made using averaged thermodynamic modeling parameters from all of the experiments that are considered in this study, regardless of bacterial species used, ionic strength, temperature, or growth condition of the experiment. The average site densities for the four discrete sites are 1.1 ?? 0.7 ?? 10-4, 9.1 ?? 3.8 ?? 10-5, 5.3 ?? 2.1 ?? 10-5, and 6.6 ?? 3.0 ?? 10-5 moles/wet gram bacteria for the sites with pKa values of 3.1, 4.7, 6.6, and 9.0, respectively. It is our hope that this thermodynamic framework for modeling bacteria-proton binding reactions will also provide the basis for the development of an internally consistent set of bacteria-metal binding constants. 'Universal' constants for bacteria-metal binding reactions can then be used in conjunction with equilibrium constants for other important metal adsorption and complexation reactions to calculate the overall distribution of metals in realistic geologic systems.

Advances in the development of bacterial vector technology.

PubMed

Kochi, Sims K; Killeen, Kevin P; Ryan, Una S

2003-02-01

The demand for new and improved vaccines against human diseases has continued unabated over the past century. While the need continues for traditional vaccines in areas such as infectious diseases, there is an increasing demand for new therapies in nontraditional areas, such as cancer treatment, bioterrorism and food safety. Prompted by these changes, there has been a renewed interest in the application and development of live, attenuated bacteria expressing foreign antigens as vaccines. The application of bacterial vector vaccines to human maladies has been studied most extensively in attenuted strains of Salmonella. Live, attenuated strains of Shigella, Listeria monocytogenes, Mycobacterium bovis-BCG and Vibrio cholerae provide unique alternatives in terms of antigen delivery and immune presentation, however and also show promise as potentially useful bacterial vectors.

Characterization of bacterial diversity in pulque, a traditional Mexican alcoholic fermented beverage, as determined by 16S rDNA analysis.

PubMed

Escalante, Adelfo; Rodríguez, María Elena; Martínez, Alfredo; López-Munguía, Agustín; Bolívar, Francisco; Gosset, Guillermo

2004-06-15

The bacterial diversity in pulque, a traditional Mexican alcoholic fermented beverage, was studied in 16S rDNA clone libraries from three pulque samples. Sequenced clones identified as Lactobacillus acidophilus, Lactobacillus strain ASF360, L. kefir, L. acetotolerans, L. hilgardii, L. plantarum, Leuconostoc pseudomesenteroides, Microbacterium arborescens, Flavobacterium johnsoniae, Acetobacter pomorium, Gluconobacter oxydans, and Hafnia alvei, were detected for the first time in pulque. Identity of 16S rDNA sequenced clones showed that bacterial diversity present among pulque samples is dominated by Lactobacillus species (80.97%). Seventy-eight clones exhibited less than 95% of relatedness to NCBI database sequences, which may indicate the presence of new species in pulque samples.

Predictive value of bacterial analysis of laparotomy wounds.

PubMed

Minutolo, Mario; Blandino, Giovanna; Arena, Manuel; Licciardello, Alessio; Di Stefano, Biagio; Lanteri, Raffaele; Puleo, Stefano; Licata, Antonio; Minutolo, Vincenzo

2014-01-01

Despite improvements in antibiotic prophylaxis, surgical site infections represent the most common postoperative complication with important clinical consequences for patients. The hypothesis that a bacterial analysis of the surgical wound in the operating room could predict the likelihood of developing a clinical infection, and might allow a tailored and preemptive approach, aimed to reduce the consequences of an infection, seems appealing. We would like to present a prospective study on the predictive value of the bacterial analysis of laparotomy wounds. Seventy eight prospective patients undergoing surgery were included in the study. To evaluate the risk factors associated with increased rate of wound infection, we performed a bacterial analysis of the wound. 48 patients out of 78 (61%) had positive cultures. 23 patients out of 32 patients (72%) who didn't receive antibiotic prophylaxis were positive to the wound culture whereas 25 patients out of 46 patients (54%) grew positive cultures in the group of patients that received antibiotic prophylaxis. None of the 30 patients with negative cultures developed clinical infection. Only 6 patients out of 48 patients who had positive cultures (12.5%) developed wound infection. Clinical infection occurred in 5 patients who had gram-negative contamination of the wound. No clinical infection occurred in patients who had gram-positive contamination. Wound cultures and their positivity are predictive tools to identify the patients that are at risk to develop wound infection. The positive predictive value of the bacterial analysis of the wound was 12.5%. Abdominal surgery, Bacterial analysis, Wound infection.

Bacterial diversity characterization in petroleum samples from Brazilian reservoirs

PubMed Central

de Oliveira, Valéria Maia; Sette, Lara Durães; Simioni, Karen Christina Marques; dos Santos Neto, Eugênio Vaz

2008-01-01

This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments. PMID:24031244

Phenotypic and molecular fingerprinting of fast growing rhizobia of field-grown pigeonpea from the eastern edge of the Brazilian Pantanal.

PubMed

Costa, F M; Schiavo, J A; Brasil, M S; Leite, J; Xavier, G R; Fernandes, P I

2014-01-21

The aim of this study was to evaluate the diversity of rhizobial isolates obtained from root nodules of pigeonpea plants grown at the eastern edge of the Brazilian Pantanal. The bacterial isolates were isolated from root nodules from field-growing pigeonpea grown in two rural settlements of the Aquidauana municipality. The bacterial isolates were characterized phenotypically by means of cultural characterization, intrinsic antibiotic resistance (IAR), salt and high incubation temperature tolerance, and amylolytic and cellulolytic activities. The molecular characterization of the bacterial isolates was carried out using amplified ribosomal DNA restriction analysis (ARDRA) and Box-polymerase chain reaction (PCR) techniques. In addition, the symbiotic performance of selected rhizobial isolates was evaluated in a greenhouse experiment using sterile substrate. The phenotypic characterization revealed that the bacterial strains obtained from pigeonpea root nodules presented characteristics that are uncommon among rhizobial isolates, indicating the presence of new species nodulating the pigeonpea plants in the Brazilian Pantanal. The molecular fingerprinting of these bacterial isolates also showed a highly diverse collection, with both techniques revealing less than 25% similarity among bacterial isolates. The evaluation of symbiotic performance also indicated the presence of microorganisms with high potential to increase the growth and nitrogen content at the shoots of pigeonpea plants. The results obtained in this study indicate the presence of a highly diversified rhizobial community nodulating the pigeonpea at the eastern edge of the Brazilian Pantanal.

An evidential example of airborne bacteria in a crowded, underground public concourse in Tokyo

NASA Astrophysics Data System (ADS)

Seino, Kaoruko; Takano, Takehito; Nakamura, Keiko; Watanabe, Masafumi

2005-01-01

We examined airborne bacteria in an underground concourse in Tokyo and investigated conditions that influenced bacterial counts. Airborne bacteria were collected by using an impactor sampler. Colonies on plate count agar (PCA) and Columbia colistin-nalidixic acid agar with 5% sheep blood (CNA agar) were enumerated. The range, geometric mean, and 95% CI of the bacterial counts (CFU m-3) on PCA and CNA agar were 150-1380, 456, 382-550 and 50-990, 237, 182-309, respectively. Bacterial counts on PCA significantly correlated with number of the pedestrians (r=0.89), relative humidity (r=0.70) and airborne dust (PM5.0) (r=0.73). Results of a multiple regression indicated independent positive association between the number of pedestrians and bacterial counts on PCA (p<0.01) after excluding the influence of relative humidity and airborne dust. Similar results were obtained with the statistical analysis for the counts of bacteria on CNA agar. Gram-positive cocci were dominant on PCA and CNA agar. Staphylococcus epidermidis and Micrococcus spp. were dominant among the 11 genera and 19 species identified in the present study. Considering the pattern of identified species and the significant independent association between number of pedestrians and bacterial counts, airborne bacteria in a crowded underground concourse were mostly originated from the pedestrians who were walking in the underground concourse. This study gave an evidential example of bacterial conditions in the air of an underground crowded public space in Tokyo.

Bacterial Endosymbionts of the Psyllid Cacopsylla pyricola (Hemiptera: Psyllidae) in the Pacific Northwestern United States.

PubMed

Cooper, W Rodney; Garczynski, Stephen F; Horton, David R; Unruh, Thomas R; Beers, Elizabeth H; Peter, W Shearer; Hilton, Richard J

2017-04-01

Insects often have facultative associations with bacterial endosymbionts, which can alter the insects' susceptibility to parasitism, pathogens, plant defenses, and certain classes of insecticides. We collected pear psylla, Cacopsylla pyricola (Förster) (Hemiptera: Psyllidae), from pear orchards in Washington and Oregon, and surveyed them for the presence of bacterial endosymbionts. Adult psyllids were collected on multiple dates to allow us to assay specimens of both the summer ("summerform") and the overwintering ("winterform") morphotypes. Two endosymbionts, Arsenophonus and Phytoplasma pyri, were detected in psyllids of both morphotypes in both states. A separate survey revealed similar associations present in psyllids collected in 1987. Arsenophonus was present in 80-100% of psyllids in all growing regions. A slightly lower proportion of summerform than winterform psyllids harbored the bacterium. Arsenophonus was present in the bacteriomes and developing oocytes of most psyllids, indicating that this endosymbiont is transovarially transmitted. This bacterium was also observed in the salivary glands and midguts of some psyllids. Phytoplasma pyri was present in a greater proportion of pear psylla from orchards near Yakima, WA, than from other regions, and was present in a higher proportion of winterforms than summerforms. We did not detect Wolbachia, Profftella, or Liberibacter europaeus, which are associated with other psyllid pests, including other species of Cacopsylla. Our study is the first to survey North American populations of C. pyricola for endosymbionts, and provides a foundation for further research on how bacterial associations may influence the ecology and management of this pest. Published by Oxford University Press on behalf of Entomological Society of America 2017. This work is written by US Government employees and is in the public domain in the US.

Protection and consolidation of stone heritage by self-inoculation with indigenous carbonatogenic bacterial communities.

PubMed

Jroundi, Fadwa; Schiro, Mara; Ruiz-Agudo, Encarnación; Elert, Kerstin; Martín-Sánchez, Inés; González-Muñoz, María Teresa; Rodriguez-Navarro, Carlos

2017-08-17

Enhanced salt weathering resulting from global warming and increasing environmental pollution is endangering the survival of stone monuments and artworks. To mitigate the effects of these deleterious processes, numerous conservation treatments have been applied that, however, show limited efficacy. Here we present a novel, environmentally friendly, bacterial self-inoculation approach for the conservation of stone, based on the isolation of an indigenous community of carbonatogenic bacteria from salt damaged stone, followed by their culture and re-application back onto the same stone. This method results in an effective consolidation and protection due to the formation of an abundant and exceptionally strong hybrid cement consisting of nanostructured bacterial CaCO 3 and bacterially derived organics, and the passivating effect of bacterial exopolymeric substances (EPS) covering the substrate. The fact that the isolated and identified bacterial community is common to many stone artworks may enable worldwide application of this novel conservation methodology.Salt weathering enhanced by global warming and environmental pollution is increasingly threatening stone monuments and artworks. Here, the authors present a bacterial self-inoculation approach with indigenous carbonatogenic bacteria and find that this technique consolidates and protects salt damaged stone.

Promiscuity in mice is associated with increased vaginal bacterial diversity

NASA Astrophysics Data System (ADS)

Macmanes, Matthew David

2011-11-01

Differences in the number of sexual partners (i.e., mating system) have the potential to exert a strong influence on the bacterial communities present in reproductive structures like the vagina. Because this structure serves as a conduit for gametes, bacteria present there may have a pronounced, direct effect on host reproductive success. As a first step towards the identification of the relationship between sexual behavior and potentially pathogenic bacterial communities inhabiting vital reproductive structures, as well as their potential effects on fitness, I sought to quantify differences in bacterial diversity in a promiscuous and monogamous mammal species. To accomplish this, I used two sympatric species of Peromyscus rodents— Peromyscus californicus and Peromyscus maniculatus that differ with regard to the number of sexual partners per individual to test the hypothesis that bacterial diversity should be greater in the promiscuous P. maniculatus relative to the monogamous P. californicus. As predicted, phylogenetically controlled and operational taxonomic unit-based indices of bacterial diversity indicated that diversity is greater in the promiscuous species. These results provide important new insights into the effects of mating system on bacterial diversity in free-living vertebrates, and may suggest a potential cost of promiscuity.

Duration of fever and markers of serious bacterial infection in young febrile children.

PubMed

Pratt, Amanda; Attia, Magdy W

2007-02-01

Despite the drastic change in the evaluation of the febrile young child due to the decreased incidence of serious bacterial infections (SBI) effected by Haemophilus influenza type B and pneumococcal vaccine, there remains a small role for blood work in the evaluation of these patients. Bacterial markers including white blood cell (WBC) count, absolute neutrophil count (ANC) and C-reactive protein (CRP) have been studied and are widely used as predictors of SBI in febrile children. It has been suggested that CRP values should be interpreted cautiously when fever has been present <12 h based on the kinetics of this biological marker. This limitation has not been previously addressed with CRP, nor was it described with other markers, specifically WBC and ANC, therefore the purpose of the present paper was to assess WBC, ANC and CRP values as predictors of SBI in relation to duration of fever. Patients who presented to a pediatric emergency department between the ages of 1 and 36 months, with fever > or =39 degrees C and no source of infection had a complete blood count (CBC) blood culture, and CRP level drawn. A urinalysis and/or urine culture was obtained when age and gender appropriate. A chest X-ray was performed at the discretion of the treating physician. The study subjects were enrolled prospectively and then divided into two groups based on duration of fever of < or = or >12 h, and compared. One hundred and twenty-eight patients were originally enrolled. Nine patients were excluded. Seventeen patients (14%) had SBI. One patient (<1%) had bacteremia, three (3%) had pneumonia, and 13 (10%) had urinary tract infections. Forty-five patients presented with fever < or =12 h and 74 patients presented with fever >12 h. Area under the curve (AUC) for WBC, ANC and CRP was significantly larger in patients with SBI presenting with fever >12 h (0.85, 0.83, 0.92 respectively) compared to patients with SBI who presented with fever for <12 h (0.37, 0.42, 0.68 respectively). Bacterial markers studied were more predictive of SBI if the duration of fever was >12 h as shown by the AUC. CRP performed better than WBC and ANC in both scenarios.

Enhanced Direct Major Histocompatibility Complex Class I Self-Antigen Presentation Induced by Chlamydia Infection

PubMed Central

Cram, Erik D.; Simmons, Ryan S.; Palmer, Amy L.; Hildebrand, William H.; Rockey, Daniel D.

2015-01-01

The direct major histocompatibility complex (MHC) class I antigen presentation pathway ensures intracellular peptides are displayed at the cellular surface for recognition of infected or transformed cells by CD8+ cytotoxic T lymphocytes. Chlamydia spp. are obligate intracellular bacteria and, as such, should be targeted by CD8+ T cells. It is likely that Chlamydia spp. have evolved mechanisms to avoid the CD8+ killer T cell responses by interfering with MHC class I antigen presentation. Using a model system of self-peptide presentation which allows for posttranslational control of the model protein's stability, we tested the ability of various Chlamydia species to alter direct MHC class I antigen presentation. Infection of the JY lymphoblastoid cell line limited the accumulation of a model host protein and increased presentation of the model-protein-derived peptides. Enhanced self-peptide presentation was detected only when presentation was restricted to defective ribosomal products, or DRiPs, and total MHC class I levels remained unaltered. Skewed antigen presentation was dependent on a bacterial synthesized component, as evidenced by reversal of the observed phenotype upon preventing bacterial transcription, translation, and the inhibition of bacterial lipooligosaccharide synthesis. These data suggest that Chlamydia spp. have evolved to alter the host antigen presentation machinery to favor presentation of defective and rapidly degraded forms of self-antigen, possibly as a mechanism to diminish the presentation of peptides derived from bacterial proteins. PMID:26597986

[Congenital skull base defect causing recurrent bacterial meningitis].

PubMed

Berliner, Elihay; Bar Meir, Maskit; Megged, Orli

2012-08-01

Bacterial meningitis is a life threatening disease. Most patients will experience only one episode throughout life. Children who experience bacterial meningitis more than once, require further immunologic or anatomic evaluation. We report a 9 year old child with five episodes of bacterial meningitis due to a congenital defect of the skull base. A two and a half year old boy first presented to our medical center with pneumococcal meningitis. He was treated with antibiotics and fully recovered. Two months later he presented again with a similar clinical picture. Streptococcus pneumoniae grew in cerebrospinal fluid (CSF) culture. CT scan and later MRI of the brain revealed a defect in the anterior middle fossa floor, with protrusion of brain tissue into the sphenoidal sinus. Corrective surgery was recommended but the parents refused. Three months later, a third episode of pneumococcal meningitis occurred. The child again recovered with antibiotics and this time corrective surgery was performed. Five years later, the boy presented once again with clinical signs and symptoms consistent with bacterial meningitis. CSF culture was positive, but the final identification of the bacteria was conducted by broad spectrum 16S ribosomal RNA PCR (16S rRNA PCR) which revealed a sequence of Neisseria lactamica. CT and MRI showed recurrence of the skull base defect with encephalocele in the sphenoid sinus. The parents again refused neurosurgical intervention. A year later the patient presented with bacterial meningitis. CSF culture obtained after initiation of antibiotics was negative, but actinobacillus was identified in the CSF by 16S rRNA PCR. The patient is scheduled for neurosurgical intervention. In patients with recurrent bacterial meningitis caused by organisms colonizing the oropharynx or nasopharynx, an anatomical defect should be carefully sought and surgically repaired.

Impact of Solar Radiation on Gene Expression in Bacteria

PubMed Central

Matallana-Surget, Sabine; Wattiez, Ruddy

2013-01-01

Microorganisms often regulate their gene expression at the level of transcription and/or translation in response to solar radiation. In this review, we present the use of both transcriptomics and proteomics to advance knowledge in the field of bacterial response to damaging radiation. Those studies pertain to diverse application areas such as fundamental microbiology, water treatment, microbial ecology and astrobiology. Even though it has been demonstrated that mRNA abundance is not always consistent with the protein regulation, we present here an exhaustive review on how bacteria regulate their gene expression at both transcription and translation levels to enable biomarkers identification and comparison of gene regulation from one bacterial species to another. PMID:28250399

Iris abscess as an unusual presentation of endogenous endophthalmitis in a patient with bacterial endocarditis.

PubMed

Ramonas, Krista M; Freilich, Benjamin D

2003-02-01

To report the clinical findings and management of a case of endogenous endophthalmitis in a patient with bacterial endocarditis presenting with a septic metastasis to the iris. Observational case report. Review of clinical findings and treatment. A 37-year-old intravenous drug user hospitalized with bacterial endocarditis secondary to methicillin-sensitive Staphylococcus aureus bacteremia presented with a painful red left eye, hypopyon, and iris abscess. Roth spots were noted in the fundus of the right eye. Aqueous culture was positive for methicillin-sensitive S aureus. The patient was treated with intravitreal, topical, and intravenous antibiotics. The hypopyon and iris abscess resolved within 2 weeks, and the patient achieved a final visual acuity of 20/25 in the left eye. Septic metastasis to the iris is a rare occurrence. To our knowledge this is the first reported case of an iris abscess secondary to bacterial endocarditis.

Uterine bacterial flora in postpartum Danish Holstein dairy cows determined using DNA-based fingerprinting: correlation to uterine condition and calving management.

PubMed

Elkjær, K; Ancker, M-L; Gustafsson, H; Friggens, N C; Waldmann, A; Mølbak, L; Callesen, H

2013-04-01

The overall aim of this study was to describe uterine bacterial flora during the postpartum period in Danish Holstein cows using the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method. This method produces a pattern of nucleic acid fragments from the microorganisms present, reflecting the "fingerprint" of the actual microbial flora. As well as characterizing changes in flora with time from calving and between herds, data were examined for strong relations between uterine bacterial flora, calving management and uterine condition. In total 125 Holstein cows from five herds were included, and for each cow calving management was recorded. Cows were clinically examined on average 8 (range 0-19) and 28 (range 22-38) days after calving, and a uterine sample was taken for bacterial identification using T-RFLP. Milk samples were taken weekly for progesterone analysis. Bacteria were found in all cows at both examinations, and the flora was composed of many species, including species not traditionally reported to be present in the bovine uterus. The bacterial composition differed according to days from calving and herd. In all five herds Fusobacterium necrophorum, Pseudomonas/Acinetobacter and Bacteroides/Sphingobacterium/Prevotellaceae were among the most common at both examinations. In four herds there was a percentage decrease of F. necrophorum from first to second examination, and in all herds there was a percentage increase of Pseudomonas/Acinetobacter from first to second examination. No differences in bacterial flora were found between cows with different uterine scores, which were influenced by herd, calving difficulty and retained placenta. Copyright © 2013 Elsevier B.V. All rights reserved.

Spectrum and Prevalence of Pathological Intracranial Magnetic Resonance Imaging Findings in Acute Bacterial Meningitis.

PubMed

Lummel, N; Koch, M; Klein, M; Pfister, H W; Brückmann, H; Linn, J

2016-06-01

Aim of this study was to determine the spectrum and prevalence of pathological intracranial magnetic resonance imaging (MRI) findings in patients with acute bacterial meningitis. We retrospectively identified all consecutive patients with cerebral spinal fluid proven bacterial meningitis who presented at our neurology department between 2007 and 2012. Pathogenic agents and clinical symptoms were noted. MR-examinations were evaluated regarding presence and localization of pathological signal alterations in the different sequences by two neuroradiologists in consensus. A total of 136 patients with purulent bacterial meningitis were identified. In 114 cases the bacterial pathogen agent was proven and in 75 patients an MRI was available. In 62 of the 75 (82.7 %) patients meningitis-associated pathologic imaging findings were evident on MRI. Overall, intraventricular signal alterations, i.e., signs of pyogenic ventriculitis, were present in 41 cases (54.7 %), while sulcal signal changes were found in 22 cases (29.3 %). Intraparenchymatous signal alterations affected the cortex in 15 cases (20 %), and the white matter in 20 patients (26.7 %). The diffusion-weighted imaging and fluid attenuated inversion recovery sequences were most sensitive in the detection of these changes and showed any pathologic findings in 67.6 and 79.6 %, respectively. Patients with streptococcal meningitis showed significantly more often (n = 29 of 34, 85.3 %) intraventricular and/or sulcal diffusion restrictions than patients with meningitis caused by other agents (n = 12 of 37, 32.4 %) (p< 0.0001). Pathological MR findings are frequently found in patients with acute bacterial meningitis. Intraventricular diffusion restrictions, i.e., signs of pyogenic ventriculitis, are more often found in patients with streptococcal, especially pneumococcal, infection.

Viral-bacterial coinfection affects the presentation and alters the prognosis of severe community-acquired pneumonia.

PubMed

Voiriot, Guillaume; Visseaux, Benoit; Cohen, Johana; Nguyen, Liem Binh Luong; Neuville, Mathilde; Morbieu, Caroline; Burdet, Charles; Radjou, Aguila; Lescure, François-Xavier; Smonig, Roland; Armand-Lefèvre, Laurence; Mourvillier, Bruno; Yazdanpanah, Yazdan; Soubirou, Jean-Francois; Ruckly, Stephane; Houhou-Fidouh, Nadhira; Timsit, Jean-François

2016-10-25

Multiplex polymerase chain reaction (mPCR) enables recovery of viruses from airways of patients with community-acquired pneumonia (CAP), although their clinical impact remains uncertain. Among consecutive adult patients who had undergone a mPCR within 72 hours following their admission to one intensive care unit (ICU), we retrospectively included those with a final diagnosis of CAP. Four etiology groups were clustered: bacterial, viral, mixed (viral-bacterial) and no etiology. A composite criterion of complicated course (hospital death or mechanical ventilation > 7 days) was used. A subgroup analysis compared patients with bacterial and viral-bacterial CAP matched on the bacterial pathogens. Among 174 patients (132 men [76 %], age 63 [53-75] years, SAPSII 38 [27;55], median PSI score 106 [78;130]), bacterial, viral, mixed and no etiology groups gathered 46 (26 %), 53 (31 %), 45 (26 %) and 30 (17 %) patients, respectively. Virus-infected patients displayed a high creatine kinase serum level, a low platelet count, and a trend toward more frequent alveolar-interstitial infiltrates. A complicated course was more frequent in the mixed group (31/45, 69 %), as compared to bacterial (18/46, 39 %), viral (15/53, 28 %) and no etiology (12/30, 40 %) groups (p < 0.01). In multivariate analysis, the mixed (viral-bacterial) infection was independently associated with complicated course (reference: bacterial pneumonia; OR, 3.58; CI 95 %, 1.16-11; p = 0.03). The subgroup analysis of bacteria-matched patients confirmed these findings. Viral-bacterial coinfection during severe CAP in adults is associated with an impaired presentation and a complicated course.

Antibacterial activity of some medicinal plants against selected human pathogenic bacteria

PubMed Central

Khan, Usman Ali; Niaz, Zeeshan; Qasim, Muhammad; Khan, Jafar; Tayyaba; Rehman, Bushra

2013-01-01

Medicinal plants are traditionally used for the treatment of human infections. The present study was undertaken to investigate Bergenia ciliata, Jasminum officinale, and Santalum album for their potential activity against human bacterial pathogens. B. ciliata, J. officinale, and S. album extracts were prepared in cold and hot water. The activity of plant extracts and selected antibiotics was evaluated against five bacterial pathogens including Staphylococcus aureus, Bacillus subtilis, Proteus vulgaris, Pseudomonas aeruginosa, and Escherichia coli using agar well diffusion method. Among the three medicinal plants, B. ciliata extracts displayed potential activity against bacterial pathogens. Cold water extract of Bergenia ciliate showed the highest activity against B. subtilis, which is comparable with a zone of inhibition exhibited by ceftriaxone and erythromycin. J. officinale and S. album extracts demonstrated variable antibacterial activity. Further studies are needed to explore the novel antibacterial bioactive molecules. PMID:24294497

Human gut microbiome: the second genome of human body.

PubMed

Zhu, Baoli; Wang, Xin; Li, Lanjuan

2010-08-01

The human body is actually a super-organism that is composed of 10 times more microbial cells than our body cells. Metagenomic study of the human microbiome has demonstrated that there are 3.3 million unique genes in human gut, 150 times more genes than our own genome, and the bacterial diversity analysis showed that about 1000 bacterial species are living in our gut and a majority of them belongs to the divisions of Firmicutes and Bacteriodetes. In addition, most people share a core microbiota that comprises 50-100 bacterial species when the frequency of abundance at phylotype level is not considered, and a core microbiome harboring more than 6000 functional gene groups is present in the majority of human gut surveyed till now. Gut bacteria are not only critical for regulating gut metabolism, but also important for host immune system as revealed by animal studies.

Marine Viruses: Truth or Dare

NASA Astrophysics Data System (ADS)

Breitbart, Mya

2012-01-01

Over the past two decades, marine virology has progressed from a curiosity to an intensely studied topic of critical importance to oceanography. At concentrations of approximately 10 million viruses per milliliter of surface seawater, viruses are the most abundant biological entities in the oceans. The majority of these viruses are phages (viruses that infect bacteria). Through lysing their bacterial hosts, marine phages control bacterial abundance, affect community composition, and impact global biogeochemical cycles. In addition, phages influence their hosts through selection for resistance, horizontal gene transfer, and manipulation of bacterial metabolism. Recent work has also demonstrated that marine phages are extremely diverse and can carry a variety of auxiliary metabolic genes encoding critical ecological functions. This review is structured as a scientific "truth or dare," revealing several well-established "truths" about marine viruses and presenting a few "dares" for the research community to undertake in future studies.

Identification of Peptides in Flowers of Sambucus nigra with Antimicrobial Activity against Aquaculture Pathogens.

PubMed

Álvarez, Claudio Andrés; Barriga, Andrés; Albericio, Fernando; Romero, María Soledad; Guzmán, Fanny

2018-04-27

The elder ( Sambucus spp.) tree has a number of uses in traditional medicine. Previous studies have demonstrated the antimicrobial properties of elderberry liquid extract against human pathogenic bacteria and also influenza viruses. These properties have been mainly attributed to phenolic compounds. However, other plant defense molecules, such as antimicrobial peptides (AMPs), may be present. Here, we studied peptide extracts from flowers of Sambucus nigra L. The mass spectrometry analyses determined peptides of 3 to 3.6 kDa, among them, cysteine-rich peptides were identified with antimicrobial activity against various Gram-negative bacteria, including recurrent pathogens of Chilean aquaculture. In addition, membrane blebbing on the bacterial surface after exposure to the cyclotide was visualized by SEM microscopy and SYTOX Green permeabilization assay showed the ability to disrupt the bacterial membrane. We postulate that these peptides exert their action by destroying the bacterial membrane.

Effect of some biotic factors on microbially-induced calcite precipitation in cement mortar.

PubMed

Al-Salloum, Yousef; Abbas, H; Sheikh, Q I; Hadi, S; Alsayed, Saleh; Almusallam, Tarek

2017-02-01

Sporosarcina pasteurii , a common soil bacterium has been tested for microbial treatment of cement mortar. The present study also seeks to investigate the effects of growth medium, bacterial concentration and different buffers concerning the preparation of bacterial suspensions on the compressive strength of cement mortar. Two growth media, six different suspensions and two bacterial concentrations were used in the study. The influence of growth medium on calcification efficiency of S. pasteurii was insignificant. Significant improvement in the compressive as well as the tensile strength of cement mortar was observed. Microbial mineral precipitation visualized by Scanning Electron Microscopy (SEM) shows fibrous material that increased the strength of cement mortar. Formation of thin strands of fillers observed through SEM micrographs improves the pore structure, impermeability and thus the compressive as well as the tensile strengths of the cement mortar. The type of substrate and its molarity have a significant influence on the strength of cement mortar.

Control of occupational exposure to phenol in industrial wastewater treatment plant of a petroleum refinery in Alexandria, Egypt: An intervention application case study.

PubMed

Zaki, Gehan R; El-Marakby, Fadia A; Ramadan, Alaa El-Din K; Issa, Ahmed I; Nofal, Faten H

2016-11-01

Phenol exposure is one of the hazards in the industrial wastewater treatment basin of any refinery. It additively interacts with hydrogen sulfide emitted from the wastewater basin. Consequently, its concentration should be greatly lower than its threshold limit value. The present study aimed at controlling occupational exposure to phenol in the work environment of wastewater treatment plant in a refinery by reducing phenolic compounds in the industrial wastewater basin. This study was conducted on both laboratory and refinery scales. The first was completed by dividing each wastewater sample from the outlets of different refinery units into three portions; the first was analyzed for phenolic compounds. The second and third were for laboratory scale charcoal and bacterial treatments. The two methods were compared regarding their simplicities, design, and removal efficiencies. Accordingly, bacterial treatment by continuous flow of sewage water containing Pseudomonas Aeruginosa was used for refinery scale treatment. Laboratory scale treatment of phenolic compounds revealed higher removal efficiency of charcoal [100.0(0.0) %] than of bacteria [99.9(0.013) %]. The refinery scale bacterial treatment was [99.8(0.013) %] efficient. Consequently, level of phenol in the work environment after refinery-scale treatment [0.069(0.802) mg/m(3)] was much lower than that before [5.700(26.050) mg/m(3)], with removal efficiency of [99.125(2.335) %]. From the present study, we can conclude that bacterial treatment of phenolic compounds in industrial wastewater of the wastewater treatment plant using continuous flow of sewage water containing Pseudomonas Aeruginosa reduces the workers' exposure to phenol.

Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study.

PubMed

Borgo, Francesca; Verduci, Elvira; Riva, Alessandra; Lassandro, Carlotta; Riva, Enrica; Morace, Giulia; Borghi, Elisa

2017-02-01

Differences in relative proportions of gut microbial communities in adults have been correlated with intestinal diseases and obesity. In this study we evaluated the gut microbiota biodiversity, both bacterial and fungal, in obese and normal-weight school-aged children. We studied 28 obese (mean age 10.03 ± 0.68) and 33 age- and sex-matched normal-weight children. BMI z-scores were calculated, and the obesity condition was defined according to the WHO criteria. Fecal samples were analyzed by 16S rRNA amplification followed by denaturing gradient gel electrophoresis (DGGE) analysis and sequencing. Real-time polymerase chain reaction (PCR) was performed to quantify the most representative microbial species and genera. DGGE profiles showed high bacterial biodiversity without significant correlations with BMI z-score groups. Compared to bacterial profiles, we observed lower richness in yeast species. Sequence of the most representative bands gave back Eubacterium rectale, Saccharomyces cerevisiae, Candida albicans, and C. glabrata as present in all samples. Debaryomyces hansenii was present only in two obese children. Obese children revealed a significantly lower abundance in Akkermansia muciniphyla, Faecalibacterium prausnitzii, Bacteroides/Prevotella group, Candida spp., and Saccharomyces spp. (P = 0.031, P = 0.044, P = 0.003, P = 0.047, and P = 0.034, respectively). Taking into account the complexity of obesity, our data suggest that differences in relative abundance of some core microbial species, preexisting or diet driven, could actively be part of its etiology. This study improved our knowledge about the fungal population in the pediatric school-age population and highlighted the need to consider the influence of cross-kingdom relationships.

Effect of Catechins, Green tea Extract and Methylxanthines in Combination with Gentamicin Against Staphylococcus aureus and Pseudomonas aeruginosa

PubMed Central

Fazly Bazzaz, Bibi Sedigheh; Sarabandi, Sahar; Khameneh, Bahman; Hosseinzadeh, Hossein

2016-01-01

Objectives: Bacterial resistant infections have become a global health challenge and threaten the society’s health. Thus, an urgent need exists to find ways to combat resistant pathogens. One promising approach to overcoming bacterial resistance is the use of herbal products. Green tea catechins, the major green tea polyphenols, show antimicrobial activity against resistant pathogens. The present study aimed to investigate the effect of catechins, green tea extract, and methylxanthines in combination with gentamicin against standard and clinical isolates of Staphylococcus aureus (S. aureus) and the standard strain of Pseudomonas aeruginosa (P. aeruginosa). Methods: The minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) values of different agents against bacterial strains were determined. The interactions of green tea extract, epigallate catechin, epigallocatechin gallate, two types of methylxanthine, caffeine, and theophylline with gentamicin were studied in vitro by using a checkerboard method and calculating the fraction inhibitory concentration index (FICI). Results: The MICs of gentamicin against bacterial strains were in the range of 0.312 - 320 μg/mL. The MIC values of both types of catechins were 62.5 - 250 μg/ mL. Green tea extract showed insufficient antibacterial activity when used alone. Methylxanthines had no intrinsic inhibitory activity against any of the bacterial strains tested. When green tea extract and catechins were combined with gentamicin, the MIC values of gentamicin against the standard strains and a clinical isolate were reduced, and synergistic activities were observed (FICI < 1). A combination of caffeine with gentamicin did not alter the MIC values of gentamicin. Conclusion: The results of the present study revealed that green tea extract and catechins potentiated the antimicrobial action of gentamicin against some clinical isolates of S. aureus and standard P. aeruginosa strains. Therefore, combinations of gentamicin with these natural compounds might be a promising approach to combat microbial resistance. PMID:28097041

Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality

PubMed Central

Van Rossum, Thea; Peabody, Michael A.; Uyaguari-Diaz, Miguel I.; Cronin, Kirby I.; Chan, Michael; Slobodan, Jared R.; Nesbitt, Matthew J.; Suttle, Curtis A.; Hsiao, William W. L.; Tang, Patrick K. C.; Prystajecky, Natalie A.; Brinkman, Fiona S. L.

2015-01-01

Select bacteria, such as Escherichia coli or coliforms, have been widely used as sentinels of low water quality; however, there are concerns regarding their predictive accuracy for the protection of human and environmental health. To develop improved monitoring systems, a greater understanding of bacterial community structure, function, and variability across time is required in the context of different pollution types, such as agricultural and urban contamination. Here, we present a year-long survey of free-living bacterial DNA collected from seven sites along rivers in three watersheds with varying land use in Southwestern Canada. This is the first study to examine the bacterial metagenome in flowing freshwater (lotic) environments over such a time span, providing an opportunity to describe bacterial community variability as a function of land use and environmental conditions. Characteristics of the metagenomic data, such as sequence composition and average genome size (AGS), vary with sampling site, environmental conditions, and water chemistry. For example, AGS was correlated with hours of daylight in the agricultural watershed and, across the agriculturally and urban-affected sites, k-mer composition clustering corresponded to nutrient concentrations. In addition to indicating a community shift, this change in AGS has implications in terms of the normalization strategies required, and considerations surrounding such strategies in general are discussed. When comparing abundances of gene functional groups between high- and low-quality water samples collected from an agricultural area, the latter had a higher abundance of nutrient metabolism and bacteriophage groups, possibly reflecting an increase in agricultural runoff. This work presents a valuable dataset representing a year of monthly sampling across watersheds and an analysis targeted at establishing a foundational understanding of how bacterial lotic communities vary across time and land use. The results provide important context for future studies, including further analyses of watershed ecosystem health, and the identification and development of biomarkers for improved water quality monitoring systems. PMID:26733955

Persistence of Clones of Coagulase-Negative Staphylococci among Premature Neonates in Neonatal Intensive Care Units: Two-Center Study of Bacterial Genotyping and Patient Risk Factors

PubMed Central

Vermont, Clementien L.; Hartwig, Nico G.; Fleer, André; de Man, Peter; Verbrugh, Henri; van den Anker, John; de Groot, Ronald; van Belkum, Alex

1998-01-01

From 1 January 1995 until 1 January 1996, we studied the molecular epidemiology of blood isolates of coagulase-negative staphylococci (CoNS) in the Neonatal Intensive Care Units (NICUs) of the Sophia Children’s Hospital (SCH; Rotterdam, The Netherlands) and the Wilhelmina Children’s Hospital (WCH; Utrecht, The Netherlands). The main goal of the present study was to detect putatively endemic clones of CoNS persisting in these NICUs. Pulsed-field gel electrophoresis was used to detect the possible presence of endemic clones of clinical significance. In addition, clinical data of patients in the SCH were analyzed retrospectively to identify risk factors for the acquisition of positive blood cultures. In both centers, endemic CoNS clones were persistently present. Thirty-three percent of the bacterial isolates derived from blood cultures in the SCH belonged to a single genotype. In the WCH, 45% of all bacterial strains belonged to a single clone. These clones were clearly different from each other, which implies that site specificity is involved. Interestingly, we observe that the clonal type in the SCH differed significantly from the incidentally occurring strains with respect to both the average pH and partial CO2 pressure of the patient’s blood at the time of bacterial culture. We found that the use of intravascular catheters, low gestational age, and a long hospital stay were important risk factors for the development of a putative CoNS infection. When the antibiotic susceptibility of the bacterial isolates was assessed, a clear correlation between the nature of the antibiotics most frequently used as a first line of defense versus the resistance profile was observed. We conclude that the intensive use of antibiotics in an NICU setting with highly susceptible patients causes selection of multiresistant clones of CoNS which subsequently become endemic. PMID:9705379

Bisphosphonates enhance bacterial adhesion and biofilm formation on bone hydroxyapatite.

PubMed

Kos, Marcin; Junka, Adam; Smutnicka, Danuta; Szymczyk, Patrycja; Gluza, Karolina; Bartoszewicz, Marzenna

2015-07-01

Because of the suspicion that bisphosphonates enhance bacterial colonization, this study evaluated adhesion and biofilm formation by Streptococcus mutans 25175, Staphylococcus aureus 6538, and Pseudomonas aeruginosa 14454 reference strains on hydroxyapatite coated with clodronate, pamidronate, or zoledronate. Bacterial strains were cultured on bisphosphonate-coated and noncoated hydroxyapatite discs. After incubation, nonadhered bacteria were removed by centrifugation. Biofilm formation was confirmed by scanning electron microscopy. Bacterial colonization was estimated using quantitative cultures compared by means with Kruskal-Wallis and post-hoc Student-Newman-Keuls tests. Modeling of the interactions between bisphosphonates and hydroxyapatite was performed using the Density Functional Theory method. Bacterial colonization of the hydroxyapatite discs was significantly higher for all tested strains in the presence of bisphosphonates vs. Adherence in the presence of pamidronate was higher than with other bisphosphonates. Density Functional Theory analysis showed that the protonated amine group of pamidronate, which are not present in clodronate or zoledronate, forms two additional hydrogen bonds with hydroxyapatite. Moreover, the reactive cationic amino group of pamidronate may attract bacteria by direct electrostatic interaction. Increased bacterial adhesion and biofilm formation can promote osteomyelitis, cause failure of dental implants or bisphosphonate-coated joint prostheses, and complicate bone surgery in patients on bisphosphonates. Copyright © 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Impact assessment of silver nanoparticles on plant growth and soil bacterial diversity.

PubMed

Pallavi; Mehta, C M; Srivastava, Rashmi; Arora, Sandeep; Sharma, A K

2016-12-01

The present study was carried out to investigate the impact of silver nanoparticles (AgNPs) on the growth of three different crop species, wheat (Triticum aestivum, var. UP2338), cowpea (Vigna sinensis, var. Pusa Komal), and Brassica (Brassica juncea, var. Pusa Jai Kisan), along with their impact on the rhizospheric bacterial diversity. Three different concentrations (0, 50 and 75 ppm) of AgNPs were applied through foliar spray. After harvesting, shoot and root parameters were compared, and it was observed that wheat was relatively unaffected by all AgNP treatments. The optimum growth promotion and increased root nodulation were observed at 50 ppm treatment in cowpea, while improved shoot parameters were recorded at 75 ppm in Brassica. To observe the impact of AgNPs on soil bacterial community, sampling was carried out from the rhizosphere of these crops at 20 and 40 days after the spraying of AgNPS. The bacterial diversity of these samples was analyzed by both cultural and molecular techniques (denaturing gradient gel electrophoresis). It is clearly evident from the results that application of AgNPs changes the soil bacterial diversity and this is further influenced by the plant species grown in that soil. Also, the functional bacterial diversity differed with different concentrations of AgNPs.

Using experimental evolution to explore natural patterns between bacterial motility and resistance to bacteriophages

PubMed Central

Koskella, Britt; Taylor, Tiffany B; Bates, Jennifer; Buckling, Angus

2011-01-01

Resistance of bacteria to phages may be gained by alteration of surface proteins to which phages bind, a mechanism that is likely to be costly as these molecules typically have critical functions such as movement or nutrient uptake. To address this potential trade-off, we combine a systematic study of natural bacteria and phage populations with an experimental evolution approach. We compare motility, growth rate and susceptibility to local phages for 80 bacteria isolated from horse chestnut leaves and, contrary to expectation, find no negative association between resistance to phages and bacterial motility or growth rate. However, because correlational patterns (and their absence) are open to numerous interpretations, we test for any causal association between resistance to phages and bacterial motility using experimental evolution of a subset of bacteria in both the presence and absence of naturally associated phages. Again, we find no clear link between the acquisition of resistance and bacterial motility, suggesting that for these natural bacterial populations, phage-mediated selection is unlikely to shape bacterial motility, a key fitness trait for many bacteria in the phyllosphere. The agreement between the observed natural pattern and the experimental evolution results presented here demonstrates the power of this combined approach for testing evolutionary trade-offs. PMID:21509046

Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome.

PubMed

Lupatini, Manoeli; Suleiman, Afnan Khalil Ahmad; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Kuramae, Eiko Eurya; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Würdig

2013-01-01

The Pampa biome is considered one of the main hotspots of the world's biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.

Seasonal changes in bacterial communities associated with healthy and diseased Porites coral in southern Taiwan.

PubMed

Lin, Chorng-Horng; Chuang, Chih-Hsiang; Twan, Wen-Hung; Chiou, Shu-Fen; Wong, Tit-Yee; Liu, Jong-Kang; Kao, Chyuan-Yao; Kuo, Jimmy

2016-12-01

We compared the bacterial communities associated with healthy scleractinian coral Porites sp. with those associated with coral infected with pink spot syndrome harvested during summer and winter from waters off the coast of southern Taiwan. Members of the bacterial community associated with the coral were characterized by means of denaturing gradient gel electrophoresis (DGGE) of a short region of the 16S rRNA gene and clone library analysis. Of 5 different areas of the 16S rRNA gene, we demonstrated that the V3 hypervariable region is most suited to represent the coral-associated bacterial community. The DNA sequences of 26 distinct bands extracted from DGGE gels and 269 sequences of the 16S rRNA gene from clone libraries were determined. We found that the communities present in diseased coral were more heterogeneous than the bacterial communities of uninfected coral. In addition, bacterial communities associated with coral harvested in the summer were more diverse than those associated with coral collected in winter, regardless of the health status of the coral. Our study suggested that the compositions of coral-associated bacteria communities are complex, and the population of bacteria varies greatly between seasons and in coral of differing health status.

The bacterial community composition of the surface microlayer in a high mountain lake.

PubMed

Hörtnagl, Paul; Pérez, Maria Teresa; Zeder, Michael; Sommaruga, Ruben

2010-09-01

The existence of bacterioneuston in aquatic ecosystems is well established, but little is known about its composition and dynamics, particularly in lakes. The bacterioneuston underlies extreme conditions at the air-water boundary, which may influence its dynamics in a different way compared with the bacterioplankton. In this study, we assessed quantitative changes in major bacterial groups of the surface microlayer (SML) (upper 900 microm) and the underlying water (ULW) (0.2-0.5 m depth) of an alpine lake during two consecutive ice-free seasons. Analysis of the bacterial community composition was done using catalyzed reporter deposition FISH with oligonucleotide probes. In addition, several physicochemical parameters were measured to characterize these two water layers. Dissolved organic carbon was consistently enriched in the SML and the dissolved organic matter pool presented clear signals of photodegradation and photobleaching. The water temperature was generally colder in the SML than in the subsurface. The bacterial community of the SML and the ULW was dominated by Betaproteobacteria and Actinobacteria. The bacterial community composition was associated with different combinations of physicochemical factors in these two layers, but temporal changes showed similar trends in both layers over the two seasons. Our results identify the SML of alpine lakes as a microhabitat where specific bacterial members such as of Betaproteobacteria seem to be efficient colonizers.

Origin-Dependent Variations in the Atmospheric Microbiome in Eastern Mediterranean Dust Storms

NASA Astrophysics Data System (ADS)

Rudich, Y.; Gat, D.

2017-12-01

Microorganisms carried by dust storms are transported through the atmosphere and may affect human health and the functionality of microbial communities in various environments. Characterizing the dust-borne microbiome in dust storms of different origins, or that followed different trajectories, provides valuable data to improve our understanding of global health and environmental impacts. We present a comparative study on the diversity of dust- borne bacterial communities in dust storms from three distinct origins—North Africa, Syria and Saudi Arabia—and compare them with local bacterial communities sampled on clear days, all collected at a single location, in Israel. Storms from different dust origins exhibited distinct bacterial communities, with signature bacterial taxa for each source. Dust storms were characterized by a lower abundance of selected antibiotic resistance genes (ARGs) compared with ambient dust, asserting that the origin of these genes is local, possibly anthropogenic. With the progression of the storm, the storm-borne bacterial community showed increasing resemblance to ambient dust, suggesting mixing with local dust. We will also discuss how exposure to dust containing biological components affect lung epithelial cells. These results show, for the first time, that dust storms from different sources display distinct bacterial communities, suggesting possible distinct effects on the environment and public health.

Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system.

PubMed

Revetta, R P; Gomez-Alvarez, V; Gerke, T L; Santo Domingo, J W; Ashbolt, N J

2016-07-01

This study examined the development of bacterial biofilms within a metropolitan distribution system. The distribution system is fed with different source water (i.e. groundwater, GW and surface water, SW) and undergoes different treatment processes in separate facilities. The biofilm community was characterized using 16S rRNA gene clone libraries and functional potential analysis, generated from total DNA extracted from coupons in biofilm annular reactors fed with onsite drinking water for up to 18 months. Differences in the bacterial community structure were observed between GW and SW. Representatives that explained the dissimilarity were associated with the classes Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Gammaproteobacteria and Firmicutes. After 9 months the biofilm bacterial community from both GW and SW were dominated by Mycobacterium species. The distribution of the dominant operational taxonomic unit (OTU) (Mycobacterium) positively correlated with the drinking water distribution system (DWDS) temperature. In this study, the biofilm community structure observed between GW and SW were dissimilar, while communities from different locations receiving SW did not show significant differences. The results suggest that source water and/or the water quality shaped by their respective treatment processes may play an important role in shaping the bacterial communities in the distribution system. In addition, several bacterial groups were present in all samples, suggesting that they are an integral part of the core microbiota of this DWDS. These results provide an ecological insight into biofilm bacterial structure in chlorine-treated drinking water influenced by different water sources and their respective treatment processes. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Bacterial components are the major contributors to the macrophage stimulating activity exhibited by extracts of common edible mushrooms.

PubMed

Tyler, Heather L; Haron, Mona H; Pugh, Nirmal D; Zhang, Jin; Jackson, Colin R; Pasco, David S

2016-10-12

Recent studies have indicated that a major contributor to the innate immune enhancing properties of some medicinal plants is derived from the cell wall components of bacteria colonizing these plants. The purpose of the current study was to assess if the bacteria present within edible and medicinal mushrooms substantially contribute to the innate immune stimulating potential of these mushrooms. Whole mushrooms from thirteen types of edible fungi and individual parts from Agaricus bisporus were analyzed for in vitro macrophage activation as well as bacterial lipopolysaccharides (LPS) content, cell load, and community composition. Substantial variation between samples was observed in macrophage activation (over 500-fold), total bacterial load (over 200-fold), and LPS content (over 10 million-fold). Both LPS content (ρ = 0.832, p < 0.0001) and total bacterial load (ρ = 0.701, p < 0.0001) correlated significantly with macrophage activation in the whole mushroom extracts. Extract activity was negated by treatment with NaOH, conditions that inactivate LPS and other bacterial components. Significant correlations between macrophage activation and total bacterial load (ρ = 0.723, p = 0.0001) and LPS content (ρ = 0.951, p < 0.0001) were also observed between different tissues of Agaricus bisporus. Pseudomonas and Flavobacterium were the most prevalent genera identified in the different tissue parts and these taxa were significantly correlated with in vitro macrophage activation (ρ = 0.697, p < 0.0001 and ρ = 0.659, p = 0.0001, respectively). These results indicate that components derived from mushroom associated bacteria contribute substantially to the innate immune enhancing activity exhibited by mushrooms and may result in similar therapeutic actions as reported for ingestion of bacterial preparations such as probiotics.

Diversity and biological activities of the bacterial community associated with the marine sponge Phorbas tenacior (Porifera, Demospongiae).

PubMed

Dupont, S; Carré-Mlouka, A; Descarrega, F; Ereskovsky, A; Longeon, A; Mouray, E; Florent, I; Bourguet-Kondracki, M L

2014-01-01

The diversity of the cultivable microbiota of the marine sponge Phorbas tenacior frequently found in the Mediterranean Sea was investigated, and its potential as a source of antimicrobial, antioxidant and antiplasmodial compounds was evaluated. The cultivable bacterial community was studied by isolation, cultivation and 16S rRNA gene sequencing. Twenty-three bacterial strains were isolated and identified in the Proteobacteria (α or γ classes) and Actinobacteria phyla. Furthermore, three different bacterial morphotypes localized extracellularly within the sponge tissues were revealed by microscopic observations. Bacterial strains were assigned to seven different genera, namely Vibrio, Photobacterium, Shewanella, Pseudomonas, Ruegeria, Pseudovibrio and Citricoccus. The strains affiliated to the same genus were differentiated according to their genetic dissimilarities using random amplified polymorphic DNA (RAPD) analyses. Eleven bacterial strains were selected for evaluation of their bioactivities. Three isolates Pseudovibrio P1Ma4, Vibrio P1MaNal1 and Citricoccus P1S7 revealed antimicrobial activity; Citricoccus P1S7 and Vibrio P1MaNal1 isolates also exhibited antiplasmodial activity, while two Vibrio isolates P1Ma8 and P1Ma5 displayed antioxidant activity. These data confirmed the importance of Proteobacteria and Actinobacteria associated with marine sponges as a reservoir of bioactive compounds. This study presents the first report on the diversity of the cultivable bacteria associated with the marine sponge Phorbas tenacior, frequently found in the Mediterranean Sea. Evaluation of the antiplasmodial, antimicrobial and antioxidant activities of the isolates has been investigated and allowed to select bacterial strains, confirming the importance of Proteobacteria and Actinobacteria as sources of bioactive compounds. © 2013 The Society for Applied Microbiology.

Presence of Bacteria in Spontaneous Achilles Tendon Ruptures.

PubMed

Rolf, Christer G; Fu, Sai-Chuen; Hopkins, Chelsea; Luan, Ju; Ip, Margaret; Yung, Shu-Hang; Friman, Göran; Qin, Ling; Chan, Kai-Ming

2017-07-01

The structural pathology of Achilles tendon (AT) ruptures resembles tendinopathy, but the causes remain unknown. Recently, a number of diseases were found to be attributed to bacterial infections, resulting in low-grade inflammation and progressive matrix disturbance. The authors speculate that spontaneous AT ruptures may also be influenced by the presence of bacteria. Bacteria are present in ruptured ATs but not in healthy tendons. Cross-sectional study; Level of evidence, 3. Patients with spontaneous AT ruptures and patients undergoing anterior cruciate ligament (ACL) reconstruction were recruited for this study. During AT surgical repair, excised tendinopathic tissue was collected, and healthy tendon samples were obtained as controls from hamstring tendon grafts used in ACL reconstruction. Half of every sample was reserved for DNA extraction and the other half for histology. Polymerase chain reaction (PCR) was conducted using 16S rRNA gene universal primers, and the PCR products were sequenced for the identification of bacterial species. A histological examination was performed to compare tendinopathic changes in the case and control samples. Five of 20 AT rupture samples were positive for the presence of bacterial DNA, while none of the 23 hamstring tendon samples were positive. Sterile operating and experimental conditions and tests on samples, controlling for harvesting and processing procedures, ruled out the chance of postoperative bacterial contamination. The species identified predominantly belonged to the Staphylococcus genus. AT rupture samples exhibited histopathological features characteristic of tendinopathy, and most healthy hamstring tendon samples displayed normal tendon features. There were no apparent differences in histopathology between the bacterial DNA-positive and bacterial DNA-negative AT rupture samples. The authors have demonstrated the presence of bacterial DNA in ruptured AT samples. It may suggest the potential involvement of bacteria in spontaneous AT ruptures.

Microbiological analysis of infected root canals from symptomatic and asymptomatic teeth with periapical periodontitis and the antimicrobial susceptibility of some isolated anaerobic bacteria.

PubMed

Jacinto, R C; Gomes, B P F A; Ferraz, C C R; Zaia, A A; Filho, F J Souza

2003-10-01

The purpose of the present study was to investigate the correlation between the composition of the bacterial flora isolated from infected root canals of teeth with apical periodontitis with the presence of clinical signs and symptoms, and to test the antibiotic susceptibility of five anaerobic bacteria mostly commonly found in the root canals of symptomatic teeth against various substances using the E-test. Microbial samples were taken from 48 root canals, 29 symptomatic and 19 asymptomatic, using adequate techniques. A total of 218 cultivable isolates were recovered from 48 different microbial species and 19 different genera. Root canals from symptomatic teeth harbored more obligate anaerobes and a bigger number of bacterial species than the asymptomatic teeth. More than 70% of the bacterial isolates were strict anaerobes. Statistical analysis used a Pearson Chi-squared test or a one-sided Fisher's Exact test as appropriate. Suggested relationships were found between specific microorganisms, especially gram-negative anaerobes, and the presence of spontaneous or previous pain, tenderness to percussion, pain on palpation and swelling amoxicillin, amoxicillin + clavulanate and cephaclor were effective against all the strains tested. The lowest susceptibility rate was presented by Prevotella intermedia/nigrescens against Penicillin G. Our results suggested that specific bacteria are associated with endodontic symptoms of infected teeth with periapical periodontitis and the majority of the anaerobic bacterial species tested were susceptible to all antibiotics studied.

Direct detection of methylation in genomic DNA

PubMed Central

Bart, A.; van Passel, M. W. J.; van Amsterdam, K.; van der Ende, A.

2005-01-01

The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene expression. Three types of methylated nucleobases are known: N6-methyladenine, 5-methylcytosine and N4-methylcytosine. The aim of this study was to develop a method to detect all three types of DNA methylation in complete genomic DNA. It was previously shown that N6-methyladenine and 5-methylcytosine in plasmid and viral DNA can be detected by intersequence trace comparison of methylated and unmethylated DNA. We extended this method to include N4-methylcytosine detection in both in vitro and in vivo methylated DNA. Furthermore, application of intersequence trace comparison was extended to bacterial genomic DNA. Finally, we present evidence that intrasequence comparison suffices to detect methylated sites in genomic DNA. In conclusion, we present a method to detect all three natural types of DNA methylation in bacterial genomic DNA. This provides the possibility to define the complete methylome of any prokaryote. PMID:16091626

Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production.

PubMed

Belila, A; El-Chakhtoura, J; Otaibi, N; Muyzer, G; Gonzalez-Gil, G; Saikaly, P E; van Loosdrecht, M C M; Vrouwenvelder, J S

2016-05-01

Microbial processes inevitably play a role in membrane-based desalination plants, mainly recognized as membrane biofouling. We assessed the bacterial community structure and diversity during different treatment steps in a full-scale seawater desalination plant producing 40,000 m(3)/d of drinking water. Water samples were taken over the full treatment train consisting of chlorination, spruce media and cartridge filters, de-chlorination, first and second pass reverse osmosis (RO) membranes and final chlorine dosage for drinking water distribution. The water samples were analyzed for water quality parameters (total bacterial cell number, total organic carbon, conductivity, pH, etc.) and microbial community composition by 16S rRNA gene pyrosequencing. The planktonic microbial community was dominated by Proteobacteria (48.6%) followed by Bacteroidetes (15%), Firmicutes (9.3%) and Cyanobacteria (4.9%). During the pretreatment step, the spruce media filter did not impact the bacterial community composition dominated by Proteobacteria. In contrast, the RO and final chlorination treatment steps reduced the Proteobacterial relative abundance in the produced water where Firmicutes constituted the most dominant bacterial group. Shannon and Chao1 diversity indices showed that bacterial species richness and diversity decreased during the seawater desalination process. The two-stage RO filtration strongly reduced the water conductivity (>99%), TOC concentration (98.5%) and total bacterial cell number (>99%), albeit some bacterial DNA was found in the water after RO filtration. About 0.25% of the total bacterial operational taxonomic units (OTUs) were present in all stages of the desalination plant: the seawater, the RO permeates and the chlorinated drinking water, suggesting that these bacterial strains can survive in different environments such as high/low salt concentration and with/without residual disinfectant. These bacterial strains were not caused by contamination during water sample filtration or from DNA extraction protocols. Control measurements for sample contamination are important for clean water studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial dynamics during production of lesser mealworms (Alphitobius diaperinus) for human consumption at industrial scale.

PubMed

Wynants, E; Crauwels, S; Verreth, C; Gianotten, N; Lievens, B; Claes, J; Van Campenhout, L

2018-04-01

In this study, the microbial dynamics during an industrial production cyle of lesser mealworms (Alphitobius diaperinus), sold for human consumption, were characterised. The microbial numbers as well as the microbial diversity were generally higher for the substrate, existing of remaining feed, faeces and exuviae, than for the larvae. Most of the species-level operational taxonomic units, identified using Illumina MiSeq sequencing, that were present in the feed were also detected in the larvae and vice versa. However, bacterial diversity decreased in the larvae during rearing. These results suggested that the feed is an important determinant of the insect bacterial community, but that some bacterial species show a competitive advantage inside the insect gut and become dominant. A blanching treatment of the larvae after harvest reduced most microbial counts, but the number of aerobic endospores remained at 4.0 log cfu/g. Whereas food pathogens Salmonella spp., Listeria monocytogenes, Bacillus cereus or coagulase-positive staphylococci were not detected in our study, fungal isolates corresponding to the genera Aspergillus and Fusarium were recovered. Therefore, it cannot be excluded that mycotoxins were present. The results of this study contribute to a better understanding of the microbial dynamics and food safety aspects during the production of edible insects. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Audiophonological evaluation of 16 children fitted with cochlear implants for sensorineural hearing loss induced by bacterial meningitis].

PubMed

Teissier, N; Doehring, I; Noel-Petroff, N; Elmaleh-Bergès, M; Viala, P; François, M; Faye, A; Van Den Abbeele, T; Lorrot, M

2013-06-01

Bacterial meningitis (BM) is the primary etiology of acquired sensorineural hearing loss (SNHL) in children and may compromise language development. Since the 1990 s, cochlear implants (CIs) have become part of the management of children with profound SNHL with encouraging results. The aim of this study was to analyze the audiophonological performance of children before and after cochlear implantation for SNHL following bacterial meningitis. Retrospective study of all children fitted with CIs for bilateral severe to profound SNHL after bacterial meningitis in the Robert-Debré pediatric ENT department between August 1990 and March 2009. Audiophonological performance was assessed using the APCEI profile. Of the 283 children receiving implants during that period, 16 children (6%; 6 boys, 10 girls) underwent CI implantation after bacterial meningitis (Streptococcus pneumoniae in 8 cases, Neisseria meningitidis in 2 cases, and Haemophilus influenzae in 4 cases). The mean time from meningitis to SNHL was 8.3 months (median, 1.5 months; range, 1 day to 13 years). The mean time from meningitis to cochlear implantation was 2 years and 3 months (median, 7 months; range, 1 month to 13 years 3 months). Twelve children (75%) presented partial cochlear and/or vestibular ossification on presurgical CT scan. Three children received bilateral implants. Thirteen children (81%) developed early SNHL in the first 3 months, whereas 3 children developed SNHL more than 10 months after meningitis. As for the benefits of cochlear implantation, 11 children presented near to normal intelligibility and optimal use of their cochlear implant; 5 children presented partial benefits due to neurological sequelae (1), a long delay before implantation (1), technical problems (2), or a social problem in relation to low socioeconomic status (1). After bacterial meningitis, audiological evaluation must be made carefully during the first 3 months to detect early SNHL, but SNHL may also develop several years later. In case of profound SNHL and a modified signal of the labyrinth on the MRI, cochlear implantation must be performed without delay before cochlear and/or vestibular ossification. Cochlear implantation is an effective technique with good long-term audiologic results. The coexistence of neurological lesions may compromise the results, but it should not contraindicate a cochlear implantation. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Intra-familial comparison of supragingival dental plaque microflora using the checkerboard DNA-DNA hybridisation technique.

PubMed

Mannaa, Alaa; Carlén, Anette; Dahlén, Gunnar; Lingström, Peter

2012-12-01

The aims of the present study were to correlate the quantified supragingival plaque bacteria between mothers and their children and identify possible microbial associations. A total of 86 mothers and their 4- to 6-year-old and 12- to 16-year-old children participated. Pooled supragingival plaque samples were obtained from interproximal sites between teeth 16/15, 25/26, 35/36 and 46/45 in mothers and older children and teeth 55/54, 64/65, 74/75 and 85/84 in younger children. All the samples were individually analysed for their content of 18 bacterial strains using checkerboard DNA-DNA hybridisation (whole genomic probes). Microbial associations were sought using cluster analysis (dendrogram) for all three age groups together, while community ordination techniques were used for each of the three groups separately. Three complexes were formed from the dendrogram in addition to associations between these complexes and remaining bacterial strains. Principal component analysis results were similar in all three groups. The correlation analyses of bacterial counts between mothers and their children showed a significant association for most of the bacterial strains (p<0.05 or 0.01). Supragingival plaque microbiota are correlated between mothers and their children. In addition, similar supragingival plaque microbial associations are present in family members.. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bacterial Community Analysis of Drinking Water Biofilms in Southern Sweden

PubMed Central

Lührig, Katharina; Canbäck, Björn; Paul, Catherine J.; Johansson, Tomas; Persson, Kenneth M.; Rådström, Peter

2015-01-01

Next-generation sequencing of the V1–V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82–87%), with 22–40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities. PMID:25739379

[Decontamination of dental unit waterlines using disinfectants and filters].

PubMed

Monarca, S; Garusi, G; Gigola, P; Spampinato, L; Zani, C; Sapelli, P L

2002-10-01

Bacterial contamination of the dental unit water system can become a health problem for patients, particularly if they are immunodepressed. The present study has had the purpose of evaluating the effectiveness of methods of chemical decontamination using different disinfectants (peracetic acid, hydrogen peroxide, silver salts, chloramine T, glutaraldehyde T4) and methods of physical decontamination using synthetic membranes for the filtration of water. A preliminary removal procedure of the biofilm present in the waterline has been followed in a dental unit prepared on purpose for the research; subsequently different 2-week long maintenance procedures were applied using disinfectants injected by a pump and finally the bacterial contamination of the water flowing from the waterline was evaluated. The physical decontamination was performed using 0.22 mm membrane filters, which have been installed also in another dental unit, and the filtered water was analyzed to detect bacterial contamination. The preliminary procedure of biofilm removal succeeded obtaining germ-free water. Among the disinfectants used for the maintenance of the water quality only glutaraldehyde T4 was able to reduce the bacterial contamination under the limit suggested by the ADA. The membrane filter system was not able to purify the water, but when a disinfectant (peracetic acid) was used in the last part of the waterline good results were obtained. At present no decontamination system of dental waterline is available, and glutaraldehyde T4 seems to be the best disinfectant only if integrated with periodic biofilm removal for the maintenance of the water quality.

Amplicon sequencing of bacterial microbiota in abortion material from cattle.

PubMed

Vidal, Sara; Kegler, Kristel; Posthaus, Horst; Perreten, Vincent; Rodriguez-Campos, Sabrina

2017-10-10

Abortions in cattle have a significant economic impact on animal husbandry and require prompt diagnosis for surveillance of epizootic infectious agents. Since most abortions are not epizootic but sporadic with often undetected etiologies, this study examined the bacterial community present in the placenta (PL, n = 32) and fetal abomasal content (AC, n = 49) in 64 cases of bovine abortion by next generation sequencing (NGS) of the 16S rRNA gene. The PL and AC from three fetuses of dams that died from non-infectious reasons were included as controls. All samples were analyzed by bacterial culture, and 17 were examined by histopathology. We observed 922 OTUs overall and 267 taxa at the genus level. No detectable bacterial DNA was present in the control samples. The microbial profiles of the PL and AC differed significantly, both in their composition (PERMANOVA), species richness and Chao-1 (Mann-Whitney test). In both organs, Pseudomonas was the most abundant genus. The combination of NGS and culture identified opportunistic pathogens of interest in placentas with lesions, such as Vibrio metschnikovii, Streptococcus uberis, Lactococcus lactis and Escherichia coli. In placentas with lesions where culturing was unsuccessful, Pseudomonas and unidentified Aeromonadaceae were identified by NGS displaying high number of reads. Three cases with multiple possible etiologies and placentas presenting lesions were detected by NGS. Amplicon sequencing has the potential to uncover unknown etiological agents. These new insights on cattle abortion extend our focus to previously understudied opportunistic abortive bacteria.

Bacterial community analysis of drinking water biofilms in southern Sweden.

PubMed

Lührig, Katharina; Canbäck, Björn; Paul, Catherine J; Johansson, Tomas; Persson, Kenneth M; Rådström, Peter

2015-01-01

Next-generation sequencing of the V1-V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82-87%), with 22-40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities.

Bacterial Biofilms in Jones Tubes.

PubMed

Ahn, Eric S; Hauck, Matthew J; Kirk Harris, Jonathan; Robertson, Charles E; Dailey, Roger A

To investigate the presence and microbiology of bacterial biofilms on Jones tubes (JTs) by direct visualization with scanning electron microscopy and polymerase chain reaction (PCR) of representative JTs, and to correlate these findings with inflammation and/or infection related to the JT. In this study, prospective case series were performed. JTs were recovered from consecutive patients presenting to clinic for routine cleaning or recurrent irritation/infection. Four tubes were processed for scanning electron microscopy alone to visualize evidence of biofilms. Two tubes underwent PCR alone for bacterial quantification. One tube was divided in half and sent for scanning electron microscopy and PCR. Symptoms related to the JTs were recorded at the time of recovery. Seven tubes were obtained. Five underwent SEM, and 3 out of 5 showed evidence of biofilms (60%). Two of the 3 biofilms demonstrated cocci and the third revealed rods. Three tubes underwent PCR. The predominant bacteria identified were Pseudomonadales (39%), Pseudomonas (16%), and Staphylococcus (14%). Three of the 7 patients (43%) reported irritation and discharge at presentation. Two symptomatic patients, whose tubes were imaged only, revealed biofilms. The third symptomatic patient's tube underwent PCR only, showing predominantly Staphylococcus (56%) and Haemophilus (36%) species. Two of the 4 asymptomatic patients also showed biofilms. All symptomatic patients improved rapidly after tube exchange and steroid antibiotic drops. Bacterial biofilms were variably present on JTs, and did not always correlate with patients' symptoms. Nevertheless, routine JT cleaning is recommended to treat and possibly prevent inflammation caused by biofilms.

Bacterial diversity indicates dietary overlap among bats of different feeding habits.

PubMed

Banskar, Sunil; Mourya, Devendra T; Shouche, Yogesh S

2016-01-01

Bats are among the most conspicuous mammals with extraordinary adaptations. They play a key role in the ecosystem. Frugivorous bats are important seed dispersing agents that help in maintaining forest tree diversity, while insectivorous bats are natural insect pest control agents. Several previous reports suggest that bats are reservoir of viruses; nonetheless their bacterial counterparts are relatively less explored. The present study describes the microbial diversity associated with the intestine of bats from different regions of India. Our observations stipulate that there is substantial sharing of bacterial communities between the insectivorous and frugivorous bats, which signifies fairly large dietary overlap. We also observed the presence of higher abundance of Mycoplasma in Cynopterus species of bats, indicating possible Mycoplasma infection. Considering the scarcity of literature related to microbial communities of bat intestinal tract, this study can direct future microbial diversity studies in bats with reference to their dietary habits, host-bacteria interaction and zoonosis. Copyright © 2015 Elsevier GmbH. All rights reserved.

Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction

PubMed Central

Asem, Dhaneshwaree; Leo, Vincent Vineeth; Passari, Ajit Kumar; Tonsing, Mary Vanlalhruaii; Joshi, J. Beslin; Uthandi, Sivakumar; Hashem, Abeer; Abd_Allah, Elsayed Fathi

2017-01-01

The gastrointestinal (GI) habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk) and a domesticated goat (Black Bengal) were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF) of D2 (alkaline pretreated pulpy biomass) using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL) and FPase (0.5 U/mL) activities (55°C, pH 8). The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion. PMID:29023528

Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction.

PubMed

Asem, Dhaneshwaree; Leo, Vincent Vineeth; Passari, Ajit Kumar; Tonsing, Mary Vanlalhruaii; Joshi, J Beslin; Uthandi, Sivakumar; Hashem, Abeer; Abd Allah, Elsayed Fathi; Singh, Bhim Pratap

2017-01-01

The gastrointestinal (GI) habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk) and a domesticated goat (Black Bengal) were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF) of D2 (alkaline pretreated pulpy biomass) using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL) and FPase (0.5 U/mL) activities (55°C, pH 8). The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.

Quasi-Instantaneous Bacterial Inactivation on Cu-Ag Nanoparticulate 3D Catheters in the Dark and Under Light: Mechanism and Dynamics.

PubMed

Rtimi, Sami; Sanjines, Rosendo; Pulgarin, Cesar; Kiwi, John

2016-01-13

The first evidence for Cu-Ag (50%/50%) nanoparticulate hybrid coatings is presented leading to a complete and almost instantaneous bacterial inactivation in the dark (≤5 min). Dark bacterial inactivation times on Cu-Ag (50%/50%) were observed to coincide with the times required by actinic light irradiation. This provides the evidence that the bimetal Cu-Ag driven inactivation predominates over a CuO/Cu2O and Ag2O oxides inducing a semiconductor driven behavior. Cu- or Ag-coated polyurethane (PU) catheters led to bacterial inactivation needing about ∼30 min. The accelerated bacterial inactivation by Cu-Ag coated on 3D catheters sputtered was investigated in a detailed way. The release of Cu/Ag ions during bacterial inactivation was followed by inductively coupled plasma mass-spectrometry (ICP-MS) and the amount of Cu and Ag-ions released were below the cytotoxicity levels permitted by the sanitary regulations. By stereomicroscopy the amount of live/dead cells were followed during the bacterial inactivation time. By Fourier transform infrared spectroscopy (FTIR), the systematic shift of the -(CH2) band stretching of the outer lipo-polysaccharide bilayer (LPS) was followed to monitor the changes leading to cell lysis. A hydrophobic to hydrophilic transformation of the Cu-Ag PU catheter surface under light was observed within 30 min followed concomitantly to a longer back transformation to the hydrophobic initial state in the dark. Physical insight is provided for the superior performance of Cu-Ag films compared to Cu or Ag films in view of the drastic acceleration of the bacterial inactivation observed on bimetal Cu-Ag films coating PU catheters. A mechanism of bacterial inactivation is suggested that is consistent with the findings reported in this study.

Antibacterial Activity of Polyphenolic Fraction of Kombucha Against Enteric Bacterial Pathogens.

PubMed

Bhattacharya, Debanjana; Bhattacharya, Semantee; Patra, Madhu Manti; Chakravorty, Somnath; Sarkar, Soumyadev; Chakraborty, Writachit; Koley, Hemanta; Gachhui, Ratan

2016-12-01

The emergence of multi-drug-resistant enteric pathogens has prompted the scientist community to explore the therapeutic potentials of traditional foods and beverages. The present study was undertaken to investigate the efficacy of Kombucha, a fermented beverage of sugared black tea, against enterotoxigenic Escherichia coli, Vibrio cholerae, Shigella flexneri and Salmonella Typhimurium followed by the identification of the antibacterial components present in Kombucha. The antibacterial activity was evaluated by determining the inhibition zone diameter, minimal inhibitory concentration and minimal bactericidal concentration. Kombucha fermented for 14 days showed maximum activity against the bacterial strains. Its ethyl acetate extract was found to be the most effective upon sequential solvent extraction of the 14-day Kombucha. This potent ethyl acetate extract was then subjected to thin layer chromatography for further purification of antibacterial ingredients which led to the isolation of an active polyphenolic fraction. Catechin and isorhamnetin were detected as the major antibacterial compounds present in this polyphenolic fraction of Kombucha by High Performance Liquid Chromatography. Catechin, one of the primary antibacterial polyphenols in tea was also found to be present in Kombucha. But isorhamnetin is not reported to be present in tea, which may thereby suggest the role of fermentation process of black tea for its production in Kombucha. To the best of our knowledge, this is the first report on the presence of isorhamnetin in Kombucha. The overall study suggests that Kombucha can be used as a potent antibacterial agent against entero-pathogenic bacterial infections, which mainly is attributed to its polyphenolic content.

Bacterial Community Assembly and Turnover within the Intestines of Developing Zebrafish

PubMed Central

Yan, Qingyun; van der Gast, Christopher J.; Yu, Yuhe

2012-01-01

Background The majority of animal associated microorganisms are present in digestive tract communities. These intestinal communities arise from selective pressures of the gut habitats as well as host's genotype are regarded as an extra ‘organ’ regulate functions that have not evolved wholly on the host. They are functionally essential in providing nourishment, regulating epithelial development, and influencing immunity in the vertebrate host. As vertebrates are born free of microorganisms, what is poorly understood is how intestinal bacterial communities assemble and develop in conjunction with the development of the host. Methodology/Principal Findings Set within an ecological framework, we investigated the bacterial community assembly and turnover within the intestinal habitats of developing zebrafish (from larvae to adult animals). Spatial and temporal species-richness relationships and Mantel and partial Mantel tests revealed that turnover was low and that richness and composition was best predicted by time and not intestinal volume (habitat size) or changes in food diet. We also observed that bacterial communities within the zebrafish intestines were deterministically assembled (reflected by the observed low turnover) switching to stochastic assembly in the later stages of zebrafish development. Conclusions/Significance This study is of importance as it provides a novel insight into how intestinal bacterial communities assemble in tandem with the host's development (from early to adult stages). It is our hope that by studying intestinal microbiota of this vertebrate model with such or some more refined approaches in the future could well provide ecological insights for clinical benefit. In addition, this study also adds to our still fledgling knowledge of how spatial and temporal species-richness relationships are shaped and provides further mounting evidence that bacterial community assembly and dynamics are shaped by both deterministic and stochastic considerations. PMID:22276219

Comparison of desiccation tolerance among Listeria monocytogenes, Escherichia coli O157:H7, Salmonella enterica, and Cronobacter sakazakii in powdered infant formula.

PubMed

Koseki, Shigenobu; Nakamura, Nobutaka; Shiina, Takeo

2015-01-01

Bacterial pathogens such as Listeria monocytogenes, Escherichia coli O157:H7, Salmonella enterica, and Cronobacter sakazakii have demonstrated long-term survival in/on dry or low-water activity (aw) foods. However, there have been few comparative studies on the desiccation tolerance among these bacterial pathogens separately in a same food matrix. In the present study, the survival kinetics of the four bacterial pathogens separately inoculated onto powdered infant formula as a model low-aw food was compared during storage at 5, 22, and 35°C. No significant differences in the survival kinetics between E. coli O157:H7 and L. monocytogenes were observed. Salmonella showed significantly higher desiccation tolerance than these pathogens, and C. sakazakii demonstrated significantly higher desiccation tolerance than all other three bacteria studied. Thus, the desiccation tolerance was represented as C. sakazakii > Salmonella > E. coli O157:H7 = L. monocytogenes. The survival kinetics of each bacterium was mathematically analyzed, and the observed kinetics was successfully described using the Weibull model. To evaluate the variability of the inactivation kinetics of the tested bacterial pathogens, the Monte Carlo simulation was performed using assumed probability distribution of the estimated fitted parameters. The simulation results showed that the storage temperature significantly influenced survival of each bacterium under the dry environment, where the bacterial inactivation became faster with increasing storage temperature. Furthermore, the fitted rate and shape parameters of the Weibull model were successfully modelled as a function of temperature. The numerical simulation of the bacterial inactivation was realized using the functions of the parameters under arbitrary fluctuating temperature conditions.

Lactobacillus-deficient vaginal microbiota dominate post-partum women in rural Malawi.

PubMed

Doyle, Ronan; Gondwe, Austridia; Fan, Yue-Mei; Maleta, Kenneth; Ashorn, Per; Klein, Nigel; Harris, Kathryn

2018-01-05

The bacterial community found in the vagina is an important determinant of a woman's health and disease. A healthy vaginal microbiota is associated with a lower species richness and high proportions of one of a number of different Lactobacillus spp.. When disrupted the resulting abnormal vaginal microbiota is associated with a number of disease states and poor pregnancy outcomes. Studies up until now have concentrated on relatively small numbers of American and European populations which may not capture the full complexity of the community, nor adequately predict what constitutes a healthy microbiota in all populations. In this study we sampled and characterised the vaginal microbiota from a cohort of 1107 women in rural Malawi found on vaginal swabs taken post-partum. We found a population dominated by Gardnerella vaginalis and devoid of the most common vaginal Lactobacillus species, even if the vagina was sampled over a year post-partum. The Lactobacillus -deficient anaerobic community commonly labelled community state type (CST) 4 could be sub-divided into four further communities. A Lactobacillus iners dominated vaginal microbiota became more common the longer after delivery the vagina was sampled, but G. vaginalis remained the dominant organism. These results outline the difficulty in all-encompassing definitions of what a healthy or abnormal vaginal microbiota is post-partum. Previous identification of community state types and associations between bacterial species, bacterial vaginosis and adverse birth outcomes may not represent the complex heterogeneity of the microbiota present. Importance A bacterial community in the vaginal tract that is dominated by small number of bacterial Lactobacillus species and when they are not present, there is a greater incidence of inflammatory conditions and adverse birth outcomes. A switch to a vaginal bacterial community lacking in Lactobacillus species is common after pregnancy. In this study we characterised the vaginal microbiota after delivery of a large group of women from a resource poor, under-sampled population in rural Malawi. The majority of women were found to have a Lactobacillus -deficient community and even after a year after delivery the majority of women still did not have Lactobacillus present in their vaginal microbiota. The effect of becoming pregnant again for those who do not revert to a Lactobacillus dominant community is unknown and could suggest that not all Lactobacillus -deficient community structures are adverse. A better understanding is needed of this complex community state type. Copyright © 2018 Doyle et al.

Culturable bacteria present in the fluid of the hooded-pitcher plant Sarracenia minor based on 16S rDNA gene sequence data.

PubMed

Siragusa, Alex J; Swenson, Janice E; Casamatta, Dale A

2007-08-01

The culturable microbial community within the pitcher fluid of 93 Sarracenia minor carnivorous plants was examined over a 2-year study. Many aspects of the plant/bacterial/insect interaction within the pitcher fluid are minimally understood because the bacterial taxa present in these pitchers have not been identified. Thirteen isolates were characterized by 16S rDNA sequencing and subsequent phylogenetic analysis. The Proteobacteria were the most abundant taxa and included representatives from Serratia, Achromobacter, and Pantoea. The Actinobacteria Micrococcus was also abundant while Bacillus, Lactococcus, Chryseobacterium, and Rhodococcus were infrequently encountered. Several isolates conformed to species identifiers (>98% rDNA gene sequence similarity) including Serratia marcescens (isolates found in 27.5% of pitchers), Achromobacter xylosoxidans (37.6%), Micrococcus luteus (40.9%), Bacillus cereus (isolates found in 10.2%), Bacillus thuringiensis (5.4%), Lactococcus lactis (17.2%), and Rhodococcus equi (2.2%). Species-area curves suggest that sampling efforts were sufficient to recover a representative culturable bacterial community. The bacteria present represent a diverse community probably as a result of introduction by insect vectors, but the ecological significance remains under explored.

Bacterial and fungal keratitis in Upper Egypt: In vitro screening of enzymes, toxins and antifungal activity

PubMed Central

Gharamah, Abdullah A; Moharram, Ahmed M; Ismail, Mady A; AL-Hussaini, Ashraf K

2014-01-01

Purpose: This work was conducted to study the ability of bacterial and fungal isolates from keratitis cases in Upper Egypt to produce enzymes, toxins, and to test the isolated fungal species sensitivity to some therapeutic agents. Materials and Methods: One hundred and fifteen patients clinically diagnosed to have microbial keratitis were investigated. From these cases, 37 bacterial isolates and 25 fungal isolates were screened for their ability to produce extra-cellular enzymes in solid media. In addition, the ability of fungal isolates to produce mycotoxins and their sensitivity to 4 antifungal agents were tested. Results: Protease, lipase, hemolysins, urease, phosphatase, and catalase were detected respectively in 48.65%, 37.84%, 59.46%, 43.24%, 67.57%, and 100% out of 37 bacterial isolates tested. Out of 25 fungal isolates tested during the present study, 80% were positive for protease, 84% for lipase and urease, 28% for blood hemolysis, and 100% for phosphatase and catalase enzymes. Thirteen fungal isolates were able to produce detectable amounts of 7 mycotoxins in culture medium (aflatoxins (B1, B2, G1, and G2), sterigmatocystin, fumagillin, diacetoxyscirpenol, zearalenone, T-2 toxin, and trichodermin). Among the antifungal agents tested in this study, terbinafine showed the highest effect against most isolates in vitro. Conclusion: In conclusion, the ability of bacterial and fungal isolates to produce extracellular enzymes and toxins may be aid in the invasion and destruction of eye tissues, which, in turn, lead to vision loss. PMID:24008795

Differentiation of etiologic agents of bacterial keratitis from presentation characteristics.

PubMed

Mascarenhas, Jeena; Srinivasan, Muthiah; Chen, Michael; Rajaraman, Revathi; Ravindran, Meenakshi; Lalitha, Prajna; Oldenburg, Catherine E; Ray, Kathryn J; Glidden, David V; Costanza, Stephanie; Lietman, Thomas M; Acharya, Nisha R

2012-12-01

Presenting characteristics of bacterial corneal ulcers may suggest particular causative organisms, helping to guide treatment decisions before cultures become available. In this study, we analyze the association between presentation demographic and clinical characteristics, using data collected as part of a randomized, controlled clinical trial. Data for this study were collected as part of the Steroids for Corneal Ulcers Trial, a randomized, placebo-controlled, double-masked trial. All patients had a culture-proven bacterial corneal ulcer. Patient history, clinical examination, and photography were performed in a standardized fashion at enrollment. Analysis of variance or Fisher's exact test was used to compare characteristics by organism. Univariate logistic regression was used to analyze predictors of the most common organisms. Five hundred patients were enrolled in the trial, of whom 488 were included in this analysis. The most common organism was Streptococcus pneumoniae (N = 248, 51 %) followed by Pseudomonas aeruginosa (N = 110, 23 %). Compared to other organisms, P. aeruginosa was significantly associated with a larger baseline infiltrate/scar size [odds ratio (OR) 1.6, 95 % confidence interval (CI) 1.4-1.8] and deeper infiltrate (OR 2.4, 95 % CI 1.5-3.8). S. pneumoniae was significantly associated with a smaller baseline infiltrate/scar size (OR 0.8, 95 % CI 0.7-0.9) and dacryocystitis (OR 7.3, 95 % CI 4.1-13.3). Nocardia spp. were significantly associated with longer duration of symptoms prior to presentation (OR 1.4, 95 % CI 1.2-1.6), more shallow infiltrate (OR 0.3, 95 % CI 0.2-0.5), and better baseline visual acuity (OR 0.4, 95 % CI 0.2-0.65). Staphylococcus spp. were less likely to be central in location (OR 0.16, 95 % CI 0.08-0.3). Baseline characteristics of bacterial ulcers may suggest the likely etiology and guide early management.

Differentiation of etiologic agents of bacterial keratitis from presentation characteristics

PubMed Central

Mascarenhas, Jeena; Srinivasan, Muthiah; Chen, Michael; Rajaraman, Revathi; Ravindran, Meenakshi; Lalitha, Prajna; Oldenburg, Catherine E.; Ray, Kathryn J.; Glidden, David V.; Costanza, Stephanie; Lietman, Thomas M.

2013-01-01

Presenting characteristics of bacterial corneal ulcers may suggest particular causative organisms, helping to guide treatment decisions before cultures become available. In this study, we analyze the association between presentation demographic and clinical characteristics, using data collected as part of a randomized, controlled clinical trial. Data for this study were collected as part of the Steroids for Corneal Ulcers Trial, a randomized, placebo-controlled, double-masked trial. All patients had a culture-proven bacterial corneal ulcer. Patient history, clinical examination, and photography were performed in a standardized fashion at enrollment. Analysis of variance or Fisher’s exact test was used to compare characteristics by organism. Univariate logistic regression was used to analyze predictors of the most common organisms. Five hundred patients were enrolled in the trial, of whom 488 were included in this analysis. The most common organism was Streptococcus pneumoniae (N = 248, 51 %) followed by Pseudomonas aeruginosa (N = 110, 23 %). Compared to other organisms, P. aeruginosa was significantly associated with a larger baseline infiltrate/scar size [odds ratio (OR) 1.6, 95 % confidence interval (CI) 1.4–1.8] and deeper infiltrate (OR 2.4, 95 % CI 1.5–3.8). S. pneumoniae was significantly associated with a smaller baseline infiltrate/scar size (OR 0.8, 95 % CI 0.7–0.9) and dacryocystitis (OR 7.3, 95 % CI 4.1–13.3). Nocardia spp. were significantly associated with longer duration of symptoms prior to presentation (OR 1.4, 95 % CI 1.2–1.6), more shallow infiltrate (OR 0.3, 95 % CI 0.2–0.5), and better baseline visual acuity (OR 0.4, 95 % CI 0.2–0.65). Staphylococcus spp. were less likely to be central in location (OR 0.16, 95 % CI 0.08–0.3). Baseline characteristics of bacterial ulcers may suggest the likely etiology and guide early management. PMID:22752605

An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

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

Song, Zhen; Kenney, Janice P.L.; Fein, Jeremy B.

2015-02-09

Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has beenmore » observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.« less

Relationship of periodontal clinical parameters with bacterial composition in human dental plaque.

PubMed

Fujinaka, Hidetake; Takeshita, Toru; Sato, Hirayuki; Yamamoto, Tetsuji; Nakamura, Junji; Hase, Tadashi; Yamashita, Yoshihisa

2013-06-01

More than 600 bacterial species have been identified in the oral cavity, but only a limited number of species show a strong association with periodontitis. The purpose of the present study was to provide a comprehensive outline of the microbiota in dental plaque related to periodontal status. Dental plaque from 90 subjects was sampled, and the subjects were clustered based on bacterial composition using the terminal restriction fragment length polymorphism of 16S rRNA genes. Here, we evaluated (1) periodontal clinical parameters between clusters; (2) the correlation of subgingival bacterial composition with supragingival bacterial composition; and (3) the association between bacterial interspecies in dental plaque using a graphical Gaussian model. Cluster 1 (C1) having high prevalence of pathogenic bacteria in subgingival plaque showed increasing values of the parameters. The values of the parameters in Cluster 2a (C2a) having high prevalence of non-pathogenic bacteria were markedly lower than those in C1. A cluster having low prevalence of non-pathogenic bacteria in supragingival plaque showed increasing values of the parameters. The bacterial patterns between subgingival plaque and supragingival plaque were significantly correlated. Chief pathogens, such as Porphyromonas gingivalis, formed a network with other pathogenic species in C1, whereas a network of non-pathogenic species, such as Rothia sp. and Lautropia sp., tended to compete with a network of pathogenic species in C2a. Periodontal status relates to non-pathogenic species as well as to pathogenic species, suggesting that the bacterial interspecies connection affects dental plaque virulence.

An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

NASA Astrophysics Data System (ADS)

Song, Zhen; Kenney, Janice P. L.; Fein, Jeremy B.; Bunker, Bruce A.

2012-06-01

Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has been observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.

Electrical conductivity measurements of bacterial nanowires from Pseudomonas aeruginosa

NASA Astrophysics Data System (ADS)

Maruthupandy, Muthusamy; Anand, Muthusamy; Maduraiveeran, Govindhan; Sait Hameedha Beevi, Akbar; Jeeva Priya, Radhakrishnan

2015-12-01

The extracellular appendages of bacteria (flagella) that transfer electrons to electrodes are called bacterial nanowires. This study focuses on the isolation and separation of nanowires that are attached via Pseudomonas aeruginosa bacterial culture. The size and roughness of separated nanowires were measured using transmission electron microscopy (TEM) and atomic force microscopy (AFM), respectively. The obtained bacterial nanowires indicated a clear image of bacterial nanowires measuring 16 nm in diameter. The formation of bacterial nanowires was confirmed by microscopic studies (AFM and TEM) and the conductivity nature of bacterial nanowire was investigated by electrochemical techniques. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS), which are nondestructive voltammetry techniques, suggest that bacterial nanowires could be the source of electrons—which may be used in various applications, for example, microbial fuel cells, biosensors, organic solar cells, and bioelectronic devices. Routine analysis of electron transfer between bacterial nanowires and the electrode was performed, providing insight into the extracellular electron transfer (EET) to the electrode. CV revealed the catalytic electron transferability of bacterial nanowires and electrodes and showed excellent redox activities. CV and EIS studies showed that bacterial nanowires can charge the surface by producing and storing sufficient electrons, behave as a capacitor, and have features consistent with EET. Finally, electrochemical studies confirmed the development of bacterial nanowires with EET. This study suggests that bacterial nanowires can be used to fabricate biomolecular sensors and nanoelectronic devices.

Bacterial detection of platelets: current problems and possible resolutions.

PubMed

Blajchman, Morris A; Beckers, Erik A M; Dickmeiss, Ebbe; Lin, Lilly; Moore, Gillian; Muylle, Ludo

2005-10-01

The greatest transfusion-transmitted disease risk facing a transfusion recipient is that of bacterial sepsis. The prevalence of bacterial contamination in platelets and red blood cells is approximately 1 in 3,000 units transfused. The available data indicate that transfusion-associated sepsis develops after 1 in 25,000 platelet transfusions and 1 in 250,000 red blood cell transfusions. One of the most widely used strategies for decreasing bacterial sepsis risk is bacterial detection. A roundtable meeting of experts was convened during the XXVIII Annual Congress of the International Society of Blood Transfusion (Edinburgh, UK, July 2004) to provide a forum for experts to share their experiences in the routine bacterial detection of platelet products. This article summarizes the presentations, discussions, and recommendations of the panel. The data presented indicate that some of the current bacterial screening technology is useful for blocking the issuance of platelet units that contain relatively high levels of contaminating bacteria. Platelet units are usually released based on a test-negative status, which often become test-positive only upon longer storage. These data thus suggest that bacterial screening may not prevent all transfusion-transmitted bacterial infections. Two transfusion-transmitted case reports further highlighted the limitation of the routine bacterial screening of platelet products. It was felt that newer technologies, such as pathogen inactivation, may represent a more reliable process, with a higher level of safety. The panel thus recommended that the Transfusion Medicine community may need to change its thinking (paradigm) about bacterial detection, toward the possibility of the pathogen inactivation of blood products, to deal with the bacterial contamination issue. It was suggested, where permitted by regulatory agencies, that blood centers should consider adopting first-generation pathogen inactivation systems as a more effective approach to reducing the risk of transfusion-associated sepsis than some of the approaches currently available.

Conventional CD4+ T cells present bacterial antigens to induce cytotoxic and memory CD8+ T cell responses.

PubMed

Cruz-Adalia, Aránzazu; Ramirez-Santiago, Guillermo; Osuna-Pérez, Jesús; Torres-Torresano, Mónica; Zorita, Virgina; Martínez-Riaño, Ana; Boccasavia, Viola; Borroto, Aldo; Martínez Del Hoyo, Gloria; González-Granado, José María; Alarcón, Balbino; Sánchez-Madrid, Francisco; Veiga, Esteban

2017-11-17

Bacterial phagocytosis and antigen cross-presentation to activate CD8 + T cells are principal functions of professional antigen presenting cells. However, conventional CD4 + T cells also capture and kill bacteria from infected dendritic cells in a process termed transphagocytosis (also known as transinfection). Here, we show that transphagocytic T cells present bacterial antigens to naive CD8 + T cells, which proliferate and become cytotoxic in response. CD4 + T-cell-mediated antigen presentation also occurs in vivo in the course of infection, and induces the generation of central memory CD8 + T cells with low PD-1 expression. Moreover, transphagocytic CD4 + T cells induce protective anti-tumour immune responses by priming CD8 + T cells, highlighting the potential of CD4 + T cells as a tool for cancer immunotherapy.

The influence of bacteria on struvite crystal habit and its importance in urinary stone formation

NASA Astrophysics Data System (ADS)

Clapham, L.; McLean, R. J. C.; Nickel, J. C.; Downey, J.; Costerton, J. W.

1990-07-01

Infection-induced urinary stones form as a result of a urinary tract infection by urease-producing bacteria. These stones are not totally crystalline in nature but rather consist of an agglomeration of bacteria, organic matrix, and crystal of struvite (MgNH 4PO 4· 6H 2O). Crystal formation is related to the ability of the bacteria to effect an increase in the urine pH. Another equally important bacterial role lies in their formation of a 'biofilm' which later becomes the organic matrix constituent of the stone. Results of the present in vitro study indicate that crystals are formed more readily if produced within the bacterial biofilm than in the surrounding urine. It is proposed that supersaturation, due in part to a bacterial-induced pH increase and in part to the metal binding tendency of the biofilm, leads to crystal formation via a gel growth mechanism within the biofilm itself. In time further bacterial cell division, microcolony.

Recognition of bacterial plant pathogens: local, systemic and transgenerational immunity.

PubMed

Henry, Elizabeth; Yadeta, Koste A; Coaker, Gitta

2013-09-01

Bacterial pathogens can cause multiple plant diseases and plants rely on their innate immune system to recognize and actively respond to these microbes. The plant innate immune system comprises extracellular pattern recognition receptors that recognize conserved microbial patterns and intracellular nucleotide binding leucine-rich repeat (NLR) proteins that recognize specific bacterial effectors delivered into host cells. Plants lack the adaptive immune branch present in animals, but still afford flexibility to pathogen attack through systemic and transgenerational resistance. Here, we focus on current research in plant immune responses against bacterial pathogens. Recent studies shed light onto the activation and inactivation of pattern recognition receptors and systemic acquired resistance. New research has also uncovered additional layers of complexity surrounding NLR immune receptor activation, cooperation and sub-cellular localizations. Taken together, these recent advances bring us closer to understanding the web of molecular interactions responsible for coordinating defense responses and ultimately resistance. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Biological disintegration of microalgae for biomethane recovery-prediction of biodegradability and computation of energy balance.

PubMed

Kavitha, S; Yukesh Kannah, R; Rajesh Banu, J; Kaliappan, S; Johnson, M

2017-11-01

The present study investigates the synergistic effect of combined bacterial disintegration on mixed microalgal biomass for energy efficient biomethane generation. The rate of microalgal biomass lysis, enhanced biodegradability, and methane generation were used as indices to assess efficiency of the disintegration. A maximal dissolvable organics release and algal biomass lysis rate of about 1100, 950 and 800mg/L and 26, 23 and 18% was achieved in PA+C (protease, amylase+cellulase secreting bacteria), C (cellulase alone) and PA (protease, amylase) microalgal disintegration. During anaerobic fermentation, a greater production of volatile fatty acids (1000mg/L) was noted in PA+C bacterial disintegration of microalgal biomass. PA+C bacterial disintegration improve the amenability of microalgal biomass to biomethanation process with higher biodegradability of about 0.27gCOD/gCOD, respectively. The energy balance analysis of this combined bacterial disintegration of microalgal biomass provides surplus positive net energy (1.14GJ/d) by compensating the input energy requirements. Copyright © 2017 Elsevier Ltd. All rights reserved.

Community Structure Analysis and Biodegradation Potential of Aniline-Degrading Bacteria in Biofilters.

PubMed

Hou, Luanfeng; Wu, Qingping; Gu, Qihui; Zhou, Qin; Zhang, Jumei

2018-07-01

Aniline has aroused general concern owing to its strong toxicity and widespread distribution in water and soil. In the present study, the bacterial community composition before and after aniline acclimation was investigated. High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the structure of the bacterial community during the aniline acclimation period. Bacillus, Lactococcus, and Enterococcus were the dominant bacteria in biologically activated carbon before acclimation. However, the proportions of Pseudomonas, Thermomonas, and Acinetobacter increased significantly and several new bacterial taxa appeared after aniline acclimation, indicating that aniline acclimation had a strong impact on the bacterial community structure of biological activated carbon samples. Strain AN-1 accounted for the highest number of colonies on incubation plates and was identified as Acinetobacter sp. according to phylogenetic analysis of the 16S ribosomal ribonucleic acid gene sequence. Strain AN-1 was able to grow on aniline at pH value 4.0-10.0 and showed high aniline-degrading ability at neutral pH.

Identification of Naegleria fowleri in warm ground water aquifers.

PubMed

Laseke, Ian; Korte, Jill; Lamendella, Regina; Kaneshiro, Edna S; Marciano-Cabral, Francine; Oerther, Daniel B

2010-01-01

The free-living amoeba Naegleria fowleri was identified as the etiological agent of primary amoebic meningoencephalitis that caused the deaths of two children in Peoria, Arizona, in autumn of 2002. It was suspected that the source of N. fowleri was the domestic water supply, which originates from ground water sources. In this study, ground water from the greater Phoenix Metropolitan area was tested for the presence of N. fowleri using a nested polymerase chain reaction approach. Phylogenetic analyses of 16S rRNA sequences of bacterial populations in the ground water were performed to examine the potential link between the presence of N. fowleri and bacterial groups inhabiting water wells. The results showed the presence of N. fowleri in five out of six wells sampled and in 26.6% of all ground water samples tested. Phylogenetic analyses showed that beta- and gamma-proteobacteria were the dominant bacterial populations present in the ground water. Bacterial community analyses revealed a very diverse community structure in ground water samples testing positive for N. fowleri.

The ancillary protein 1 of Streptococcus pyogenes FCT-1 pili mediates cell adhesion and biofilm formation through heterophilic as well as homophilic interactions

PubMed Central

Becherelli, Marco; Manetti, Andrea G O; Buccato, Scilla; Viciani, Elisa; Ciucchi, Laura; Mollica, Giulia; Grandi, Guido; Margarit, Imma

2012-01-01

Summary Gram-positive pili are known to play a role in bacterial adhesion to epithelial cells and in the formation of biofilm microbial communities. In the present study we undertook the functional characterization of the pilus ancillary protein 1 (AP1_M6) from Streptococcus pyogenes isolates expressing the FCT-1 pilus variant, known to be strong biofilm formers. Cell binding and biofilm formation assays using S. pyogenes in-frame deletion mutants, Lactococcus expressing heterologous FCT-1 pili and purified recombinant AP1_M6, indicated that this pilin is a strong cell adhesin that is also involved in bacterial biofilm formation. Moreover, we show that AP1_M6 establishes homophilic interactions that mediate inter-bacterial contact, possibly promoting bacterial colonization of target epithelial cells in the form of three-dimensional microcolonies. Finally, AP1_M6 knockout mutants were less virulent in mice, indicating that this protein is also implicated in GAS systemic infection. PMID:22320452

Stratification Modelling of Key Bacterial Taxa Driven by Metabolic Dynamics in Meromictic Lakes.

PubMed

Zhu, Kaicheng; Lauro, Federico M; Su, Haibin

2018-06-22

In meromictic lakes, the water column is stratified into distinguishable steady layers with different physico-chemical properties. The bottom portion, known as monimolimnion, has been studied for the functional stratification of microbial populations. Recent experiments have reported the profiles of bacterial and nutrient spatial distributions, but quantitative understanding is invoked to unravel the underlying mechanism of maintaining the discrete spatial organization. Here a reaction-diffusion model is developed to highlight the spatial pattern coupled with the light-driven metabolism of bacteria, which is resilient to a wide range of dynamical correlation between bacterial and nutrient species at the molecular level. Particularly, exact analytical solutions of the system are presented together with numerical results, in a good agreement with measurements in Ace lake and Rogoznica lake. Furthermore, one quantitative prediction is reported here on the dynamics of the seasonal stratification patterns in Ace lake. The active role played by the bacterial metabolism at microscale clearly shapes the biogeochemistry landscape of lake-wide ecology at macroscale.

Influence of nanoscale topology on bactericidal efficiency of black silicon surfaces

NASA Astrophysics Data System (ADS)

Linklater, Denver P.; Khuong Duy Nguyen, Huu; Bhadra, Chris M.; Juodkazis, Saulius; Ivanova, Elena P.

2017-06-01

The nanostructuring of materials to create bactericidal and antibiofouling surfaces presents an exciting alternative to common methods of preventing bacterial adhesion. The fabrication of synthetic bactericidal surfaces has been inspired by the anti-wetting and anti-biofouling properties of insect wings, and other topologies found in nature. Black silicon is one such synthetic surfaces which has established bactericidal properties. In this study we show that time-dependent plasma etching of silicon wafers using 15, 30, and 45 min etching intervals, is able to produce different surface geometries with linearly increasing heights of approximately 280, 430, and 610 nm, respectively. After incubation on these surfaces with Gram-positive Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa bacterial cells it was established that smaller, more densely packed pillars exhibited the greatest bactericidal activity with 85% and 89% inactivation of bacterial cells, respectively. The decrease in the pillar heights, pillar cap diameter and inter-pillar spacing corresponded to a subsequent decrease in the number of attached cells for both bacterial species.

Subcellular Localization of Pseudomonas syringae pv. tomato Effector Proteins in Plants.

PubMed

Aung, Kyaw; Xin, Xiufang; Mecey, Christy; He, Sheng Yang

2017-01-01

Animal and plant pathogenic bacteria use type III secretion systems to translocate proteinaceous effectors to subvert innate immunity of their host organisms. Type III secretion/effector systems are a crucial pathogenicity factor in many bacterial pathogens of plants and animals. Pseudomonas syringae pv. tomato (Pst) DC3000 injects a total of 36 protein effectors that target a variety of host proteins. Studies of a subset of Pst DC3000 effectors demonstrated that bacterial effectors, once inside the host cell, are localized to different subcellular compartments, including plasma membrane, cytoplasm, mitochondria, chloroplast, and Trans-Golgi network, to carry out their virulence functions. Identifying the subcellular localization of bacterial effector proteins in host cells could provide substantial clues to understanding the molecular and cellular basis of the virulence activities of effector proteins. In this chapter, we present methods for transient or stable expression of bacterial effector proteins in tobacco and/or Arabidopsis thaliana for live cell imaging as well as confirming the subcellular localization in plants using fluorescent organelle markers or chemical treatment.

Contingent interactions among biofilm-forming bacteria determine preservation or decay in the first steps toward fossilization of marine embryos.

PubMed

Raff, Elizabeth C; Andrews, Mary E; Turner, F Rudolf; Toh, Evelyn; Nelson, David E; Raff, Rudolf A

2013-01-01

Fossils of soft tissues provide important records of early animals and embryos, and there is substantial evidence for a role for microbes in soft tissue fossilization. We are investigating the initial events in interactions of bacteria with freshly dead tissue, using marine embryos as a model system. We previously found that microbial invasion can stabilize embryo tissue that would otherwise disintegrate in hours or days by generating a bacterial pseudomorph, a three dimensional biofilm that both replaces the tissue and replicates its morphology. In this study, we sampled seawater at different times and places near Sydney, Australia, and determined the range and frequency of different taphonomic outcomes. Although destruction was most common, bacteria in 35% of seawater samples yielded morphology‐preserving biofilms. We could replicate the taphonomic pathways seen with seawater bacterial communities using single cultured strains of marine gammaproteobacteria. Each given species reproducibly generated a consistent taphonomic outcome and we identified species that yielded each of the distinct pathways produced by seawater bacterial communities. Once formed,bacterial pseudomorphs are stable for over a year and resist attack by other bacteria and destruction by proteases and other lytic enzymes. Competition studies showed that the initial action of a pseudomorphing strain can be blocked by a strain that destroys tissues. Thus embryo preservation in nature may depend on contingent interactions among bacterial species that determine if pseudomorphing occurs.We used Artemia nauplius larvae to show that bacterial biofilm replacement of tissue is not restricted to embryos, but is relevant for preservation of small multicellular organisms. We present a model for bacterial self‐assembly of large‐scale three‐dimensional tissue pseudomorphs, based on smallscaleinteractions among individual bacterial cells to form local biofilms at structural boundaries within the tissue. Localbiofilms then conjoin to generate the pseudomorph.

Bacterial Viability within Dental Calculus: An Untrodden, Inquisitive Clinico-Patho- Microbiological Research.

PubMed

Gupta, Swati; Jain, P K; Kumra, Madhumani; Rehani, Shweta; Mathias, Yulia; Gupta, Ramakant; Mehendiratta, Monica; Chander, Anil

2016-07-01

Chronic inflammatory periodontal diseases i.e. gingivitis and periodontitis are one of the most common afflictions faced by human beings. Dental plaque, which is a pool of pathogenic microorganisms, remains to be current mainstay in etiopathogenesis. Dental calculus, which is a mineralized product of this plaque remains ignored and is considered merely as an ash heap of minor significance. However, the intriguing array in disease etiopathogenesis bulldozed researchers to suspect the role of calculus in disease chrysalis but still the viability of bacteria inside calculus and thus its pathogenicity remains an intricacy; the answer to which lies in the Pandora's Box. The present study was undertaken to investigate the viability of bacteria within dental calculus along with their identification. Also, to classify dental calculus on the basis of mineralization and to observe the variation of viable microflora found in dental calculus with the extent of mineralization and disease severity. A total of 60 samples were obtained, by harvesting two samples of supragingival calculus from each patient having chronic inflammatory periodontal disease. These samples were divided into two groups (Group A and Group B). Samples of Group A were kept non-irradiated and samples of Group B were exposed to UV radiation. The samples were categorized into less, moderately and highly mineralized according to the force required for crushing them. All the crushed calculus samples were then divided into three parts. These were used for dark-field microscopy, gram staining and bacterial cultures. Bacterial identification of the cultures obtained was also carried out by performing various biochemical assays. The present study revealed the presence of motile spirochaetes within the samples under dark-field microscope. Gram staining revealed presence of numerous gram positive cocci and gram negative bacilli. Bacterial cultures showed growth of variety of aerobic and capnophilic microorganisms. The present study concludes the presence of viable aerobic and capnophilic bacteria inside dental calculus which may reside within the lacunae and channels in the calculus.

Acute bacterial prostatitis with osteomyelitis

PubMed Central

Nargund, V H; Stewart, P A Hamilton

1995-01-01

This short case presentation concerns the simultaneous occurrence of acute bacterial prostatitis and osteomyelitis due to staphylococcal bacteraemia hitherto unrecorded in the literature. ImagesFigure 1Figure 2 PMID:7629772

Predictive value of decoy receptor 3 in postoperative nosocomial bacterial meningitis.

PubMed

Liu, Yong-Juan; Shao, Li-Hua; Wang, Qian; Zhang, Jian; Ma, Rui-Ping; Liu, Hai-Hong; Dong, Xiao-Meng; Ma, Li-Xian

2014-11-03

Nosocomial bacterial meningitis requires timely treatment, but what is difficult is the prompt and accurate diagnosis of this disease. The aim of this study was to assess the potential role of decoy receptor 3 (DcR3) levels in the differentiation of bacterial meningitis from non-bacterial meningitis. A total of 123 patients were recruited in this study, among them 80 patients being with bacterial meningitis and 43 patients with non-bacterial meningitis. Bacterial meningitis was confirmed by bacterial culture of cerebrospinal fluid (CSF) culture and enzyme-linked immunosorbent assay (ELISA) was used to detect the level of DcR3 in CSF. CSF levels of DcR3 were statistically significant between patients with bacterial meningitis and those with non-bacterial meningitis (p<0.001). A total of 48.75% of patients with bacterial meningitis received antibiotic>24 h before CSF sampling, which was much higher than that of non-bacterial meningitis. CSF leucocyte count yielded the highest diagnostic value, with an area under the receiver operating characteristic curve (ROC) of 0.928, followed by DcR3. At a critical value of 0.201 ng/mL for DcR3, the sensitivity and specificity were 78.75% and 81.40% respectively. DcR3 in CSF may be a valuable predictor for differentiating patients with bacterial meningitis from those with non-bacterial meningitis. Further studies are needed for the validation of this study.

Macrophage Autophagy and Bacterial Infections

PubMed Central

Bah, Aïcha; Vergne, Isabelle

2017-01-01

Autophagy is a well-conserved lysosomal degradation pathway that plays key roles in bacterial infections. One of the most studied is probably xenophagy, the selective capture and degradation of intracellular bacteria by lysosomes. However, the impact of autophagy goes beyond xenophagy and involves intensive cross-talks with other host defense mechanisms. In addition, autophagy machinery can have non-canonical functions such as LC3-associated phagocytosis. In this review, we intend to summarize the current knowledge on the many functions of autophagy proteins in cell defenses with a focus on bacteria–macrophage interaction. We also present the strategies developed by pathogens to evade or to exploit this machinery in order to establish a successful infection. Finally, we discuss the opportunities and challenges of autophagy manipulation in improving therapeutics and vaccines against bacterial pathogens. PMID:29163544

Cultivation of a bacterial consortium with the potential to degrade total petroleum hydrocarbon using waste activated sludge.

PubMed

Sivakumar, S; Song, Y C; Kim, S H; Jang, S H

2015-11-01

Waste activated sludge was aerobically treated to demonstrate multiple uses such as cultivating an oil degrading bacterial consortium; studying the influence of a bulking agent (peat moss) and total petroleum hydrocarbon concentration on bacterial growth and producing a soil conditioner using waste activated sludge. After 30 days of incubation, the concentration of oil-degrading bacteria was 4.3 x 10(8) CFU g(-1) and 4.5 x 10(8) CFU g(-1) for 5 and 10 g of total petroleum hydrocarbon, respectively, in a mixture of waste activated sludge (1 kg) and peat moss (0.1 kg). This accounts for approximately 88.4 and 91.1%, respectively, of the total heterotrophic bacteria (total-HB). The addition of bulking agent enhanced total-HB population and total petroleum hydrocarbon-degrading bacterial population. Over 90% of total petroleum hydrocarbon degradation was achieved by the mixture of waste activated sludge, bulking agent and total petroleum hydrocarbon. The results of physico-chemical parameters of the compost (waste activated sludge with and without added peat moss compost) and a substantial reduction in E. coli showed that the use of this final product did not exhibit risk when used as soil conditioner. Finally, the present study demonstrated that cultivation of total petroleum hydrocarbon-degrading bacterial consortium and production of compost from waste activated sludge by aerobic treatment was feasible.

Molecular analysis of bacterial communities in raw cow milk and the impact of refrigeration on its structure and dynamics.

PubMed

Raats, Dina; Offek, Maya; Minz, Dror; Halpern, Malka

2011-05-01

The impact of refrigeration on raw cow milk bacterial communities in three farm bulk tanks and three dairy plant silo tanks was studied using two methods: DGGE and cloning. Both methods demonstrated that bacterial taxonomic diversity decreased during refrigeration. Gammaproteobacteria, especially Pseudomonadales, dominated the milk after refrigeration. Farm samples and dairy plant samples differed in their microbial community composition, the former showing prevalence of Gram-positive bacteria affiliated with the classes Bacilli, Clostridia and Actinobacteria, the latter showing prevalence of Gram-negative species belonging to the Gammaproteobacteria class. Actinobacteria prevalence in the farm milk samples immediately after collection stood at about 25% of the clones. A previous study had found that psychrotolerant Actinobacteria identified in raw cow milk demonstrated both lipolytic and proteolytic enzymatic activity. Thus, we conclude that although Pseudomonadales play an important role in milk spoilage after long periods of cold incubation, Actinobacteria occurrence may play an important role when assessing the quality of milk arriving at the dairy plant from different farms. As new cooling technologies reduce the initial bacterial counts of milk to very low levels, more sensitive and efficient methods to evaluate the bacterial quality of raw milk are required. The present findings are an important step towards achieving this goal. Copyright © 2010 Elsevier Ltd. All rights reserved.

A new mathematical model of bacterial interactions in two-species oral biofilms

PubMed Central

Martin, Bénédicte; Tamanai-Shacoori, Zohreh; Bronsard, Julie; Ginguené, Franck; Meuric, Vincent

2017-01-01

Periodontitis are bacterial inflammatory diseases, where the bacterial biofilms present on the tooth-supporting tissues switch from a healthy state towards a pathogenic state. Among bacterial species involved in the disease, Porphyromonas gingivalis has been shown to induce dysbiosis, and to induce virulence of otherwise healthy bacteria like Streptococcus gordonii. During biofilm development, primary colonizers such as S. gordonii first attach to the surface and allow the subsequent adhesion of periodontal pathogens such as P. gingivalis. Interactions between those two bacteria have been extensively studied during the adhesion step of the biofilm. The aim of the study was to understand interactions of both species during the growing phase of the biofilm, for which little knowledge is available, using a mathematical model. This two-species biofilm model was based on a substrate-dependent growth, implemented with damage parameters, and validated thanks to data obtained on experimental biofilms. Three different hypothesis of interactions were proposed and assayed using this model: independence, competition between both bacteria species, or induction of toxicity by one species for the other species. Adequacy between experimental and simulated biofilms were found with the last hypothetic mathematical model. This new mathematical model of two species bacteria biofilms, dependent on different substrates for growing, can be applied to any bacteria species, environmental conditions, or steps of biofilm development. It will be of great interest for exploring bacterial interactions in biofilm conditions. PMID:28253369

Simultaneous amplification of two bacterial genes: more reliable method of Helicobacter pylori detection in microbial rich dental plaque samples.

PubMed

Chaudhry, Saima; Idrees, Muhammad; Izhar, Mateen; Butt, Arshad Kamal; Khan, Ayyaz Ali

2011-01-01

Polymerase Chain reaction (PCR) assay is considered superior to other methods for detection of Helicobacter pylori (H. pylori) in oral cavity; however, it also has limitations when sample under study is microbial rich dental plaque. The type of gene targeted and number of primers used for bacterial detection in dental plaque samples can have a significant effect on the results obtained as there are a number of closely related bacterial species residing in plaque biofilm. Also due to high recombination rate of H. pylori some of the genes might be down regulated or absent. The present study was conducted to determine the frequency of H. pylori colonization of dental plaque by simultaneously amplifying two genes of the bacterium. One hundred dental plaque specimens were collected from dyspeptic patients before their upper gastrointestinal endoscopy and presence of H. pylori was determined through PCR assay using primers targeting two different genes of the bacterium. Eighty-nine of the 100 samples were included in final analysis. With simultaneous amplification of two bacterial genes 51.6% of the dental plaque samples were positive for H. pylori while this prevalence increased to 73% when only one gene amplification was used for bacterial identification. Detection of H. pylori in dental plaque samples is more reliable when two genes of the bacterium are simultaneously amplified as compared to one gene amplification only.

Experimental warming effects on the bacterial community structure and diversity

NASA Astrophysics Data System (ADS)

Kim, W.; Han, S.; Adams, J.; Son, Y.

2014-12-01

The objective of this study is to investigate the responses of soil bacterial community to future temperature increase by conducting open-field warming experiment. We conducted an open-field experimental warming system using infra-red heater in 2011 and regulated the temperature of warmed plots by 3oC higher than that of control plots constantly. The seeds of Pinus densiflora, Abies holophylla, Abies koreana, Betula costata, Quercus variabilis, Fraxinus rhynchophylla, and Zelkova serrata were planted in each 1 m × 1 m plot (n=3) in April, 2012. We collected soil samples from the rhizosphere of 7 tree species. DNA was extracted and PCR-amplified for the bacterial 16S gene targeting V1-V3 region. The paired-end sequencing was performed at Beijing Genome Institute (BGI, Hong Kong, China) using 2× 100 bp Hiseq2000 (Illumina). This study aimed to answer the following prediction/hypothesis: 1) Experimental warming will change the structure of soil bacterial community, 2) There will be distinct 'indicator group' which response to warming treatment relatively more sensitive than other groups. 3) Warming treatment will enhance the microbial activity in terms of soil respiration. 4) The rhizoplane bacterial communities for each of 7 tree species will show different response pattern to warming treatment. Since the sequence data does not arrive before the submission deadline, therefore, we would like to present the results and discussions on December 2014, AGU Fall Meeting.

Epidemiological study of relapsing fever borreliae detected in Haemaphysalis ticks and wild animals in the western part of Japan.

PubMed

Furuno, Kiwa; Lee, Kyunglee; Itoh, Yukie; Suzuki, Kazuo; Yonemitsu, Kenzo; Kuwata, Ryusei; Shimoda, Hiroshi; Watarai, Masahisa; Maeda, Ken; Takano, Ai

2017-01-01

The genus Borrelia comprises arthropod-borne bacteria, which are infectious agents in vertebrates. They are mainly transmitted by ixodid or argasid ticks. In Hokkaido, Japan, Borrelia spp. were found in deer and Haemaphysalis ticks between 2011 and 2013; however, the study was limited to a particular area. Therefore, in the present study, we conducted large-scale surveillance of ticks and wild animals in the western part of the main island of Japan. We collected 6,407 host-seeking ticks from two regions and 1,598 larvae obtained from 32 engorged female ticks and examined them to elucidate transovarial transmission. In addition, we examined whole blood samples from 190 wild boars and 276 sika deer, as well as sera from 120 wild raccoons. We detected Borrelia spp. in Haemaphysalis flava, Haemaphysalis megaspinosa, Haemaphysalis kitaokai, Haemaphysalis longicornis, and Haemaphysalis formosensis. In addition, we isolated a strain from H. megaspinosa using Barbour-Stoenner-Kelly medium. The minimum infection rate of ticks was less than 5%. Transovarial transmission was observed in H. kitaokai. Phylogenetic analysis of the isolated strain and DNA fragments amplified from ticks identified at least four bacterial genotypes, which corresponded to the tick species detected. Bacteria were detected in 8.4%, 15%, and 0.8% of wild boars, sika deer, and raccoons, respectively. In this study, we found seasonal differences in the prevalence of bacterial genotypes in sika deer during the winter and summer. The tick activity season corresponds to the season with a high prevalence of animals. The present study suggests that a particular bacterial genotype detected in this study are defined by a particular tick species in which they are present.

Characterizing endophytic competence and plant growth promotion of bacterial endophytes inhabiting the seed endosphere of Rice.

PubMed

Walitang, Denver I; Kim, Kiyoon; Madhaiyan, Munusamy; Kim, Young Kee; Kang, Yeongyeong; Sa, Tongmin

2017-10-26

Rice (Oryza sativa L. ssp. indica) seeds as plant microbiome present both an opportunity and a challenge to colonizing bacterial community living in close association with plants. Nevertheless, the roles and activities of bacterial endophytes remain largely unexplored and insights into plant-microbe interaction are compounded by its complexity. In this study, putative functions or physiological properties associated with bacterial endophytic nature were assessed. Also, endophytic roles in plant growth and germination that may allow them to be selectively chosen by plants were also studied. The cultivable seed endophytes were dominated by Proteobacteria particularly class Gammaproteobacteria. Highly identical type strains were isolated from the seed endosphere regardless of the rice host's physiological tolerance to salinity. Among the type strains, Flavobacterium sp., Microbacterium sp. and Xanthomonas sp. were isolated from the salt-sensitive and salt-tolerant cultivars. PCA-Biplot ordination also showed that specific type strains isolated from different rice cultivars have distinguishing similar characteristics. Flavobacterium sp. strains are phosphate solubilizers and indole-3-acetic acid producers with high tolerance to salinity and osmotic stress. Pseudomonas strains are characterized as high siderophore producers while Microbacterium sp. and Xanthomonas sp. strains have very high pectinase and cellulase activity. Among the physiological traits of the seed endophytes, bacterial pectinase and cellulase activity are positively correlated as well as salt and osmotic tolerance. Overall characterization shows that majority of the isolates could survive in 4-8% salt concentration as well as in 0.6 M and 1.2 M sucrose solution. The activities of catalase, pectinase and cellulase were also observed in almost all of the isolates indicating the importance of these characteristics for survival and colonization into the seed endosphere. Seed bacterial endophytes also showed promising plant growth promoting activities including hormone modulation, nitrogen fixation, siderophore production and phosphate solubilization. Though many of the isolates possess similar PGP and endophytic physiological traits, this study shows some prominent and distinguishing traits among bacterial groups indicating key determinants for their success as endophytes in the rice seed endosphere. Rice seeds are also inhabited by bacterial endophytes that promote growth during early seedling development.

IMPACT OF MICROBIOLOGICAL CHANGES ON SPONTANEOUS BACTERIAL PERITONITIS IN THREE DIFFERENT PERIODS OVER 17 YEARS.

PubMed

Almeida, Paulo Roberto Lerias de; Leão, Gabriel Stefani; Gonçalves, Charlles David Gonçalves; Picon, Rafael Veiga; Tovo, Cristiane Valle

2018-01-01

Spontaneous bacterial peritonitis is a serious complication in cirrhotic patients, and changes in the microbiological characteristics reported in the last years are impacting the choice of antibiotic used for treatment. The aim of the present study is to evaluate the changes in the epidemiology and bacterial resistance of the germs causing spontaneous bacterial peritonitis over three different periods over 17 years. All cirrhotic patients with spontaneous bacterial peritonitis and positive culture of ascites fluid were retrospectively studied in a reference Hospital in Southern Brazil. Three periods were ramdomly evaluated: 1997-1998, 2002-2003 and 2014-2015. The most frequent infecting organisms and the sensitivity in vitro to antibiotics were registered. In the first period (1997-1998) there were 33 cases, the most common were: E. coli in 13 (36.11%), Staphylococcus coagulase-negative in 6 (16.66%), K. pneumoniae in 5 (13.88%), S. aureus in 4 (11.11%) and S. faecalis in 3 (8.33%). In the second period (2002-2003), there were 43 cases, the most frequent were: Staphylococus coagulase-negative in 16 (35.55%), S. aureus in 8 (17.77%), E. coli in 7 (15.55%) and K. pneumoniae in 3 (6.66%). In the third period (2014-2015) there were 58 cases (seven with two bacteria), the most frequent were: E. coli in 15 (23.1%), S. viridans in 12 (18.5%), K. pneumoniae in 10 (15.4%) and E. faecium 5 (7.7%). No one was using antibiotic prophylaxis. Considering all staphylococci, the prevalence increased to rates of the order of 50% in the second period, with a reduction in the third period evaluated. Likewise, the prevalence of resistant E. coli increased, reaching 14%. There was a modification of the bacterial population causing spontaneous bacterial peritonitis, with high frequency of gram-positive organisms, as well as an increase in the resistance to the traditionally recommended antibiotics. This study suggests a probable imminent inclusion of a drug against gram-positive organisms in the empiric treatment of spontaneous bacterial peritonitis.

Death Becomes Them: Bacterial Community Dynamics and Stilbene Antibiotic Production in Cadavers of Galleria mellonella Killed by Heterorhabditis and Photorhabdus spp.

PubMed Central

Wollenberg, Amanda C.; Slough, Greg; Hoinville, Megan E.

2016-01-01

ABSTRACT Insect larvae killed by entomopathogenic nematodes are thought to contain bacterial communities dominated by a single bacterial genus, that of the nematode's bacterial symbiont. In this study, we used next-generation sequencing to profile bacterial community dynamics in greater wax moth (Galleria mellonella) larvae cadavers killed by Heterorhabditis nematodes and their Photorhabdus symbionts. We found that, although Photorhabdus strains did initially displace an Enterococcus-dominated community present in uninfected G. mellonella insect larvae, the cadaver community was not static. Twelve days postinfection, Photorhabdus shared the cadaver with Stenotrophomonas species. Consistent with this result, Stenotrophomonas strains isolated from infected cadavers were resistant to Photorhabdus-mediated toxicity in solid coculture assays. We isolated and characterized a Photorhabdus-produced antibiotic from G. mellonella cadavers, produced it synthetically, and demonstrated that both the natural and synthetic compounds decreased G. mellonella-associated Enterococcus growth, but not Stenotrophomonas growth, in vitro. Finally, we showed that the Stenotrophomonas strains described here negatively affected Photorhabdus growth in vitro. Our results add an important dimension to a broader understanding of Heterorhabditis-Photorhabdus biology and also demonstrate that interspecific bacterial competition likely characterizes even a theoretically monoxenic environment, such as a Heterorhabditis-Photorhabdus-parasitized insect cadaver. IMPORTANCE Understanding, and eventually manipulating, both human and environmental health depends on a complete accounting of the forces that act on and shape microbial communities. One of these underlying forces is hypothesized to be resource competition. A resource that has received little attention in the general microbiological literature, but likely has ecological and evolutionary importance, is dead/decaying multicellular organisms. Metazoan cadavers, including those of insects, are ephemeral and nutrient-rich environments, where resource competition might shape interspecific macrobiotic and microbiotic interactions. This study is the first to use a next-generation sequencing approach to study the community dynamics of bacteria within a model insect cadaver system: insect larvae parasitized by entomopathogenic nematodes and their bacterial symbionts. By integrating bioinformatic, biochemical, and classic in vitro microbiological approaches, we have provided mechanistic insight into how antibiotic-mediated bacterial interactions may shape community dynamics within insect cadavers. PMID:27451445

Effects of Bacterial Microflora of the Lower Digestive Tract of Free-Range Waterfowl on Influenza Virus Activation ▿

PubMed Central

King, Marcus D.; Guentzel, M. Neal; Arulanandam, Bernard P.; Bodour, Adria A.; Brahmakshatriya, Vinayak; Lupiani, Blanca; Chambers, James P.

2011-01-01

Proteolytic cleavage activation of influenza virus hemagglutinin (HA0) is required for cell entry via receptor-mediated endocytosis. Despite numerous studies describing bacterial protease-mediated influenza A viral activation in mammals, very little is known about the role of intestinal bacterial flora of birds in hemagglutinin cleavage/activation. Therefore, the cloaca of wild waterfowl was examined for (i) representative bacterial types and (ii) their ability to cleave in a “trypsin-like” manner the precursor viral hemagglutinin molecule (HA0). Using radiolabeled HA0, bacterial secretion-mediated trypsin-like conversion of HA0 to HA1 and HA2 peptide products was observed to various degrees in 42 of 44 bacterial isolates suggestive of influenza virus activation in the cloaca of wild waterfowl. However, treatment of uncleaved virus with all bacterial isolates gave rise to substantially reduced emergent virus progeny compared with what was expected. Examination of two isolates exhibiting pronounced trypsin-like conversion of HA0 to HA1 and HA2 peptide products and low infectivity revealed lipase activity to be present. Because influenza virus possesses a complex lipid envelope, the presence of lipid hydrolase activity could in part account for the observed less-than-expected level of viable progeny. A thorough characterization of respective isolate protease HA0 hydrolysis products as well as other resident activities (i.e., lipase) is ongoing such that the role of these respective contributors in virus activation/inactivation can be firmly established. PMID:21531837

454 pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas.

PubMed

Li, Yuanyuan; Chen, Longqian; Wen, Hongyu; Zhou, Tianjian; Zhang, Ting; Gao, Xiali

2014-03-28

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coalmining reclamation areas was suggested.

Substrate utilization profiles of bacterial strains in plankton from the River Warnow, a humic and eutrophic river in north Germany.

PubMed

Freese, Heike M; Eggert, Anja; Garland, Jay L; Schumann, Rhena

2010-01-01

Bacteria are very important degraders of organic substances in aquatic environments. Despite their influential role in the carbon (and many other element) cycle(s), the specific genetic identity of active bacteria is mostly unknown, although contributing phylogenetic groups had been investigated. Moreover, the degree to which phenotypic potential (i. e., utilization of environmentally relevant carbon substrates) is related to the genomic identity of bacteria or bacterial groups is unclear. The present study compared the genomic fingerprints of 27 bacterial isolates from the humic River Warnow with their ability to utilize 14 environmentally relevant substrates. Acetate was the only substrate utilized by all bacterial strains. Only 60% of the strains respired glucose, but this substrate always stimulated the highest bacterial activity (respiration and growth). Two isolates, both closely related to the same Pseudomonas sp., also had very similar substrate utilization patterns. However, similar substrate utilization profiles commonly belonged to genetically different strains (e.g., the substrate profile of Janthinobacterium lividum OW6/RT-3 and Flavobacterium sp. OW3/15-5 differed by only three substrates). Substrate consumption was sometimes totally different for genetically related isolates. Thus, the genomic profiles of bacterial strains were not congruent with their different substrate utilization profiles. Additionally, changes in pre-incubation conditions strongly influenced substrate utilization. Therefore, it is problematic to infer substrate utilization and especially microbial dissolved organic matter transformation in aquatic systems from bacterial molecular taxonomy.

Biogeographic Patterns Between Bacterial Phyllosphere Communities of the Southern Magnolia (Magnolia grandiflora) in a Small Forest.

PubMed

Stone, Bram W G; Jackson, Colin R

2016-05-01

The phyllosphere presents a unique system of discrete and easily replicable surfaces colonized primarily by bacteria. However, the biogeography of bacteria in the phyllosphere is little understood, especially at small to intermediate scales. Bacterial communities on the leaves of 91 southern magnolia (Magnolia grandiflora) trees 1-452 m apart in a small forest plot were analyzed and fragments of the 16S ribosomal RNA (rRNA) gene sequenced using the Illumina platform. Assemblages were dominated by members of the Alphaproteobacteria, Bacteroidetes, and Acidobacteria. Patterns in community composition were measured by both relative abundance (theta) and presence-absence (Jaccard) dissimilarity metrics. Distance-based Moran's eigenvector map analyses of the distance-decay relationship found a significant, positive relationship between each dissimilarity metric and significant eigenfunctions derived from geographic distance between trees, indicating trees that were closer together had more similar bacterial phyllosphere communities. Indirect gradient analyses revealed that several environmental parameters (canopy cover, tree elevation, and the slope and aspect of the ground beneath trees) were significantly related to multivariate ordination scores based on relative bacterial sequence abundances; however, these relationships were not significant when looking at the incidence of bacterial taxa. This suggests that bacterial growth and abundance in the phyllosphere is shaped by different assembly mechanisms than bacterial presence or absence. More broadly, this study demonstrates that the distance-decay relationship applies to phyllosphere communities at local scales, and that environmental parameters as well as neutral forces may both influence spatial patterns in the phyllosphere.

Nanomaterials from bacterial cellulose for antimicrobial wound dressing

NASA Astrophysics Data System (ADS)

Liyaskina, E.; Revin, V.; Paramonova, E.; Nazarkina, M.; Pestov, N.; Revina, N.; Kolesnikova, S.

2017-01-01

Bacterial nanocellulose (BNC) is widely used in biomedical applications. BNC has attracted increasing attention as a novel wound dressing material, but it has no antimicrobial activity. To get over this problem in the present study the BNC was saturated with antibiotic fusidic acid (FA). The subject of the experiment was BNC, produced by bacteria Gluconacetobacter sucrofermentans B-11267. The resulting biocomposites have high antibiotic activity against Staphylococcus aureus and can be used in medicine as a wound dressing. The structure of BNC was analyzed by atomic force microscopy (AFM) and Fourier transform infrared spectroscopy (FTIR).

Pathogenesis of Bacterial Vaginosis: Discussion of Current Hypotheses

PubMed Central

Muzny, Christina A.; Schwebke, Jane R.

2016-01-01

In April 2015, the Division of Microbiology and Infectious Diseases of the National Institute of Allergy and Infectious Diseases hosted an experts technical consultation on bacterial vaginosis (BV), where data regarding controversies over the pathogenesis of BV were discussed. The discussion on the epidemiology and pathogenesis of BV is presented here, and several hypotheses on its pathogenesis are critiqued. Rigorous hypothesis-driven studies are needed to ultimately determine the cause of BV. This information is vital for the prevention and control of this important infection and its adverse public health consequences. PMID:27449868

Chitosanase purified from bacterial isolate Bacillus licheniformis of ruined vegetables displays broad spectrum biofilm inhibition.

PubMed

Muslim, Sahira Nsayef; Al-Kadmy, Israa M S; Hussein, Nadheema Hammood; Mohammed Ali, Alaa Naseer; Taha, Buthainah Mohammed; Aziz, Sarah Naji; Kheraif, Abdulaziz Abdullah Al; Divakar, Darshan Devang; Ramakrishnaiah, Ravikumar

2016-11-01

A number of bacterial species produces chitosanases which has variety of applications because of its high biodegradability, non-toxicity and antimicrobial assets. In the present study chitosanase is purified from new bacterial species Bacillus licheniformis from spoiled vegetable. This novel strain of Bacillus licheniformis isolated from spoilt cucumber and pepper samples has the ability to produce the chitosanase enzyme when grown on chitosan substrate. Study also examined its antibiofilm properties against diverse bacterial species with biofilm forming ability. The purified chitosanase inhibited the biofilm formation ability for all Gram-negative and Gram-positive biofilm-forming bacteria [biofilm producers] tested in this study in congo red agar and microtiter plate's methods. Highly antibiofilm activity of chitosanase was recorded against Pseudomonas aeruginosa followed by Klebsiella pneumoniae with reduction of biofilm formation upto 22 and 29%, respectively compared with [100] % of control. Biofilm formation has multiple role including ability to enhance resistance and self-protection from external stress. This chitosanase has promising benefit as antibiofilm agent against biofilm forming pathogenic bacteria and has promising application as alternative antibiofilm agents to combat the growing number of multidrug resistant pathogen-associated infections, especially in situation where biofilms are involved. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano

PubMed Central

Banskar, Sunil; Bhute, Shrikant S.; Suryavanshi, Mangesh V.; Punekar, Sachin; Shouche, Yogesh S.

2016-01-01

Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals. PMID:27845426

Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano.

PubMed

Banskar, Sunil; Bhute, Shrikant S; Suryavanshi, Mangesh V; Punekar, Sachin; Shouche, Yogesh S

2016-11-15

Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals.

Response of Aquatic Bacterial Communities to Hydraulic Fracturing in Northwestern Pennsylvania: A Five-Year Study.

PubMed

Ulrich, Nikea; Kirchner, Veronica; Drucker, Rebecca; Wright, Justin R; McLimans, Christopher J; Hazen, Terry C; Campa, Maria F; Grant, Christopher J; Lamendella, Regina

2018-04-09

Horizontal drilling and hydraulic fracturing extraction procedures have become increasingly present in Pennsylvania where the Marcellus Shale play is largely located. The potential for long-term environmental impacts to nearby headwater stream ecosystems and aquatic bacterial assemblages is still incompletely understood. Here, we perform high-throughput sequencing of the 16 S rRNA gene to characterize the bacterial community structure of water, sediment, and other environmental samples (n = 189) from 31 headwater stream sites exhibiting different histories of fracking activity in northwestern Pennsylvania over five years (2012-2016). Stream pH was identified as a main driver of bacterial changes within the streams and fracking activity acted as an environmental selector for certain members at lower taxonomic levels within stream sediment. Methanotrophic and methanogenic bacteria (i.e. Methylocystaceae, Beijerinckiaceae, and Methanobacterium) were significantly enriched in sites exhibiting Marcellus shale activity (MSA+) compared to MSA- streams. This study highlighted potential sentinel taxa associated with nascent Marcellus shale activity and some of these taxa remained as stable biomarkers across this five-year study. Identifying the presence and functionality of specific microbial consortia within fracking-impacted streams will provide a clearer understanding of the natural microbial community's response to fracking and inform in situ remediation strategies.

Effect of oral supplementation of the probiotic capsule UB-01BV in the treatment of patients with bacterial vaginosis.

PubMed

Sudha, M Ratna; Maurya, A K

2012-06-01

Bacterial vaginosis (BV) is a common condition affecting millions of women annually and is characterised by a reduction in native lactobacilli. Antimicrobial therapy used to cure the disease is often found to be ineffective. We postulate that the potential probiotic capsule UB-01BV might be efficient in the treatment of BV. In the present study, 30 Indian women diagnosed with BV presenting symptoms such as white discharge, pH greater than 4.7, increased discharge, odour, colour of discharge and pruritus were included. All subjects were assigned to receive two potential probiotic capsules UB-01BV a day for 7 days. At the end of the treatment all subjects showed significant (P<0.001) positive response as revealed by a reduction in vaginosis symptoms. Therefore, the results of the present study provide the first preliminary evidence that the potential probiotic capsule UB-01BV can exert a significant reduction in vaginal infection.

Molecular characterization of soil bacterial community in a perhumid, low mountain forest.

PubMed

Lin, Yu-Te; Whitman, William B; Coleman, David C; Chih-Yu, Chiu

2011-01-01

Forest disturbance often results in changes in soil properties and microbial communities. In the present study, we characterized a soil bacterial community subjected to disturbance using 16S rRNA gene clone libraries. The community was from a disturbed broad-leaved, low mountain forest ecosystem at Huoshaoliao (HSL) located in northern Taiwan. This locality receives more than 4,000 mm annual precipitation, one of the highest precipitations in Taiwan. Based on the Shannon diversity index, Chao1 estimator, richness and rarefaction curve analysis, the bacterial community in HSL forest soils was more diverse than those previously investigated in natural and disturbed forest soils with colder or less humid weather conditions. Analysis of molecular variance also revealed that the bacterial community in disturbed soils significantly differed from natural forest soils. Most of the abundant operational taxonomic units (OTUs) in the disturbed soil community at HSL were less abundant or absent in other soils. The disturbances influenced the composition of bacterial communities in natural and disturbed forests and increased the diversity of the disturbed forest soil community. Furthermore, the warmer and humid weather conditions could also increase community diversity in HSL soils.

Bacterial microleakage at the abutment-implant interface, in vitro study.

PubMed

Larrucea, Carlos; Conrado, Aparicio; Olivares, Denise; Padilla, Carlos; Barrera, Andrea; Lobos, Olga

2018-02-15

In implant rehabilitation, a microspace is created at the abutment-implant interface (AII). Previous research has shown that oral microbiome can proliferate in this microspace and affect periimplant tissues, causing inflammation in peri-implant tissues. Preventing microbial leakages through the AII is therefore an important goal in implantology. To determine the presence of marginal bacterial microleakage at the AII according to the torque applied to the prosthetic implant in vitro. Twenty-five Ticare Inhex internal conical implants (MG Mozo-Grau, Valladolid, España) were connected to a prosthetic abutment using torques of <10, 10, 20, 30, and 30 N and then sealed. The samples were submitted to cycles of occlusal loads and thermocycling, then one sample of each group was observed by micro TC, while the rest were mounted on devices according to the bacterial leakage model with Porphyromonas gingivalis. Bacterial leakage was observed only in the <10 and 10 N torque samples, and the same groups presented poor abutment/implant adjustment as determined by micro-CT. The different torques applied to the abutment-implant system condition the bacterial leakage at the implant interface. No microleakage was observed at 20 and 30 N. © 2018 Wiley Periodicals, Inc.

Human Milk Oligosaccharides Promote the Growth of Staphylococci

PubMed Central

Hunt, K. M.; Preuss, J.; Nissan, C.; Davlin, C. A.; Williams, J. E.; Shafii, B.; Richardson, A. D.; McGuire, M. K.; Bode, L.

2012-01-01

Human milk oligosaccharides (HMO), which constitute a major component of human milk, promote the growth of particular bacterial species in the infant's gastrointestinal tract. We hypothesized that HMO also interact with the bacterial communities present in human milk. To test this hypothesis, two experiments were conducted. First, milk samples were collected from healthy women (n = 16); culture-independent analysis of the bacterial communities was performed, HMO content was analyzed, and the relation between these factors was investigated. A positive correlation was observed between the relative abundance of Staphylococcus and total HMO content (r = 0.66). In a follow-up study, we conducted a series of in vitro growth curve experiments utilizing Staphylococcus aureus or Staphylococcus epidermidis and HMO isolated from human milk. HMO exhibited stimulatory effects on bacterial growth under various nutritional conditions. Analysis of culture supernatants from these experiments revealed that HMO did not measurably disappear from the culture medium, indicating that the growth-enhancing effects were not a result of bacterial metabolism of the HMO. Instead, stimulation of growth caused greater utilization of amino acids in minimal medium. Collectively, the data provide evidence that HMO may promote the growth of Staphylococcus species in the lactating mammary gland. PMID:22562995

Gardnerella vaginalis and anaerobic bacteria in the etiology of bacterial (nonspecific) vaginosis.

PubMed

Spiegel, C A; Davick, P; Totten, P A; Chen, K C; Eschenbach, D A; Amsel, R; Holmes, K K

1983-01-01

G. vaginalis was originally described as the etiologic agent of bacterial vaginosis (nonspecific vaginitis) because it was recovered only from women with signs and symptoms of "bacterial vaginitis" and not from normal controls. Recent data have shown that G. vaginalis is present in normal women but at concentrations lower than the limit of sensitivity of the media formerly used. Detection of low concentrations of G. vaginalis in normal controls has been made possible by development of a selective and differential medium (HBT). Anaerobically performed studies of the vaginal flora have indicated that while lactobacilli predominate in the normal vagina with or without G. vaginalis, anaerobic bacteria including Bacteroides spp., Peptococcus spp., Eubacterium spp. and curved rods as well as G. vaginalis predominate in bacterial vaginosis. Anaerobic bacteria and G. vaginalis are decreased after appropriate therapy. After treatment with metronidazole, lactobacilli again predominate. Lactobacilli are less prevalent after treatment with ampicillin or amoxicillin. These data suggest that as in infections at other mucous membrane sites, bacterial vaginosis is a mixed infection involving a finite number of facultative and anaerobic species. The data also suggest an important role for facultative lactobacilli.

Evidence for a bacterial lipopolysaccharide-recognizing G-protein-coupled receptor in the bacterial engulfment by Entamoeba histolytica.

PubMed

Brewer, Matthew T; Agbedanu, Prince N; Zamanian, Mostafa; Day, Tim A; Carlson, Steve A

2013-11-01

Entamoeba histolytica is the causative agent of amoebic dysentery, a worldwide protozoal disease that results in approximately 100,000 deaths annually. The virulence of E. histolytica may be due to interactions with the host bacterial flora, whereby trophozoites engulf colonic bacteria as a nutrient source. The engulfment process depends on trophozoite recognition of bacterial epitopes that activate phagocytosis pathways. E. histolytica GPCR-1 (EhGPCR-1) was previously recognized as a putative G-protein-coupled receptor (GPCR) used by Entamoeba histolytica during phagocytosis. In the present study, we attempted to characterize EhGPCR-1 by using heterologous GPCR expression in Saccharomyces cerevisiae. We discovered that bacterial lipopolysaccharide (LPS) is an activator of EhGPCR-1 and that LPS stimulates EhGPCR-1 in a concentration-dependent manner. Additionally, we demonstrated that Entamoeba histolytica prefers to engulf bacteria with intact LPS and that this engulfment process is sensitive to suramin, which prevents the interactions of GPCRs and G-proteins. Thus, EhGPCR-1 is an LPS-recognizing GPCR that is a potential drug target for treatment of amoebiasis, especially considering the well-established drug targeting to GPCRs.

Titanium Surface Chemical Composition Interferes in the Pseudomonas aeruginosa Biofilm Formation.

PubMed

Nunes Filho, Antonio; Aires, Michelle de Medeiros; Braz, Danilo Cavalcante; Hinrichs, Ruth; Macedo, Alexandre José; Alves, Clodomiro

2018-02-01

Bacterial adhesion on three different surfaces: untreated Ti, plasma nitriding, and plasma carbonitriding Ti substrates were investigated. The samples were placed in bacterial cultures of Pseudomonas aeruginosa to assess biofilm formation. The correlation between the amount of bacteria attached to the surface after a lapse of time with nanotopography and physicochemical properties was performed. TiN showed the highest capacity to avoid bacterial adhesion, while presenting intermediate roughness and wettability. Although the surface of TiCN had the highest surface roughness and low contact angle (high wettability), bacterial adhesion was intermediate on this sample. Untreated Ti, even though presenting a smooth surface and low wettability, had the highest tendency to form biofilms. © 2018 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Comparison of Scrub Typhus Meningitis with Acute Bacterial Meningitis and Tuberculous Meningitis.

PubMed

Kakarlapudi, Svas Raju; Chacko, Anila; Samuel, Prasanna; Verghese, Valsan Philip; Rose, Winsley

2018-01-15

To compare scrub typhus meningitis with bacterial and tuberculous meningitis. Children aged <15 years admitted with meningitis were screened and those who fit criteria for diagnosis of scrub typhus meningitis (n=48), bacterial meningitis (n=44) and tuberculous meningitis (n=31) were included for analysis. Clinical features, investigations and outcomes were compared between the three types of meningitis. Mean age, duration of fever at presentation, presence of headache and, altered sensorium and presence of hepatomegaly/splenomegaly were statistically significantly different between the groups. Scrub typhus had statistically significant thrombocytopenia, shorter hospital stay and a better neurological and mortality outcome. Sub-acute presentation of meningitis in older age group children, and good outcome is associated with scrub typhus when compared to bacterial and tuberculous meningitis.

Succession of bacterial and fungal communities within biofilms of a chlorinated drinking water distribution system.

PubMed

Douterelo, I; Fish, K E; Boxall, J B

2018-09-15

Understanding the temporal dynamics of multi-species biofilms in Drinking Water Distribution Systems (DWDS) is essential to ensure safe, high quality water reaches consumers after it passes through these high surface area reactors. This research studied the succession characteristics of fungal and bacterial communities under controlled environmental conditions fully representative of operational DWDS. Microbial communities were observed to increase in complexity after one month of biofilm development but they did not reach stability after three months. Changes in cell numbers were faster at the start of biofilm formation and tended to decrease over time, despite the continuing changes in bacterial community composition. Fungal diversity was markedly less than bacterial diversity and had a lag in responding to temporal dynamics. A core-mixed community of bacteria including Pseudomonas, Massillia and Sphingomonas and the fungi Acremonium and Neocosmopora were present constantly and consistently in the biofilms over time and conditions studied. Monitoring and managing biofilms and such ubiquitous core microbial communities are key control strategies to ensuring the delivery of safe drinking water via the current ageing DWDS infrastructure. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Reagent-free bacterial identification using multivariate analysis of transmission spectra

NASA Astrophysics Data System (ADS)

Smith, Jennifer M.; Huffman, Debra E.; Acosta, Dayanis; Serebrennikova, Yulia; García-Rubio, Luis; Leparc, German F.

2012-10-01

The identification of bacterial pathogens from culture is critical to the proper administration of antibiotics and patient treatment. Many of the tests currently used in the clinical microbiology laboratory for bacterial identification today can be highly sensitive and specific; however, they have the additional burdens of complexity, cost, and the need for specialized reagents. We present an innovative, reagent-free method for the identification of pathogens from culture. A clinical study has been initiated to evaluate the sensitivity and specificity of this approach. Multiwavelength transmission spectra were generated from a set of clinical isolates including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Spectra of an initial training set of these target organisms were used to create identification models representing the spectral variability of each species using multivariate statistical techniques. Next, the spectra of the blinded isolates of targeted species were identified using the model achieving >94% sensitivity and >98% specificity, with 100% accuracy for P. aeruginosa and S. aureus. The results from this on-going clinical study indicate this approach is a powerful and exciting technique for identification of pathogens. The menu of models is being expanded to include other bacterial genera and species of clinical significance.

Polymorphism in Bacterial Flagella Suspensions

NASA Astrophysics Data System (ADS)

Schwenger, Walter J.

Bacterial flagella are a type of biological polymer studied for its role in bacterial motility and the polymorphic transitions undertaken to facilitate the run and tumble behavior. The naturally rigid, helical shape of flagella gives rise to novel colloidal dynamics and material properties. This thesis studies methods in which the shape of bacterial flagella can be controlled using in vitro methods and the changes the shape of the flagella have on both single particle dynamics and bulk material properties. We observe individual flagellum in both the dilute and semidilute regimes to observe the effects of solvent condition on the shape of the filament as well as the effect the filament morphology has on reptation through a network of flagella. In addition, we present rheological measurements showing how the shape of filaments effects the bulk material properties of flagellar suspensions. We find that the individual particle dynamics in suspensions of flagella can vary with geometry from needing to reptate linearly via rotation for helical filaments to the prevention of long range diffusion for block copolymer filaments. Similarly, for bulk material properties of flagella suspensions, helical geometries show a dramatic enhancement in elasticity over straight filaments while block copolymers form an elastic gel without the aid of crosslinking agents.

Anti-bacterial activity of recombinant human β-defensin-3 secreted in the milk of transgenic goats produced by somatic cell nuclear transfer.

PubMed

Liu, Jun; Luo, Yan; Ge, Hengtao; Han, Chengquan; Zhang, Hui; Wang, Yongsheng; Su, Jianmin; Quan, Fusheng; Gao, Mingqing; Zhang, Yong

2013-01-01

The present study was conducted to determine whether recombinant human β-defensin-3 (rHBD3) in the milk of transgenic goats has an anti-bacterial activity against Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Streptococcus agalactiae (S. agalactiae) that could cause mastitis. A HBD3 mammary-specific expression vector was transfected by electroporation into goat fetal fibroblasts which were used to produce fourteen healthy transgenic goats by somatic cell nuclear transfer. The expression level of rHBD3 in the milk of the six transgenic goats ranged from 98 to 121 µg/ml at 15 days of lactation, and was maintained at 90-111 µg/ml during the following 2 months. Milk samples from transgenic goats showed an obvious inhibitory activity against E. coli, S. aureus and S. agalactiae in vitro. The minimal inhibitory concentrations of rHBD3 in milk against E. coli, S. aureus and S. agalactiae were 9.5-10.5, 21.8-23.0 and 17.3-18.5 µg/mL, respectively, which was similar to those of the HBD3 standard (P>0.05). The in vivo anti-bacterial activities of rHBD3 in milk were examined by intramammary infusion of viable bacterial inoculums. We observed that 9/10 and 8/10 glands of non-transgenic goats infused with S. aureus and E. coli became infected. The mean numbers of viable bacteria went up to 2.9×10(3) and 95.4×10(3) CFU/ml at 48 h after infusion, respectively; the mean somatic cell counts (SCC) in infected glands reached up to 260.4×10(5) and 622.2×10(5) cells/ml, which were significantly higher than the SCC in uninfected goat glands. In contrast, no bacteria was presented in glands of transgenic goats and PBS-infused controls, and the SSC did not significantly change throughout the period. Moreover, the compositions and protein profiles of milk from transgenic and non-transgenic goats were identical. The present study demonstrated that HBD3 were an effective anti-bacterial protein to enhance the mastitis resistance of dairy animals.

Identification and Antimicrobial Resistance of Bacteria Isolated from Probiotic Products Used in Shrimp Culture.

PubMed

Noor Uddin, Gazi Md; Larsen, Marianne Halberg; Christensen, Henrik; Aarestrup, Frank M; Phu, Tran Minh; Dalsgaard, Anders

2015-01-01

Probiotics are increasingly used in aquaculture to control diseases and improve feed digestion and pond water quality; however, little is known about the antimicrobial resistance properties of such probiotic bacteria and to what extent they may contribute to the development of bacterial resistance in aquaculture ponds. Concerns have been raised that the declared information on probiotic product labels are incorrect and information on bacterial composition are often missing. We therefore evaluated seven probiotics commonly used in Vietnamese shrimp culture for their bacterial species content, phenotypic antimicrobial resistance and associated transferable resistance genes. The bacterial species was established by 16S rRNA sequence analysis of 125 representative bacterial isolates. MIC testing was done for a range of antimicrobials and whole genome sequencing of six multiple antimicrobial resistant Bacillus spp. used to identify resistance genes and genetic elements associated with horizontal gene transfer. Thirteen bacterial species declared on the probiotic products could not be identified and 11 non-declared Bacillus spp. were identified. Although our culture-based isolation and identification may have missed a few bacterial species present in the tested products this would represent minor bias, but future studies may apply culture independent identification methods like pyro sequencing. Only 6/60 isolates were resistant to more than four antimicrobials and whole genome sequencing showed that they contained macrolide (ermD), tetracycline (tetL), phenicol (fexA) and trimethoprim (dfrD, dfrG and dfrK) resistance genes, but not known structures associated with horizontal gene transfer. Probiotic bacterial strains used in Vietnamese shrimp culture seem to contribute with very limited types and numbers of resistance genes compared to the naturally occurring bacterial species in aquaculture environments. Approval procedures of probiotic products must be strengthened through scientific-based efficacy trials and product labels should allow identification of individual bacterial strains and inform the farmer on specific purpose, dosage and correct application measures.

Widespread presence of "bacterial-like" PPP phosphatases in eukaryotes.

PubMed

Andreeva, Alexandra V; Kutuzov, Mikhail A

2004-11-19

In eukaryotes, PPP (protein phosphatase P) family is one of the two known protein phosphatase families specific for Ser and Thr. The role of PPP phosphatases in multiple signaling pathways in eukaryotic cell has been extensively studied. Unlike eukaryotic PPP phosphatases, bacterial members of the family have broad substrate specificity or may even be Tyr-specific. Moreover, one group of bacterial PPPs are diadenosine tetraphosphatases, indicating that bacterial PPP phosphatases may not necessarily function as protein phosphatases. We describe the presence in eukaryotes of three groups of expressed genes encoding "non-conventional" phosphatases of the PPP family. These enzymes are more closely related to bacterial PPP phosphatases than to the known eukaryotic members of the family. One group, found exclusively in land plants, is most closely related to PPP phosphatases from some alpha-Proteobacteria, including Rhizobiales, Rhodobacterales and Rhodospirillaceae. This group is therefore termed Rhizobiales / Rhodobacterales / Rhodospirillaceae-like phosphatases, or Rhilphs. Phosphatases of the other group are found in Viridiplantae, Rhodophyta, Trypanosomatidae, Plasmodium and some fungi. They are structurally related to phosphatases from psychrophilic bacteria Shewanella and Colwellia, and are termed Shewanella-like phosphatases, or Shelphs. Phosphatases of the third group are distantly related to ApaH, bacterial diadenosine tetraphosphatases, and are termed ApaH-like phosphatases, or Alphs. Patchy distribution of Alphs in animals, plants, fungi, diatoms and kinetoplasts suggests that these phosphatases were present in the common ancestor of eukaryotes but were independently lost in many lineages. Rhilphs, Shelphs and Alphs form PPP clades, as divergent from "conventional" eukaryotic PPP phosphatases as they are from each other and from major bacterial clades. In addition, comparison of primary structures revealed a previously unrecognised (I/L/V)D(S/T)G motif, conserved in all bacterial and "bacterial-like" eukaryotic PPPs, but not in "conventional" eukaryotic and archaeal PPPs. Our findings demonstrate that many eukaryotes possess diverse "bacterial-like" PPP phosphatases, the enzymatic characteristics, physiological roles and precise evolutionary history of which have yet to be determined.

Bacterial inosine 5'-monophosphate dehydrogenase ("IMPDH") DNA as a dominant selectable marker in mammals and other eukaryotes

DOEpatents

Huberman, Eliezer [Chicago, IL; Baccam, Mekhine J [Woodridge, IL

2007-02-27

The present invention relates to a nucleic acid sequence and its corresponding protein sequence useful as a dominant selectable marker in eukaryotes. More specifically the invention relates to a nucleic acid encoding a bacterial IMPDH gene that has been engineered into a eukaryotic expression vectors, thereby permitting bacterial IMPDH expression in mammalian cells. Bacterial IMPDH expression confers resistance to MPA which can be used as dominant selectable marker in eukaryotes including mammals. The invention also relates to expression vectors and cells that express the bacterial IMPDH gene as well as gene therapies and protein synthesis.

Nanobarium Titanate As Supplement To Accelerate Plastic Waste Biodegradation By Indigenous Bacterial Consortia

NASA Astrophysics Data System (ADS)

Kapri, Anil; Zaidi, M. G. H.; Goel, Reeta

2009-06-01

Plastic waste biodegradation studies have seen several developmental phases from the discovery of potential microbial cultures, inclusion of photo-oxidizable additives into the polymer chain, to the creation of starch-embedded biodegradable plastics. The present study deals with the supplementation of nanobarium titanate (NBT) in the minimal broth in order to alter the growth-profiles of the Low-density polyethylene (LDPE) degrading consortia. The pro-bacterial influence of the nanoparticles could be seen by substantial changes such as shortening of the lag phase and elongation of the exponential as well as stationary growth phases, respectively, which eventually increase the biodegradation efficiency. In-vitro biodegradation studies revealed better dissolution of LDPE in the presence of NBT as compared to control. Significant shifting in λ-max values was observed in the treated samples through UV-Vis spectroscopy, while Fourier transform infrared spectroscopy (FTIR) and simultaneous thermogravimetric-differential thermogravimetry-differential thermal analysis (TG-DTG-DTA) further confirmed the breakage and formation of bonds in the polymer backbone. Therefore, this study suggests the implementation of NBT as nutritional additive for plastic waste management through bacterial growth acceleration.

Variability in bacterial community structure during upwelling in the coastal ocean

USGS Publications Warehouse

Kerkhof, L.J.; Voytek, M.A.; Sherrell, Robert M.; Millie, D.; Schofield, O.

1999-01-01

Over the last 30 years, investigations at the community level of marine bacteria and phytoplankton populations suggest they are tightly coupled. However, traditional oceanographic approaches cannot assess whether associations between specific bacteria and phytoplankton exist. Recently, molecular based approaches have been implemented to characterize specific members of different marine bacterial communities. Yet, few molecular-based studies have examined coastal upwelling situations. This is important since upwelling systems provide a unique opportunity for analyzing the association between specific bacteria and specific phytoplankton in the ocean. It is widely believed that upwelling can lead to changes in phytoplankton populations (blooms). Thus, if specific associations exist, we would expect to observe changes in the bacterial population triggered by the bloom. In this paper, we present preliminary data from coastal waters off New Jersey that confirm a shift in bacterial communities during a 1995 upwelling event recorded at a long-term earth observatory (LEO-15) in the Mid-Atlantic Bight. Using PCR amplification and cloning, specific bacterial 16S ribosomal RNA sequences were found which were present in upwelling samples during a phytoplankton bloom, but were not detected in non-bloom samples (surface seawater, offshore sites or sediment samples) collected at the same time or in the same area. These findings are consistent with the notion of specific associations between bacteria and phytoplankton in the ocean. However, further examination of episodic events, such as coastal upwelling, are needed to confirm the existence of specific associations. Additionally, experiments need to be performed to elucidate the mechanisms leading to the specific linkages between a group of bacteria and a group of phytoplankton.

Bisphosphocins: novel antimicrobials for enhanced killing of drug-resistant and biofilm-forming bacteria.

PubMed

Wong, Jonathan P; DiTullio, Paul; Parkinson, Steve

2015-01-01

The global prevalence of antibiotic resistance and the threat posed by drug-resistant superbugs are a leading challenge confronting modern medicine in the 21st century. However, the progress on the development of novel antibiotics to combat this problem is severely lagging. A more concerted effort to develop novel therapeutic agents with robust activity and unique mechanisms of action will be needed to overcome the problem of drug resistance. Furthermore, biofilm forming bacteria are known to be increasingly resistant to the actions of antibiotics and are a leading cause of mortality or morbidity in nosocomial infections. Bisphosphocins (also scientifically known as nubiotics) are novel small protonated deoxynucleotide molecules, and exert their antibacterial activity by depolarization of the bacterial cell membrane, causing bacterial cell death. Bisphosphocins may represent an effective weapon against antibiotic-resistant and biofilm-forming pathogenic bacteria. Preclinical efficacy studies in animals have shown that the compounds are safe and, efficacious against various bacterial infections, including drug-resistant pathogens. In vitro biochemical analysis confirmed that the bactericidal activity of bisphosphocins is mediated by depolarization of the bacterial cell membrane, and these compounds are better able to penetrate through bacterial biofilm and kill the biofilm encased bacteria. This article will cover the structure, mode of action, safety, efficacy and the current state of development of bisphosphocins. Together, the information presented here will present a strong case for bisphosphocins to be considered for use as new weapons to complement the existing arsenal of antimicrobial drugs and as a first line defence against drug-resistant and biofilm-forming bacteria.

A Nonluminescent and Highly Virulent Vibrio harveyi Strain Is Associated with “Bacterial White Tail Disease” of Litopenaeus vannamei Shrimp

PubMed Central

Zhou, Junfang; Fang, Wenhong; Yang, Xianle; Zhou, Shuai; Hu, Linlin; Li, Xincang; Qi, Xinyong; Su, Hang; Xie, Layue

2012-01-01

Recurrent outbreaks of a disease in pond-cultured juvenile and subadult Litopenaeus vannamei shrimp in several districts in China remain an important problem in recent years. The disease was characterized by “white tail” and generally accompanied by mass mortalities. Based on data from the microscopical analyses, PCR detection and 16S rRNA sequencing, a new Vibrio harveyi strain (designated as strain HLB0905) was identified as the etiologic pathogen. The bacterial isolation and challenge tests demonstrated that the HLB0905 strain was nonluminescent but highly virulent. It could cause mass mortality in affected shrimp during a short time period with a low dose of infection. Meanwhile, the histopathological and electron microscopical analysis both showed that the HLB0905 strain could cause severe fiber cell damages and striated muscle necrosis by accumulating in the tail muscle of L. vannamei shrimp, which led the affected shrimp to exhibit white or opaque lesions in the tail. The typical sign was closely similar to that caused by infectious myonecrosis (IMN), white tail disease (WTD) or penaeid white tail disease (PWTD). To differentiate from such diseases as with a sign of “white tail” but of non-bacterial origin, the present disease was named as “bacterial white tail disease (BWTD)”. Present study revealed that, just like IMN and WTD, BWTD could also cause mass mortalities in pond-cultured shrimp. These results suggested that some bacterial strains are changing themselves from secondary to primary pathogens by enhancing their virulence in current shrimp aquaculture system. PMID:22383954

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps.

PubMed

Yashiro, Erika; Pinto-Figueroa, Eric; Buri, Aline; Spangenberg, Jorge E; Adatte, Thierry; Niculita-Hirzel, Hélène; Guisan, Antoine; van der Meer, Jan Roelof

2016-11-01

Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km 2 area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change. This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700-km 2 study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Adaptive self-organization during growth of bacterial colonies

NASA Astrophysics Data System (ADS)

Ben-Jacob, Eshel; Shmueli, Haim; Shochet, Ofer; Tenenbaum, Adam

1992-09-01

We present a study of interfacial pattern formation during diffusion-limited growth of Bacillus subtilis. It is demonstrated that bacterial colonies can develop patterns similar to morphologies observed during diffusion-limited growth in non-living (azoic) systems such as solidification and electro-chemical deposition. The various growth morphologies, that is the global structure of the colony, are observed as we vary the growth conditions. These include fractal growth, dense-branching growth, compact growth, dendritic growth and chiral growth. The results demonstrate the action of a singular interplay between the micro-level (individual bacterium) and macro-level (the colony) in selecting the observed morphologies as is understood for non-living systems. Furthermore, the observed morphologies can be organized within a morphology diagram indicating the existence of a morphology selection principle similar to the one proposed for azoic systems. We propose a phase-field-like model (the phase being the bacterial concentration and the field being the nutrient concentration) to describe the growth. The bacteria-bacteria interaction is manifested as a phase dependent diffusion constant. Growth of a bacterial colony presents an inherent additional level of complexity compared to azoic systems, since the building blocks themselves are living systems. Thus, our studies also focus on the transition between morphologies. We have observed extended morphology transitions due to phenotypic changes of the bacteria, as well as bursts of new morphologies resulting from genotypic changes. In addition, we have observed extended and heritable transitions (mainly between dense branching growth and chiral growth) as well as phenotypic transitions that turn genotypic over time. We discuss the implications of our results in the context of the evolving picture of genome cybernetics. Diffusion limited growth of bacterial colonies combined with new understanding of pattern formation in azoic systems provide new tools for the study of adaptive self-organization and mutation in the presence of selective pressures. We include brief reviews of both the recent developments in the study of interfacial pattern formation in non-living systems and the current trends in the view of mutation dynamics.

Effects of probiotics on the recurrence of bacterial vaginosis: a review.

PubMed

Homayouni, Aziz; Bastani, Parvin; Ziyadi, Somayeh; Mohammad-Alizadeh-Charandabi, Sakineh; Ghalibaf, Morad; Mortazavian, Amir Mohammad; Mehrabany, Elnaz Vaghef

2014-01-01

Bacterial vaginosis (BV) is a common cause of genital discomfort in women in reproductive ages, which causes many complications. Bacterial vaginosis is usually treated by metronidazole and clindamycin. However, this protocol does not prevent its recurrence, which is a main complaint of the patients. The number of lactobacilli in the vagina of women with BV is significantly lower than that in healthy women. Hence, efforts have been made to normalize vaginal flora by oral or vaginal administration of lactobacilli. The objective of the present study was to review clinical evidences available regarding the efficacy of probiotics in the prevention and treatment of BV. Published randomized controlled trials were searched in PubMed, Science Direct, and the Cochrane Database between 1990 and 2011. Search terms included bacterial vaginosis, urinary tract infection, lactobacillus, and probiotics. Orally consumed probiotics are believed to ascend to the vaginal tract after they are excreted from the rectum; vaginal administration allows for direct replacement of the probiotics for unhealthy vaginal microbiota and occupation of specific adhesion sites at the epithelial surface of the urinary tract, which consequently results in maintenance of a low pH and production of antimicrobial substances like acids and hydrogen peroxide. Receiving Lactobacillus acidophilus, Lactobacillus rhamnosus GR-1, and Lactobacillus fermentum RC-14 at a dose of at least 10 CFU/day for 2 months has been shown to present the patients with better results. Although the results of different studies are controversial, most studies have been in favor of the probiotics in the prevention or treatment of BV, and no adverse effects have been reported. Therefore, it may be helpful to recommend daily consumption of probiotic products to improve public health among women.

Arthropod-borne bacterial diseases in pregnancy.

PubMed

Dotters-Katz, Sarah K; Kuller, Jeffrey; Heine, R Phillips

2013-09-01

Arthropod-borne bacterial diseases affect more than 25,000 Americans every year and thousands more around the world. These infections present a diagnostic dilemma for clinicians because they mimic many other pathologic conditions and are often low on or absent from the differential diagnosis list. Diagnosis is particularly challenging during pregnancy, as these infections may mimic common pregnancy-specific conditions, such as typical and atypical preeclampsia, or symptoms of pregnancy itself. Concerns regarding the safety in pregnancy of some indicated antibiotics add a therapeutic challenge for the prescriber, requiring knowledge of alternative therapeutic options for many arthropod-borne bacterial diseases. Physicians, especially those in endemic areas, must keep this class of infections in mind, particularly when the presentation does not appear classic for more commonly seen conditions. This article discusses presentation, diagnosis, and treatment of the most common of these arthropod-borne bacterial diseases, including Lyme disease, Rocky Mountain spotted fever, tick-borne relapsing fever, typhus, plague, cat-scratch disease, and Carrión disease.

Predictive Value of Decoy Receptor 3 in Postoperative Nosocomial Bacterial Meningitis

PubMed Central

Liu, Yong-Juan; Shao, Li-Hua; Wang, Qian; Zhang, Jian; Ma, Rui-Ping; Liu, Hai-Hong; Dong, Xiao-Meng; Ma, Li-Xian

2014-01-01

Nosocomial bacterial meningitis requires timely treatment, but what is difficult is the prompt and accurate diagnosis of this disease. The aim of this study was to assess the potential role of decoy receptor 3 (DcR3) levels in the differentiation of bacterial meningitis from non-bacterial meningitis. A total of 123 patients were recruited in this study, among them 80 patients being with bacterial meningitis and 43 patients with non-bacterial meningitis. Bacterial meningitis was confirmed by bacterial culture of cerebrospinal fluid (CSF) culture and enzyme-linked immunosorbent assay (ELISA) was used to detect the level of DcR3 in CSF. CSF levels of DcR3 were statistically significant between patients with bacterial meningitis and those with non-bacterial meningitis (p < 0.001). A total of 48.75% of patients with bacterial meningitis received antibiotic >24 h before CSF sampling, which was much higher than that of non-bacterial meningitis. CSF leucocyte count yielded the highest diagnostic value, with an area under the receiver operating characteristic curve (ROC) of 0.928, followed by DcR3. At a critical value of 0.201 ng/mL for DcR3, the sensitivity and specificity were 78.75% and 81.40% respectively. DcR3 in CSF may be a valuable predictor for differentiating patients with bacterial meningitis from those with non-bacterial meningitis. Further studies are needed for the validation of this study. PMID:25372942

Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment.

PubMed

Avena, Christine V; Parfrey, Laura Wegener; Leff, Jonathan W; Archer, Holly M; Frick, Winifred F; Langwig, Kate E; Kilpatrick, A Marm; Powers, Karen E; Foster, Jeffrey T; McKenzie, Valerie J

2016-01-01

Bats are geographically widespread and play an important role in many ecosystems, but relatively little is known about the ecology of their associated microbial communities and the role microbial taxa play in bat health, development, and evolution. Moreover, few vertebrate animal skin microbiomes have been comprehensively assessed, and thus characterizing the bat skin microbiome will yield valuable insight into the variability of vertebrate skin microbiomes as a whole. The recent emergence of the skin fungal disease white-nose syndrome highlights the potentially important role bat skin microbial communities could play in bat health. Understanding the determinant of bat skin microbial communities could provide insight into important factors allowing individuals to persist with disease. We collected skin swabs from a total of 11 bat species from the eastern United States ( n = 45) and Colorado ( n = 119), as well as environmental samples ( n = 38) from a subset of sites, and used 16S rRNA marker gene sequencing to observe bacterial communities. In addition, we conducted a literature survey to compare the skin microbiome across vertebrate groups, including the bats presented in this study. Host species, region, and site were all significant predictors of the variability across bat skin bacterial communities. Many bacterial taxa were found both on bats and in the environment. However, some bacterial taxa had consistently greater relative abundances on bat skin relative to their environments. Bats shared many of their abundant taxa with other vertebrates, but also hosted unique bacterial lineages such as the class Thermoleophilia (Actinobacteria). A strong effect of site on the bat skin microbiome indicates that the environment very strongly influences what bacteria are present on bat skin. Bat skin microbiomes are largely composed of site-specific microbiota, but there do appear to be important host-specific taxa. How this translates to differences in host-microbial interactions and bat health remains an important knowledge gap, but this work suggests that habitat variability is very important. We identify some bacterial groups that are more consistent on bats despite site differences, and these may be important ones to study in terms of their function as potential core microbiome members.

Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment

PubMed Central

Avena, Christine V.; Parfrey, Laura Wegener; Leff, Jonathan W.; Archer, Holly M.; Frick, Winifred F.; Langwig, Kate E.; Kilpatrick, A. Marm; Powers, Karen E.; Foster, Jeffrey T.; McKenzie, Valerie J.

2016-01-01

Bats are geographically widespread and play an important role in many ecosystems, but relatively little is known about the ecology of their associated microbial communities and the role microbial taxa play in bat health, development, and evolution. Moreover, few vertebrate animal skin microbiomes have been comprehensively assessed, and thus characterizing the bat skin microbiome will yield valuable insight into the variability of vertebrate skin microbiomes as a whole. The recent emergence of the skin fungal disease white-nose syndrome highlights the potentially important role bat skin microbial communities could play in bat health. Understanding the determinant of bat skin microbial communities could provide insight into important factors allowing individuals to persist with disease. We collected skin swabs from a total of 11 bat species from the eastern United States (n = 45) and Colorado (n = 119), as well as environmental samples (n = 38) from a subset of sites, and used 16S rRNA marker gene sequencing to observe bacterial communities. In addition, we conducted a literature survey to compare the skin microbiome across vertebrate groups, including the bats presented in this study. Host species, region, and site were all significant predictors of the variability across bat skin bacterial communities. Many bacterial taxa were found both on bats and in the environment. However, some bacterial taxa had consistently greater relative abundances on bat skin relative to their environments. Bats shared many of their abundant taxa with other vertebrates, but also hosted unique bacterial lineages such as the class Thermoleophilia (Actinobacteria). A strong effect of site on the bat skin microbiome indicates that the environment very strongly influences what bacteria are present on bat skin. Bat skin microbiomes are largely composed of site-specific microbiota, but there do appear to be important host-specific taxa. How this translates to differences in host-microbial interactions and bat health remains an important knowledge gap, but this work suggests that habitat variability is very important. We identify some bacterial groups that are more consistent on bats despite site differences, and these may be important ones to study in terms of their function as potential core microbiome members. PMID:27909426

Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.

PubMed

Kahlke, Tim; Goesmann, Alexander; Hjerde, Erik; Willassen, Nils Peder; Haugen, Peik

2012-05-10

The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups. The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin. The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.

Antibacterial Au nanostructured surfaces

NASA Astrophysics Data System (ADS)

Wu, Songmei; Zuber, Flavia; Brugger, Juergen; Maniura-Weber, Katharina; Ren, Qun

2016-01-01

We present here a technological platform for engineering Au nanotopographies by templated electrodeposition on antibacterial surfaces. Three different types of nanostructures were fabricated: nanopillars, nanorings and nanonuggets. The nanopillars are the basic structures and are 50 nm in diameter and 100 nm in height. Particular arrangement of the nanopillars in various geometries formed nanorings and nanonuggets. Flat surfaces, rough substrate surfaces, and various nanostructured surfaces were compared for their abilities to attach and kill bacterial cells. Methicillin-resistant Staphylococcus aureus, a Gram-positive bacterial strain responsible for many infections in health care system, was used as the model bacterial strain. It was found that all the Au nanostructures, regardless their shapes, exhibited similar excellent antibacterial properties. A comparison of live cells attached to nanotopographic surfaces showed that the number of live S. aureus cells was <1% of that from flat and rough reference surfaces. Our micro/nanofabrication process is a scalable approach based on cost-efficient self-organization and provides potential for further developing functional surfaces to study the behavior of microbes on nanoscale topographies.We present here a technological platform for engineering Au nanotopographies by templated electrodeposition on antibacterial surfaces. Three different types of nanostructures were fabricated: nanopillars, nanorings and nanonuggets. The nanopillars are the basic structures and are 50 nm in diameter and 100 nm in height. Particular arrangement of the nanopillars in various geometries formed nanorings and nanonuggets. Flat surfaces, rough substrate surfaces, and various nanostructured surfaces were compared for their abilities to attach and kill bacterial cells. Methicillin-resistant Staphylococcus aureus, a Gram-positive bacterial strain responsible for many infections in health care system, was used as the model bacterial strain. It was found that all the Au nanostructures, regardless their shapes, exhibited similar excellent antibacterial properties. A comparison of live cells attached to nanotopographic surfaces showed that the number of live S. aureus cells was <1% of that from flat and rough reference surfaces. Our micro/nanofabrication process is a scalable approach based on cost-efficient self-organization and provides potential for further developing functional surfaces to study the behavior of microbes on nanoscale topographies. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06157a

[Value of lumbar puncture after a first febrile seizure in children aged less than 18 months. A retrospective study of 157 cases].

PubMed

Casasoprana, A; Hachon Le Camus, C; Claudet, I; Grouteau, E; Chaix, Y; Cances, C; Karsenty, C; Cheuret, E

2013-06-01

Because meningitis symptoms are not very specific under the age of 18 months, lumbar puncture (LP) was widely recommended in children presenting a febrile seizure (FS). Recent retrospective studies have challenged this age criterion. In 2011, the American Academy of Pediatrics updated its guidelines for the first episode of simple FS: LP is indicated if signs suggestive of meningitis are present and remains "an option" in case of prior antibiotic treatment or between the age of 6 and 12 months if the child is not properly vaccinated against Haemophilus and Streptococcus pneumoniae. Because the meningitis epidemiology and the vaccination coverage are different, the objective of this study was to evaluate whether these new guidelines were applicable in France. Between 2009 and 2010, we conducted a retrospective single-center study including 157 children aged less than 18 months admitted to the pediatric emergency department (Children's Hospital, Toulouse, France) for their first febrile seizure. The data collected were: type of seizure, knowledge of prior antibiotic treatment, neurological status, signs of central nervous system infection, and biological results (LP, blood cultures). Lumbar puncture was performed in 40% of cases (n=63). The diagnosis of meningitis/encephalitis was selected in eight cases: three cases of viral meningitis, three bacterial meningitis (Streptococcus pneumoniae), and two non-herpetic viral encephalitis. The incidence of bacterial meningitis in our study was 1.9%. The risk of serious infection, bacterial meningitis or encephalitis, was increased when there was a complex FS (14% versus 0% with a simple FS, P=0.06). The presence of other suggestive clinical symptoms was strongly associated with a risk of bacterial meningitis/encephalitis (36% in case of clinical orientation versus 0% in the absence of such signs, P<0.001). All severe clinical presentations were associated with complex FS (prolonged, focal, and/or repeated seizures) and the presence of other suggestive clinical signs (impaired consciousness lasting longer than 1h after the seizure, septic aspect, behavior disorders, hypotonia, bulging fontanel, neck stiffness, petechial purpura). The risk of bacterial meningitis or encephalitis associated with a simple FS and followed by a strictly normal clinical examination is extremely low. After a simple febrile seizure without any other suggestive signs of meningitis, systematic lumbar puncture is not necessary even in children younger than 18 months. LP remains absolutely indicated if clinical symptoms concentrate on central nervous system infection and should be discussed in case of complex seizures, prior antibiotic treatment, or incomplete vaccination. Copyright © 2013. Published by Elsevier SAS.

Restructuring of Endophytic Bacterial Communities in Grapevine Yellows-Diseased and Recovered Vitis vinifera L. Plants ▿

PubMed Central

Bulgari, Daniela; Casati, Paola; Crepaldi, Paola; Daffonchio, Daniele; Quaglino, Fabio; Brusetti, Lorenzo; Bianco, Piero Attilio

2011-01-01

Length heterogeneity-PCR assays, combined with statistical analyses, highlighted that the endophytic bacterial community associated with healthy grapevines was characterized by a greater diversity than that present in diseased and recovered plants. The findings suggest that phytoplasmas can restructure the bacterial community by selecting endophytic strains that could elicit a plant defense response. PMID:21622794

Restructuring of endophytic bacterial communities in grapevine yellows-diseased and recovered Vitis vinifera L. plants.

PubMed

Bulgari, Daniela; Casati, Paola; Crepaldi, Paola; Daffonchio, Daniele; Quaglino, Fabio; Brusetti, Lorenzo; Bianco, Piero Attilio

2011-07-01

Length heterogeneity-PCR assays, combined with statistical analyses, highlighted that the endophytic bacterial community associated with healthy grapevines was characterized by a greater diversity than that present in diseased and recovered plants. The findings suggest that phytoplasmas can restructure the bacterial community by selecting endophytic strains that could elicit a plant defense response.

Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome

PubMed Central

Lupatini, Manoeli; Suleiman, Afnan Khalil Ahmad; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Kuramae, Eiko Eurya; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Würdig

2013-01-01

The Pampa biome is considered one of the main hotspots of the world’s biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated. PMID:24146873

The role of magnetic iron oxide nanoparticles in the bacterially induced calcium carbonate precipitation.

PubMed

Seifan, Mostafa; Ebrahiminezhad, Alireza; Ghasemi, Younes; Samani, Ali Khajeh; Berenjian, Aydin

2018-04-01

Recently, magnetic iron oxide nanoparticles (IONs) have been used to control and modify the characteristics of concrete and mortar. Concrete is one of the most used materials in the world; however, it is susceptible to cracking. Over recent years, a sustainable biotechnological approach has emerged as an alternative approach to conventional techniques to heal the concrete cracks by the incorporation of bacterial cells and nutrients into the concrete matrix. Once cracking occurs, CaCO 3 is induced and the crack is healed. Considering the positive effects of IONs on the concrete properties, the effect of these nanoparticles on bacterial growth and CaCO 3 biosynthesis needs to be evaluated for their possible application in bio self-healing concrete. In the present work, IONs were successfully synthesized and characterized using various techniques. The presence of IONs showed a significant effect on both bacterial growth and CaCO 3 precipitation. The highest bacterial growth was observed in the presence of 150 μg/mL IONs. The highest concentration of induced CaCO 3 (34.54 g/L) was achieved when the bacterial cells were immobilized with 300 μg/mL of IONs. This study provides new data and supports the possibility of using IONs as a new tool in designing the next generation of bio self-healing concrete.

In Situ Analysis of Bacterial Lipopeptide Antibiotics by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging.

PubMed

Debois, Delphine; Ongena, Marc; Cawoy, Hélène; De Pauw, Edwin

2016-01-01

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a technique developed in the late 1990s enabling the two-dimensional mapping of a broad variety of biomolecules present at the surface of a sample. In many applications including pharmaceutical studies or biomarker discovery, the distribution of proteins, lipids or drugs, and metabolites may be visualized within tissue sections. More recently, MALDI MSI has become increasingly applied in microbiology where the versatility of the technique is perfectly suited to monitor the metabolic dynamics of bacterial colonies. The work described here is focused on the application of MALDI MSI to map secondary metabolites produced by Bacilli, especially lipopeptides, produced by bacterial cells during their interaction with their environment (bacteria, fungi, plant roots, etc.). This chapter addresses the advantages and challenges that the implementation of MALDI MSI to microbiological samples entails, including detailed protocols on sample preparation (from both microbiologist and mass spectrometrist points of view), matrix deposition, and data acquisition and interpretation. Lipopeptide images recorded from confrontation plates are also presented.

Study of Bacterial Samples Using Laser Induced Breakdown Spectroscopy

NASA Astrophysics Data System (ADS)

W, A. Farooq; M, Atif; W, Tawfik; M, S. Alsalhi; Z, A. Alahmed; M, Sarfraz; J, P. Singh

2014-12-01

Laser-induced breakdown spectroscopy (LIBS) technique has been applied to investigate two different types of bacteria, Escherichia coli (B1) and Micrococcus luteus (B2) deposited on glass slides using Spectrolaser 7000. LIBS spectra were analyzed using spectrolaser software. LIBS spectrum of glass substrate was compared with bacteria spectra. Ca, Mg, Na, K, P, S, Cl, Fe, Al, Mn, Cu, C, H and CN-band appeared in bacterial samples in air. Two carbon lines at 193.02 nm, 247.88 nm and one hydrogen line at 656.28 nm with intensity ratios of 1.9, 1.83 and 1.53 appeared in bacterial samples B1 and B2 respectively. Carbon and hydrogen are the important components of the bio-samples like bacteria and other cancer cells. Investigation on LIBS spectra of the samples in He and Ar atmospheres is also presented. Ni lines appeared only in B2 sample in Ar atmosphere. From the present experimental results we are able to show that LIBS technique has a potential in the identification and discrimination of different types of bacteria.

Antibiotic Conditioned Growth Medium of Pseudomonas Aeruginosa

ERIC Educational Resources Information Center

Benathen, Isaiah A.; Cazeau, Barbara; Joseph, Njeri

2004-01-01

A simple method to study the consequences of bacterial antibiosis after interspecific competition between microorganisms is presented. Common microorganisms are used as the test organisms and Pseudomonas aeruginosa are used as the source of the inhibitor agents.

Bacterial infections in horses: a retrospective study at the University Equine Clinic of Bern.

PubMed

Panchaud, Y; Gerber, V; Rossano, A; Perreten, V

2010-04-01

Bacterial infections present a major challenge in equine medicine. Therapy should be based on bacteriological diagnosis to successfully minimize the increasing number of infections caused by multidrug-resistant bacteria. The present study is a retrospective analysis of bacteriological results from purulent infections in horses admitted at the University Equine Clinic of Bern from 2004 to 2008. From 378 samples analyzed, 557 isolates were identified, of which Staphylococcus aureus, Streptococcus equi subsp. zooepidemicus and coliforms were the most common. Special attention was paid to infections with methicillin-resistant S. aureus (MRSA) ST398 and a non-MRSA, multidrug-resistant S. aureus clone ST1 (BERN100). Screening of newly-admitted horses showed that 2.2 % were carriers of MRSA. Consequent hygiene measures taken at the Clinic helped to overcome a MRSA outbreak and decrease the number of MRSA infections.

Lactoferricin/verbascoside topical emulsion: a possible alternative treatment for atopic dermatitis in dogs.

PubMed

Biasibetti, Elena; Bruni, Natascia; Bigliati, Mauro; Capucchio, Maria Teresa

2017-08-28

Atopic dermatitis affects 3-15% of the general dog population and it has been diagnosed by veterinarians up to 58% of dogs affected with skin disease. It is usually a life-long pathology which can be controlled, but it can be seldom cured. The present investigation describes a case study in which lactoferricin and verbascoside are part of a formulation to obtain a dermatological lotion for canine dermatitis treatment. The study was an open-label trial design of two-week treatment. Thirty-eight dogs (23 females and 15 males), with atopic dermatitis and secondary bacterial or yeast overgrowth have been included. During treatment period the total clinical score progressively decreased associated with an improvement in clinical signs. No adverse effects were reported in any of the treated dogs. The present research suggests that daily applications of tested emulsion are effective in reducing bacterial overgrowth and clinical signs in skin folds and atopic dermatitis.

Bacterial adenosine triphosphate as a measure of urinary tract infection

NASA Technical Reports Server (NTRS)

Chappelle, E. W.; Picciolo, G. L.

1971-01-01

Procedure detects and counts bacteria present in urine samples. Method also determines bacterial levels in other aqueous body fluids including lymph fluid, plasma, blood, spinal fluid, saliva and mucous.

Assessing the Robustness of Complete Bacterial Genome Segmentations

NASA Astrophysics Data System (ADS)

Devillers, Hugo; Chiapello, Hélène; Schbath, Sophie; El Karoui, Meriem

Comparison of closely related bacterial genomes has revealed the presence of highly conserved sequences forming a "backbone" that is interrupted by numerous, less conserved, DNA fragments. Segmentation of bacterial genomes into backbone and variable regions is particularly useful to investigate bacterial genome evolution. Several software tools have been designed to compare complete bacterial chromosomes and a few online databases store pre-computed genome comparisons. However, very few statistical methods are available to evaluate the reliability of these software tools and to compare the results obtained with them. To fill this gap, we have developed two local scores to measure the robustness of bacterial genome segmentations. Our method uses a simulation procedure based on random perturbations of the compared genomes. The scores presented in this paper are simple to implement and our results show that they allow to discriminate easily between robust and non-robust bacterial genome segmentations when using aligners such as MAUVE and MGA.

Colorimetric and fluorimetric detection of Hg2 + and Cr3 + by boronic acid conjugated rhodamine derivatives: Mechanistic aspects and their bio-imaging application in bacterial cells

NASA Astrophysics Data System (ADS)

Vallu, Rama Krishna; Velugula, Krishna; Doshi, Sejal; Chinta, Jugun Prakash

2018-01-01

Colorimetric and fluorimetric detection of toxic metal ions such as Hg2 + and Cr3 + has gained tremendous popularity over the conventional methods due to their operational simplicity, high selectivity, and speediness. Although numerous colorimetric and fluorescent receptors for Hg2 + or Cr3 + were reported in the literature, boronic acid-based receptors for these metal ions are rather scarce in the literature. Hence, in the present study dual function boronic acid conjugated rhodamine derivatives were developed, and their toxic metal ion detection abilities were studied by absorption, emission and visual detection methods. Absorption and emission spectral studies revealed that these derivatives displayed selectivity towards Hg2 +, Cr3 + and Fe3 + among the other metal ions studied by forming new absorption band. Both the derivatives exhibited colorimetric response towards Hg2 + and Cr3 + by the change in color of the solution to pink and reddish pink with Fe3 +. The detailed mechanism involved in the detection of Hg2 + was deduced by 1H NMR and ESI-MS studies. Further, these derivatives were used for fluorescence imaging of Hg2 + and Cr3 + in S. aureus bacterial cells. Thus the present manuscript demonstrated the use of boronic acid conjugated rhodamine derivatives as a dual function (colorimetric and fluorescent) probes and as imaging agents for Hg2 + and Cr3 +, which are known for their toxic influence on bacterial cells.

Geography and Location Are the Primary Drivers of Office Microbiome Composition

PubMed Central

Chase, John; Fouquier, Jennifer; Zare, Mahnaz; Sonderegger, Derek L.; Knight, Rob; Kelley, Scott T.; Siegel, Jeffrey

2016-01-01

ABSTRACT In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidate several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ on the basis of surface material (e.g., ceiling tile or carpet) but do differ on the basis of the location in a room (e.g., ceiling or floor), two features that are often conflated but that we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material was likely detecting differences based on different usage patterns. Next, we find that offices have city-specific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but office-specific bacterial communities are less apparent. This differs from previous work, which has suggested office-specific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces. IMPORTANCE Our study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, disturbance due to repeated sampling, though detectable, is small compared to that due to other variables, opening up a range of longitudinal study designs in the BE. Next, studies requiring more samples than can be sequenced on a single sequencing run (which is increasingly common) must control for run effects by including some of the same samples in all of the sequencing runs as technical replicates. Finally, detailed tracking of indoor and material environment covariates is likely not essential for BE microbiome studies, as the normal range of indoor environmental conditions is likely not large enough to impact bacterial communities. PMID:27822521

Bacterial Diversity in the Soda Saline Crater Lake from Isabel Island, Mexico.

PubMed

Aguirre-Garrido, José Félix; Ramírez-Saad, Hugo César; Toro, Nicolás; Martínez-Abarca, Francisco

2016-01-01

Isabel Lake is a moderate saline soda crater lake located in Isabel Island in the eastern tropical Pacific coast of Mexico. Lake is mainly formed by rainfall and is strongly affected by evaporation and high input of nutrients derived from excretions of a large bird community inhabiting the island. So far, only the island macrobiota has been studied. The knowledge of the prokaryotic biota inhabiting the upper layers of this meromictic lake can give clues for the maintenance of this ecosystem. We assessed the diversity and composition of prokaryotic community in sediments and water of the lake by DGGE profiling, 16S rRNA gene amplicon pyrosequencing, and cultivation techniques. The bacterial community is largely dominated by halophilic and halotolerant microorganisms. Alpha diversity estimations reveal higher value in sediments than in water (P > 0.005). The lake water is dominated by γ-Proteobacteria belonging to four main families where Halomonadaceae presents the highest abundance. Aerobic, phototrophic, and halotolerant prokaryotes such as Cyanobacteria GPIIa, Halomonas, Alcanivorax, Idiomarina, and Cyclobacterium genera are commonly found. However, in sediment samples, Formosa, Muricauda, and Salegentibacter genera corresponding to Flavobacteriaceae family accounted for 15-20 % of the diversity. Heterotrophs like those involved in sulfur cycle, Desulfotignum, Desulfuromonas, Desulfofustis, and Desulfopila, appear to play an important role in sediments. Finally, a collection of aerobic halophilic bacterial isolates was created from these samples; members of the genus Halomonas were predominantly isolated from lake water. This study contributes to state the bacterial diversity present in this particular soda saline crater lake.

Evaluation of changes in periodontal bacteria in healthy dogs over 6 months using quantitative real-time PCR.

PubMed

Maruyama, N; Mori, A; Shono, S; Oda, H; Sako, T

2018-03-01

Porphyromonas gulae, Tannerella forsythia and Campylobacter rectus are considered dominant periodontal pathogens in dogs. Recently, quantitative real-time PCR (qRT-PCR) methods have been used for absolute quantitative determination of oral bacterial counts. The purpose of the present study was to establish a standardized qRT-PCR procedure to quantify bacterial counts of the three target periodontal bacteria (P. gulae, T. forsythia and C. rectus). Copy numbers of the three target periodontal bacteria were evaluated in 26 healthy dogs. Then, changes in bacterial counts of the three target periodontal bacteria were evaluated for 24 weeks in 7 healthy dogs after periodontal scaling. Analytical evaluation of each self-designed primer indicated acceptable analytical imprecision. All 26 healthy dogs were found to be positive for P. gulae, T. forsythia and C. rectus. Median total bacterial counts (copies/ng) of each target genes were 385.612 for P. gulae, 25.109 for T. forsythia and 5.771 for C. rectus. Significant differences were observed between the copy numbers of the three target periodontal bacteria. Periodontal scaling reduced median copy numbers of the three target periodontal bacteria in 7 healthy dogs. However, after periodontal scaling, copy numbers of all three periodontal bacteria significantly increased over time (p<0.05, Kruskal-Wallis test) (24 weeks). In conclusion, our results demonstrated that qRT-PCR can accurately measure periodontal bacteria in dogs. Furthermore, the present study has revealed that qRT-PCR method can be considered as a new objective evaluation system for canine periodontal disease. Copyright© by the Polish Academy of Sciences.

Capturing Early Changes in the Marine Bacterial Community as a Result of Crude Oil Pollution in a Mesocosm Experiment

PubMed Central

Krolicka, Adriana; Boccadoro, Catherine; Nilsen, Mari Mæland; Baussant, Thierry

2017-01-01

The results of marine bacterial community succession from a short-term study of seawater incubations at 4°C to North Sea crude oil are presented herein. Oil was used alone (O) or in combination with a dispersant (OD). Marine bacterial communities resulting from these incubations were characterized by a fingerprinting analysis and pyrosequencing of the 16S rRNA gene with the aim of 1) revealing differences in bacterial communities between the control, O treatment, and OD treatment and 2) identifying the operational taxonomic units (OTUs) of early responders in order to define the bacterial gene markers of oil pollution for in situ monitoring. After an incubation for 1 d, the distribution of the individual ribotypes of bacterial communities in control and oil-treated (O and OD) tanks differed. Differences related to the structures of bacterial communities were observed at later stages of the incubation. Among the early responders identified (Pseudoalteromonas, Sulfitobacter, Vibrio, Pseudomonas, Glaciecola, Neptunomonas, Methylophaga, and Pseudofulvibacter), genera that utilize a disintegrated biomass or hydrocarbons as well as biosurfactant producers were detected. None of these genera included obligate hydrocarbonoclastic bacteria (OHCB). After an incubation for 1 d, the abundances of Glaciecola and Pseudofulvibacter were approximately 30-fold higher in the OD and O tanks than in the control tank. OTUs assigned to the Glaciecola genus were represented more in the OD tank, while those of Pseudofulvibacter were represented more in the O tank. We also found that 2 to 3% of the structural community shift originated from the bacterial community in the oil itself, with Polaribacter being a dominant bacterium. PMID:29187706

Capturing Early Changes in the Marine Bacterial Community as a Result of Crude Oil Pollution in a Mesocosm Experiment.

PubMed

Krolicka, Adriana; Boccadoro, Catherine; Nilsen, Mari Mæland; Baussant, Thierry

2017-12-27

The results of marine bacterial community succession from a short-term study of seawater incubations at 4°C to North Sea crude oil are presented herein. Oil was used alone (O) or in combination with a dispersant (OD). Marine bacterial communities resulting from these incubations were characterized by a fingerprinting analysis and pyrosequencing of the 16S rRNA gene with the aim of 1) revealing differences in bacterial communities between the control, O treatment, and OD treatment and 2) identifying the operational taxonomic units (OTUs) of early responders in order to define the bacterial gene markers of oil pollution for in situ monitoring.After an incubation for 1 d, the distribution of the individual ribotypes of bacterial communities in control and oil-treated (O and OD) tanks differed. Differences related to the structures of bacterial communities were observed at later stages of the incubation. Among the early responders identified (Pseudoalteromonas, Sulfitobacter, Vibrio, Pseudomonas, Glaciecola, Neptunomonas, Methylophaga, and Pseudofulvibacter), genera that utilize a disintegrated biomass or hydrocarbons as well as biosurfactant producers were detected. None of these genera included obligate hydrocarbonoclastic bacteria (OHCB). After an incubation for 1 d, the abundances of Glaciecola and Pseudofulvibacter were approximately 30-fold higher in the OD and O tanks than in the control tank. OTUs assigned to the Glaciecola genus were represented more in the OD tank, while those of Pseudofulvibacter were represented more in the O tank. We also found that 2 to 3% of the structural community shift originated from the bacterial community in the oil itself, with Polaribacter being a dominant bacterium.

Non-pathogenic microflora of a spring water with regenerative properties.

PubMed

Nicoletti, Giovanni; Corbella, Marta; Jaber, Omar; Marone, Piero; Scevola, Daniele; Faga, Angela

2015-11-01

The Comano spring water (Comano, Italy) has been demonstrated to improve skin regeneration, not only by increasing keratinocyte proliferation and migration, but also by modulating the regenerated collagen and elastic fibers in the dermis. However, such biological properties may not be entirely explained by its mineral composition only. As the non-pathogenic bacterial populations have demonstrated an active role in different biological processes, the potential presence of non-pathogenic bacterial species within the Comano spring water was investigated in order to identify any possible correlation between these bacterial populations and the demonstrated biological properties of this water. The water was collected at the spring using an aseptic procedure and multiple cultures were carried out. A total of 9 different strains were isolated, which were Aeromonas hydrophila , Brevundimonas vesicularis , Chromobacterium violaceum , Citrobacter youngae , Empedobacter brevis , Pantoea agglomerans , Pseudomonas putida , Pseudomonas stutzeri and Streptococcus mitis . All the isolated bacterial strains, although showing a rare potential virulence, demonstrated peculiar and favorable metabolic attitudes in controlling environmental pollution. The therapeutical effects of certain spring waters are currently being proven as correlated not only to their peculiar mineral composition, but also to the complex activity of their resident non-pathogenic bacterial populations. Although the present study provided only preliminary data, some of the non-pathogenic bacterial populations that were identified in the Comano spring water are likely to produce molecular mediators with a role in the wound healing process that, thus far, remain unknown. Numerous other unknown bacterial species, comprehensively termed DNA-rich 'dark matter', are likely to contribute to the Comano water regenerative properties as well. Therefore, the non-pathogenic bacterial populations of the Comano spring water are possibly credited for its demonstrated regenerative properties.

Drying bacterial biosaline patterns capable of vital reanimation upon rehydration: novel hibernating biomineralogical life formations.

PubMed

Gómez Gómez, José María; Medina, Jesús; Hochberg, David; Mateo-Martí, Eva; Martínez-Frías, Jesús; Rull, Fernando

2014-07-01

Water is the fundamental molecule for life on Earth. Thus, the search for hibernating life-forms in waterless environments is an important research topic for astrobiology. To date, however, the organizational patterns containing microbial life in extremely dry places, such as the deserts of Earth, the Dry Valleys of Antarctica, or Mars analog regolith, have been poorly characterized. Here, we report on the formation of bacterial biosaline self-organized drying patterns formed over plastic surfaces. These emerge during the evaporation of sessile droplets of aqueous NaCl salt 0.15 M solutions containing Escherichia coli cells. In the present study, scanning electron microscopy (SEM) and energy dispersive X-ray spectrometry (EDS) analyses indicated that the bacterial cells and the NaCl in these biosaline formations are organized in a two-layered characteristic 3-D architectural morphology. A thin filmlike top layer formed by NaCl conjugated to, and intermingled with, "mineralized" bacterial cells covers a bottom layer constructed by the bulk of the nonmineralized bacterial cells; both layers have the same morphological pattern. In addition, optical microscopic time-lapsed movies show that the formation of these patterns is a kinetically fast process that requires the coupled interaction between the salt and the bacterial cells. Apparently, this mutual interaction drives the generative process of self-assembly that underlies the drying pattern formation. Most notably, the bacterial cells inside these drying self-assembled patterns enter into a quiescent suspended anhydrobiotic state resistant to complete desiccation and capable of vital reanimation upon rehydration. We propose that these E. coli biosaline drying patterns represent an excellent experimental model for understanding different aspects of anhydrobiosis phenomena in bacteria as well as for revealing the mechanisms of bacterially induced biomineralization, both highly relevant topics for the search of life in extraterrestrial locations.

New target for inhibition of bacterial RNA polymerase: 'switch region'.

PubMed

Srivastava, Aashish; Talaue, Meliza; Liu, Shuang; Degen, David; Ebright, Richard Y; Sineva, Elena; Chakraborty, Anirban; Druzhinin, Sergey Y; Chatterjee, Sujoy; Mukhopadhyay, Jayanta; Ebright, Yon W; Zozula, Alex; Shen, Juan; Sengupta, Sonali; Niedfeldt, Rui Rong; Xin, Cai; Kaneko, Takushi; Irschik, Herbert; Jansen, Rolf; Donadio, Stefano; Connell, Nancy; Ebright, Richard H

2011-10-01

A new drug target - the 'switch region' - has been identified within bacterial RNA polymerase (RNAP), the enzyme that mediates bacterial RNA synthesis. The new target serves as the binding site for compounds that inhibit bacterial RNA synthesis and kill bacteria. Since the new target is present in most bacterial species, compounds that bind to the new target are active against a broad spectrum of bacterial species. Since the new target is different from targets of other antibacterial agents, compounds that bind to the new target are not cross-resistant with other antibacterial agents. Four antibiotics that function through the new target have been identified: myxopyronin, corallopyronin, ripostatin, and lipiarmycin. This review summarizes the switch region, switch-region inhibitors, and implications for antibacterial drug discovery. Copyright © 2011 Elsevier Ltd. All rights reserved.

[Bacterial meningitis].

PubMed

Brouwer, M C; van de Beek, D

2012-05-01

Bacterial meningitis is a severe disease which affects 35.000 Europeans each year and has a mortality rate of about 20%. During the past 25 years the epidemiology of bacterial meningitis has changed significantly due to the implementation of vaccination against Haemophilus influenzae, Neisseria meningtidis group C and Streptococcus pneumoniae. Due to these vaccines, meningitis is now predominantly a disease occurring in adults, caused especially by Streptococcus pneumoniae, while it was formerly a child disease which was largely caused by Haemophilus influenzae. Bacterial meningitis is often difficult to recognize since the classical presentation with neck stiffness, reduced awareness and fever occurs in less than half of the patients. The only way to diagnose or exclude bacterial meningitis is by performing low-threshold cerebrospinal fluid examination with a suspicion of bacterial meningitis. The treatment consists of the prescription of antibiotics and dexamethasone.

[Community acquired bacterial meningitis in patients over 60].

PubMed

Mora Mora, Luis A; Arco Espinosa, Micke E de; Plumet, Javier; Micheli, Federico

2015-01-01

Acute bacterial meningitis has a global mortality rate of 135000 cases per year. In Argentina over the last 12 years, the annual incidence rate has been 5.5/100 000. About 20% of patients present neurological sequelae, which are more common in patients aged 60 or older. Our objective here is to determine the clinical characteristics, the most common causes and to measure evolution in patients over 60 years old diagnosed with meningitis and treated at the Hospital de Clinicas José de San Martín. This is a retrospective study based on a review of medical records from 2003 to 2013 that takes into account patients older than 60 who were diagnosed with acute bacterial meningitis acquired in the community by a microbiological diagnosis of CSF or those included due to a high suspicion of bacterial meningitis (pleocitosis > 2000 cells/mm3, proteins > 220 mg/dl, glycorrhachia < 34 mg/dl, glycorrhachia/glucose index < 0.23). Cases of TB meningitis, nosocomial, postoperative and other nonbacterial meningitis were excluded. Sixty nine patients were included, 45 (65%) were women with an average age of 78 ± 10.6 years. Only 40% had the triad of classical meningitis symptoms (stiff neck, fever and altered mental status). In 52% of the patients germs developed in the CSF, the most frequent being Streptococcus pneumoniae present in 47% of cases. Lethality rate was 41%, all of them by methicillin-sensitive Staphylococcus aureus. Only 24 (35%) cases were admitted into intensive care. The main sequelae present were motor disorders (12%) and hearing loss (5%).

Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples.

PubMed

Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

2014-04-01

Kombucha is a sweetened tea beverage that, as a consequence of fermentation, contains ethanol, carbon dioxide, a high concentration of acid (gluconic, acetic and lactic) as well as a number of other metabolites and is thought to contain a number of health-promoting components. The sucrose-tea solution is fermented by a symbiosis of bacteria and yeast embedded within a cellulosic pellicle, which forms a floating mat in the tea, and generates a new layer with each successful fermentation. The specific identity of the microbial populations present has been the focus of attention but, to date, the majority of studies have relied on culture-based analyses. To gain a more comprehensive insight into the kombucha microbiota we have carried out the first culture-independent, high-throughput sequencing analysis of the bacterial and fungal populations of 5 distinct pellicles as well as the resultant fermented kombucha at two time points. Following the analysis it was established that the major bacterial genus present was Gluconacetobacter, present at >85% in most samples, with only trace populations of Acetobacter detected (<2%). A prominent Lactobacillus population was also identified (up to 30%), with a number of sub-dominant genera, not previously associated with kombucha, also being revealed. The yeast populations were found to be dominated by Zygosaccharomyces at >95% in the fermented beverage, with a greater fungal diversity present in the cellulosic pellicle, including numerous species not identified in kombucha previously. Ultimately, this study represents the most accurate description of the microbiology of kombucha to date. Copyright © 2013 Elsevier Ltd. All rights reserved.

[ABOUT UNIFICATION OF LABORATORY CRITERIA OF DIFFERENTIATION OF BACTERIAL VAGINOSIS].

PubMed

Mavzutov, A R; Tsvetkova, A V; Muretdinova, L A

2015-06-01

The article presents analysis of laboratory criteria and classifcations used to interpret results of laboratory analysis by technique of microscopy on bacterial vaginosis or dysbacteriosis of vagina. Their advantages and restrictions are demonstrated The unified criteria of evaluation are proposed concerning results of microscopy of mucosal discharge of vagina and corresponding classification. Thereafter, three degrees of bacterial vaginosis (dysbacteriosis of vagina) are differentiated: first degree--compensated dysbacteriosis of vagina, second degree--sub compensated dysbacteriosis of vagina and third degree--decompensated dysbacteriosis of vagina. The corresponding laboratory report of physician is formulated. The proposals are presented concerning development of common unified requirements to stages (pre-analytical, analytical, post-analytical) of laboratory diagnostic of bacterial vaginosis (dysbacteriosis of vagina) with purpose of their unambiguous understanding by clinicians and hence their decision making concerning necessity and tactics of management of patient.

Acute bacterial and viral meningitis.

PubMed

Bartt, Russell

2012-12-01

Most cases of acute meningitis are infectious and result from a potentially wide range of bacterial and viral pathogens. The organized approach to the patient with suspected meningitis enables the prompt administration of antibiotics, possibly corticosteroids, and diagnostic testing with neuroimaging and spinal fluid analysis. Acute meningitis is infectious in most cases and caused by a potentially wide range of bacterial and viral pathogens. Shifts in the epidemiology of bacterial pathogens have been influenced by changes in vaccines and their implementation. Seasonal and environmental changes influence the likely viral and rickettsial pathogens. The organized approach to the patient with suspected meningitis enables the prompt administration of antibiotics, possibly corticosteroids, and diagnostic testing with neuroimaging and spinal fluid analysis. Pertinent testing and treatment can vary with the clinical presentation, season, and possible exposures. This article reviews the epidemiology, clinical presentation, diagnosis, and treatment of acute meningitis.

Bacterial and fungal endophthalmitis in upper Egypt: related species and risk factors.

PubMed

Gharamah, A A; Moharram, A M; Ismail, M A; Al-Hussaini, A K

2012-08-01

To study risk factors, contributing factors of bacterial and fungal endophthalmitis in Upper Egypt, test the isolated species sensitive to some therapeutic agents, and to investigate the air-borne bacteria and fungi in opthalmology operating rooms. Thirty one cases of endophthalmitis were clinically diagnosed and microbiologically studied. Indoor air-borne bacteria and fungi inside four air-conditioned operating rooms in the Ophthalmology Department at Assiut University Hospitals were also investigated. The isolated microbes from endophthalmitis cases were tested for their ability to produce some extracellular enzymes including protease, lipase, urease, phosphatase and catalase. Also the ability of 5 fungal isolates from endophthalmitis origin to produce mycotoxins and their sensitivity to some therapeutic agents were studied. Results showed that bacteria and fungi were responsihle for infection in 10 and 6 cases of endophthalmitis, respectively and only 2 cases produced a mixture of bacteria and fungi. Trauma was the most prevalent risk factor of endophthalmitis where 58.1% of the 31 cases were due to trauma. In ophthalmology operating rooms, different bacterial and fungal species were isolated. 8 bacterial and 5 fungal isolates showed their ability to produce enzymes while only 3 fungal isolates were able to produce mycotoxins. Terbinafine showed the highest effect against most isolates in vitro. The ability of bacterial and fungal isolates to produce extracellular enzymes and mycotoxins may be aid in the invasion and destruction of eye tissues. Microbial contamination of operating rooms with air-borne bacteria and fungi in the present work may be a source of postoperative endophthalmitis.

Olfactory ensheathing cells: nitric oxide production and innate immunity.

PubMed

Harris, Julie A; West, Adrian K; Chuah, Meng Inn

2009-12-01

Olfactory nerves extend from the nasal cavity to the central nervous system and provide therefore, a direct route for pathogenic infection of the brain. Since actual infection by this route remains relatively uncommon, powerful endogenous mechanisms for preventing microbial infection must exist, but these remain poorly understood. Our previous studies unexpectedly revealed that the unique glial cells that ensheath olfactory nerves, olfactory ensheathing cells (OECs), expressed components of the innate immune response. In this study, we show that OECs are able to detect and respond to bacterial challenge via the synthesis of nitric oxide. In vitro studies revealed that inducible nitric oxide synthase (iNOS) mRNA and protein were present in Escherichia coli- and Staphylococcus aureus-incubated OECs, but were barely detectable in untreated OECs. Neuronal NOS and endothelial NOS were not expressed by OECs pre- and post-bacterial incubation. Nuclear translocation of nuclear factor kappa B (NFkappaB), detectable in the majority of OECs 1 h following bacterial incubation, preceded iNOS induction which resulted in the production of nitric oxide. N(G)-methyl-L-arginine significantly attenuated nitric oxide (P < 0.001) and nitrite production (P < 0.001) by OECs. In rat olfactory mucosa which was compromised by irrigation with 0.17M zinc sulfate or 0.7% Triton X-100 to facilitate bacterial infiltration, OECs contributed to a robust synthesis of iNOS. These data strongly support the hypothesis that OECs are an essential component of the innate immune response against bacterial invasion of the central nervous system via olfactory nerves.

Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary.

PubMed

Wei, Guangshan; Li, Mingcong; Li, Fenge; Li, Han; Gao, Zheng

2016-11-01

There are close exchanges between sediment and water in estuaries; however, the patterns of prokaryotic community assembly in these two habitat types are still unclear. This study investigated the bacterial and archaeal abundance, diversity, and community composition in the sediment and the overlying water of the Yellow River estuary. Notably higher prokaryotic abundance and diversity were detected in the sediment than in the water, and bacterial abundance and diversity were remarkably higher than those of archaea. Furthermore, the ratio of bacterial to archaeal 16S rRNA gene abundance was significantly lower in the sediment than in the water. Bacterial communities at different taxonomic levels were apparently distinct between the sediment and water, but archaeal communities were not. The most dominant bacteria were affiliated with Deltaproteobacteria and Gammaproteobacteria in sediment and with Alphaproteobacteria and Betaproteobacteria in water. Euryarchaeota and Thaumarchaeota were the most abundant archaea in both habitats. Although distinct prokaryotic distribution patterns were observed, most of the dominant bacteria and archaea present were related to carbon, nitrogen, and sulfur cycling processes, such as methanogenesis, ammonia oxidation, and sulfate reduction. Unexpectedly, prokaryotes from the water showed a higher sensitivity to environmental factors, while only a few factors affected sediment communities. Additionally, some potential co-occurrence relationships between prokaryotes were also found in this study. These results suggested distinct distribution patterns of bacterial and archaeal communities between sediment and overlying water in this important temperate estuary, which may serve as a useful community model for the further ecological and evolutionary study of prokaryotes in estuarine ecosystems.

Antibacterial activity of polyphenolic fraction of Kombucha against Vibrio cholerae: targeting cell membrane.

PubMed

Bhattacharya, D; Ghosh, D; Bhattacharya, S; Sarkar, S; Karmakar, P; Koley, H; Gachhui, R

2018-02-01

The present study was undertaken to determine the mechanism of antibacterial activity of a polyphenolic fraction, composed of mainly catechin and isorhamnetin, previously isolated from Kombucha, a 14-day fermented beverage of sugared black tea, against the enteropathogen Vibrio cholerae N16961. Bacterial growth was found to be seriously impaired by the polyphenolic fraction in a dose-dependent manner. Scanning Electron Microscopy demonstrated morphological alterations in bacterial cells when exposed to the polyphenolic fraction in a concentration-dependent manner. Permeabilization assays confirmed that the fraction disrupted bacterial membrane integrity in both time- and dose-dependent manners, which were proportional to the production of intracellular reactive oxygen species (ROS). Furthermore, each of the polyphenols catechin and isorhamnetin showed the ability to permeate bacterial cell membranes by generating oxidative stress, thereby suggesting their role in the antibacterial potential of Kombucha. Thus, the basic mechanism of antibacterial activity of the Kombucha polyphenolic fraction against V. cholerae involved bacterial membrane permeabilization and morphological changes, which might be due to the generation of intracellular ROS. To the best of our knowledge, this is the first report on the investigation of antibacterial mechanism of Kombucha, which is mostly attributed to its polyphenolic content. The emergence of multidrug-resistant Vibrio cholerae strains has hindered an efficient anti-Vibrio therapy. This study has demonstrated the membrane damage-mediated antibacterial mechanism of Kombucha, a popular fermented beverage of sugared tea, which is mostly attributed to its polyphenolic content. This study also implies the exploitation of Kombucha as a potential new source of bioactive polyphenols against V. cholerae. © 2017 The Society for Applied Microbiology.

Bacterial Urease and its Role in Long-Lasting Human Diseases

PubMed Central

Konieczna, Iwona; Żarnowiec, Paulina; Kwinkowski, Marek; Kolesińska, Beata; Frączyk, Justyna; Kamiński, Zbigniew; Kaca, Wiesław

2012-01-01

Urease is a virulence factor found in various pathogenic bacteria. It is essential in colonization of a host organism and in maintenance of bacterial cells in tissues. Due to its enzymatic activity, urease has a toxic effect on human cells. The presence of ureolytic activity is an important marker of a number of bacterial infections. Urease is also an immunogenic protein and is recognized by antibodies present in human sera. The presence of such antibodies is connected with progress of several long-lasting diseases, like rheumatoid arthritis, atherosclerosis or urinary tract infections. In bacterial ureases, motives with a sequence and/or structure similar to human proteins may occur. This phenomenon, known as molecular mimicry, leads to the appearance of autoantibodies, which take part in host molecules destruction. Detection of antibodies-binding motives (epitopes) in bacterial proteins is a complex process. However, organic chemistry tools, such as synthetic peptide libraries, are helpful in both, epitope mapping as well as in serologic investigations. In this review, we present a synthetic report on a molecular organization of bacterial ureases - genetic as well as structural. We characterize methods used in detecting urease and ureolytic activity, including techniques applied in disease diagnostic processes and in chemical synthesis of urease epitopes. The review also provides a summary of knowledge about a toxic effect of bacterial ureases on human body and about occurrence of anti-urease antibodies in long-lasting diseases. PMID:23305365

Biofilms in chronic suppurative otitis media and cholesteatoma: scanning electron microscopy findings.

PubMed

Saunders, James; Murray, Michael; Alleman, Anthony

2011-01-01

Biofilms play a role in the pathogenesis of a variety of otorhinolaryngologic diseases, including otitis media and cholesteatoma. Despite this, relatively few studies have undertaken to demonstrate the presence of biofilms tissues from patients with chronic otitis media or infected cholesteatoma. Our objective is to detect evidence of biofilms human chronic ear infections with scanning electron microscopy (SEM). We hypothesized that bacterial biofilms are present in patients with chronic otitis media. We performed prospective collection of tissue collected during middle ear surgery from 16 patients undergoing middle ear or mastoid surgery with chronic ear infections. A total of 31 middle and mastoid tissue samples were harvested at the time of surgery and processed with critical point drying for SEM analysis. Samples were then searched for evidence of biofilms. Bacterial-shaped objects were identified that displayed both surface binding and the presence of a glycocalyx in 4 patients, findings consistent with bacterial biofilms. Most of these (3 of 4) were in patients with infected cholesteatoma, and biofims were identified in 60% of cholesteatoma cases (3 of 5). On the other hand, only 1 of 7 cases with chronic suppurative otitis media had evidence of biofilms. SEM supports the hypothesis that bacterial biofilms are common in chronic infections associated with cholesteatoma and are present in some cases of chronic suppurative otitis media without cholesteatoma. Copyright © 2011 Elsevier Inc. All rights reserved.

Unraveling the Enzymatic Activity of Oxygenated Carbon Nanotubes and Their Application in the Treatment of Bacterial Infections.

PubMed

Wang, Huan; Li, Penghui; Yu, Dongqin; Zhang, Yan; Wang, Zhenzhen; Liu, Chaoqun; Qiu, Hao; Liu, Zhen; Ren, Jinsong; Qu, Xiaogang

2018-05-17

Carbon nanotubes (CNTs) and their derivatives have emerged as a series of efficient biocatalysts to mimic the function of natural enzymes in recent years. However, the unsatisfiable enzymatic efficiency usually limits their practical usage ranging from materials science to biotechnology. Here, for the first time, we present the synthesis of several oxygenated-group-enriched carbon nanotubes (o-CNTs) via a facile but green approach, as well as their usage as high-performance peroxidase mimics for biocatalytic reaction. Exhaustive characterizations of the enzymatic activity of o-CNTs have been provided by exploring the accurate effect of various oxygenated groups on their surface including carbonyl, carboxyl, and hydroxyl groups. Because of the "competitive inhibition" effect among all of these oxygenated groups, the catalytic efficiency of o-CNTs is significantly enhanced by weakening the presence of noncatalytic sites. Furthermore, the admirable enzymatic activity of these o-CNTs has been successfully applied in the treatment of bacterial infections, and the results of both in vitro and in vivo nanozyme-mediated bacterial clearance clearly demonstrate the feasibility of o-CNTs as robust peroxidase mimics to effectively decrease the bacterial viability under physiological conditions. We believe that the present study will not only facilitate the construction of novel efficient nanozymes by rationally adjusting the degree of the "competitive inhibition" effect, but also broaden the biological usage of o-CNT-based nanomaterials via their satisfactory enzymatic activity.

Population dynamics of bacteria associated with different strains of the pine wood nematode Bursaphelenchus xylophilus after inoculation in maritime pine (Pinus pinaster).

PubMed

Roriz, Mariana; Santos, Carla; Vasconcelos, Marta W

2011-08-01

For a long time it was thought that Bursaphelenchus xylophilus was the only agent of the pine wilt disease. Recently, it was discovered that there are bacteria associated with the nematodes that contribute to the pathogenesis of this disease, mainly through the release of toxins that promote the death of the pines. Among the species most commonly found, are bacteria belonging to the Bacillus, Pantoea, Pseudomonas and Xanthomonas genera. The main objective of this work was to study the effect of inoculation of maritime pine (Pinus pinaster) with four different nematode isolates, in the bacterial population of nematodes and trees, at different stages of disease progression. The monitoring of progression of disease symptoms was also recorded. Also, the identification of bacteria isolated from the xylem of trees and the surface of nematodes was performed by classical identification methods, by the API20E identification system and by sequencing of bacterial DNA. The results showed that for the symptoms progression, the most striking difference was observed for the pines inoculated with the avirulent isolate, C14-5, which led to a slower and less severe aggravation of symptoms than in pines inoculated with the virulent isolates. In general, it was found that bacterial population, inside the tree, increased with disease progression. A superior bacterial quantity was isolated from pines inoculated with the nematode isolates HF and 20, and, comparatively, few bacteria were isolated from pines inoculated with the avirulent isolate. The identification system API20E was insufficient in the identification of bacterial species; Enterobacter cloacae species was identified in 79% of the isolated bacterial colonies and seven of these colonies could not be identified by this method. Molecular identification methods, through bacterial DNA sequencing, allowed a more reliable identification: eleven different bacterial species within the Bacillus, Citrobacter, Enterobacter, Escherichia, Klebsiella, Paenibacillus, Pantoea and Terribacillus genera were identified. General bacterial diversity increased with the progression of the disease. Bacillus spp. were predominant at the earlier stage of disease progression and Klebsiella oxytoca at the later stages. Furthermore, bacterial species isolated from the surface of nematodes were similar to those isolated from the xylem of pines. In the present work new bacterial species were identified which have never been reported before in this type of study and may be associated with their geographical origin (Portugal). P. pinaster, the pine species used in this study, was different from those commonly grown in Japan and China. Furthermore, it was the first time that bacteria were isolated and identified from an avirulent pine wood nematode isolate. Copyright © 2011 Elsevier Inc. All rights reserved.

Diversity and function of bacterial microbiota in the mosquito holobiont

PubMed Central

2013-01-01

Mosquitoes (Diptera: Culicidae) have been shown to host diverse bacterial communities that vary depending on the sex of the mosquito, the developmental stage, and ecological factors. Some studies have suggested a potential role of microbiota in the nutritional, developmental and reproductive biology of mosquitoes. Here, we present a review of the diversity and functions of mosquito-associated bacteria across multiple variation factors, emphasizing recent findings. Mosquito microbiota is considered in the context of possible extended phenotypes conferred on the insect hosts that allow niche diversification and rapid adaptive evolution in other insects. These kinds of observations have prompted the recent development of new mosquito control methods based on the use of symbiotically-modified mosquitoes to interfere with pathogen transmission or reduce the host life span and reproduction. New opportunities for exploiting bacterial function for vector control are highlighted. PMID:23688194

Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India.

PubMed

Sha, Shankar Prasad; Jani, Kunal; Sharma, Avinash; Anupma, Anu; Pradhan, Pooja; Shouche, Yogesh; Tamang, Jyoti Prakash

2017-09-08

Marcha and thiat are traditionally prepared amylolytic starters use for production of various ethnic alcoholic beverages in Sikkim and Meghalaya states in India. In the present study we have tried to investigate the bacterial and fungal community composition of marcha and thiat by using high throughput sequencing. Characterization of bacterial community depicts phylum Proteobacteria is the most dominant in both marcha (91.4%) and thiat (53.8%), followed by Firmicutes, and Actinobacteria. Estimates of fungal community composition showed Ascomycota as the dominant phylum. Presence of Zygomycota in marcha distinguishes it from the thiat. The results of NGS analysis revealed dominance of yeasts in marcha whereas molds out numbers in case of thiat. This is the first report on microbial communities of traditionally prepared amylolytic starters of India using high throughput sequencing.

The Drosophila melanogaster host model

PubMed Central

Igboin, Christina O.; Griffen, Ann L.; Leys, Eugene J.

2012-01-01

The deleterious and sometimes fatal outcomes of bacterial infectious diseases are the net result of the interactions between the pathogen and the host, and the genetically tractable fruit fly, Drosophila melanogaster, has emerged as a valuable tool for modeling the pathogen–host interactions of a wide variety of bacteria. These studies have revealed that there is a remarkable conservation of bacterial pathogenesis and host defence mechanisms between higher host organisms and Drosophila. This review presents an in-depth discussion of the Drosophila immune response, the Drosophila killing model, and the use of the model to examine bacterial–host interactions. The recent introduction of the Drosophila model into the oral microbiology field is discussed, specifically the use of the model to examine Porphyromonas gingivalis–host interactions, and finally the potential uses of this powerful model system to further elucidate oral bacterial-host interactions are addressed. PMID:22368770

Antifouling activities of marine bacteria associated with sponge ( Sigmadocia sp.)

NASA Astrophysics Data System (ADS)

Satheesh, S.; Soniamby, A. R.; Sunjaiy Shankar, C. V.; Mary Josephine Punitha, S.

2012-09-01

The present study aimed at assessing the antifouling activity of bacteria associated with marine sponges. A total of eight bacterial strains were isolated from the surface of sponge Sigmadocia sp., of them, SS02, SS05 and SS06 showed inhibitory activity against biofilm-forming bacteria. The extracts of these 3 strains considerably affected the extracellular polymeric substance producing ability and adhesion of biofilm-forming bacterial strains. In addition to disc diffusion assay, microalgal settlement assay was carried out with the extracts mixed with polyurethane wood polish and coated onto stainless steel coupons. The extract of strain SS05 showed strong microalgal settlement inhibitory activity. Strain SS05 was identified as Bacillus cereus based on its 16S rRNA gene. Metabolites of the bacterial strains associated with marine invertebrates promise to be developed into environment-friendly antifouling agents.

Influence of nanophase titania topography on bacterial attachment and metabolism

PubMed Central

Park, Margaret R; Banks, Michelle K; Applegate, Bruce; Webster, Thomas J

2008-01-01

Surfaces with nanophase compared to conventional (or nanometer smooth) topographies are known to have different properties of area, charge, and reactivity. Previously published research indicates that the attachment of certain bacteria (such as Pseudomonas fluorescens 5RL) is higher on surfaces with nanophase compared to conventional topographies, however, their effect on bacterial metabolism is unclear. Results presented here show that the adhesion of Pseudomonas fluorescens 5RL and Pseudomonas putida TVA8 was higher on nanophase than conventional titania. Importantly, in terms of metabolism, bacteria attached to the nanophase surfaces had higher bioluminescence rates than on the conventional surfaces under all nutrient conditions. Thus, the results from this study show greater select bacterial metabolism on nanometer than conventional topographies, critical results with strong consequences for the design of improved biosensors for bacteria detection. PMID:19337418

Isolation and identification of bacteria from marine market fish Scomberomorus guttatus (Bloch and Schneider, 1801) from Madurai district, Tamil Nadu, India.

PubMed

Karthiga Rani, M; Chelladurai, G; Jayanthi, G

2016-09-01

The present study was conducted to evaluate the hygienic quality and freshness of fish Indo-pacific King Mackerel "Scomberomorus guttatus" through the investigation of the occurrence of bacteria which is an indicator for fish quality. Fishes were collected every fortnight from Madurai fish market on monthly twice of January 2014 to March 2014. Skin surface of the fish was examined. Escherichia coli, Proteus vulgaris, Bacillus subtilis, Klebsiella pneumonia, Pseudomonas aeruginosa and Staphylococcus aureus were identified by Biochemical tests (IMViC Tests). Among the six bacterial species E. coli and K. pneumonia were found in all the collected samples where as other bacterial species were not found. The result of this study revealed that raw fish sold in Madurai fish market has high contamination so the presence of the bacterial species has strongly suggested the urgent need to improve the quality control systems in Madurai fish market.

Enhancement of biogas production from microalgal biomass through cellulolytic bacterial pretreatment.

PubMed

Kavitha, S; Subbulakshmi, P; Rajesh Banu, J; Gobi, Muthukaruppan; Tae Yeom, Ick

2017-06-01

Generation of bioenergy from microalgal biomass has been a focus of interest in recent years. The recalcitrant nature of microalgal biomass owing to its high cellulose content limits methane generation. Thus, the present study investigates the effect of bacterial-based biological pretreatment on liquefaction of the microalga Chlorella vulgaris prior to anaerobic biodegradation to gain insights into energy efficient biomethanation. Liquefaction of microalgae resulted in a higher biomass stress index of about 18% in the experimental (pretreated with cellulose-secreting bacteria) vs. 11.8% in the control (non-pretreated) group. Mathematical modelling of the biomethanation studies implied that bacterial pretreatment had a greater influence on sustainable methane recovery, with a methane yield of about 0.08 (g Chemical Oxygen Demand/g Chemical Oxygen Demand), than did control pretreatment, with a yield of 0.04 (g Chemical Oxygen Demand/g Chemical Oxygen Demand). Energetic analysis of the proposed method of pretreatment showed a positive energy ratio of 1.04. Copyright © 2017 Elsevier Ltd. All rights reserved.

Isolation, screening, and characterization of surface-active agent-producing, oil-degrading marine bacteria of Mumbai Harbor.

PubMed

Mohanram, Rajamani; Jagtap, Chandrakant; Kumar, Pradeep

2016-04-15

Diverse marine bacterial species predominantly found in oil-polluted seawater produce diverse surface-active agents. Surface-active agents produced by bacteria are classified into two groups based on their molecular weights, namely biosurfactants and bioemulsifiers. In this study, surface-active agent-producing, oil-degrading marine bacteria were isolated using a modified Bushnell-Haas medium with high-speed diesel as a carbon source from three oil-polluted sites of Mumbai Harbor. Surface-active agent-producing bacterial strains were screened using nine widely used methods. The nineteen bacterial strains showed positive results for more than four surface-active agent screening methods; further, these strains were characterized using biochemical and nucleic acid sequencing methods. Based on the results, the organisms belonged to the genera Acinetobacter, Alcanivorax, Bacillus, Comamonas, Chryseomicrobium, Halomonas, Marinobacter, Nesterenkonia, Pseudomonas, and Serratia. The present study confirmed the prevalence of surface-active agent-producing bacteria in the oil-polluted waters of Mumbai Harbor. Copyright © 2016 Elsevier Ltd. All rights reserved.

1,2-Benzisoselenazol-3(2H)-one Derivatives As a New Class of Bacterial Urease Inhibitors.

PubMed

Macegoniuk, Katarzyna; Grela, Ewa; Palus, Jerzy; Rudzińska-Szostak, Ewa; Grabowiecka, Agnieszka; Biernat, Monika; Berlicki, Łukasz

2016-09-08

Urease inhibitors are considered promising compounds for the treatment of ureolytic bacterial infections, particularly infections resulting from Helicobacter pylori in the gastric tract. Herein, we present the synthesis and the inhibitory activity of novel and highly effective organoselenium compounds as inhibitors of Sporosarcina pasteurii and Helicobacter pylori ureases. These studied compounds represent a class of competitive reversible urease inhibitors. The most active compound, 2-phenyl-1,2-benzisoselenazol-3(2H)-one (ebselen), displayed Ki values equal to 2.11 and 226 nM against S. pasteurii and H. pylori enzymes, respectively, indicating ebselen as one of the most potent low-molecular-weight inhibitors of bacterial ureases reported to date. Most of these molecules penetrated through the cell membrane of the Gram-negative bacteria Escherichia coli (pGEM::ureOP) in vitro. Furthermore, whole-cell studies on the H. pylori J99 reference strain confirmed the high efficiency of the examined organoselenium compounds as urease inhibitors against pathogenic bacteria.

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review.

PubMed

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using four factors: temperature, relative humidity (RH), air exchange rate, and occupant density, as a minimum requirement. We also summarize the relevant legislation by country. Choice of factors to measure remain controversial are discussed.

Plaque bacterial microbiome diversity in children younger than 30 months with or without caries prior to eruption of second primary molars.

PubMed

Xu, He; Hao, Wenjing; Zhou, Qiong; Wang, Wenhong; Xia, Zhongkui; Liu, Chuan; Chen, Xiaochi; Qin, Man; Chen, Feng

2014-01-01

Our primary objective is to phylogenetically characterize the supragingival plaque bacterial microbiome of children prior to eruption of second primary molars by pyrosequencing method for studying etiology of early childhood caries. Supragingival plaque samples were collected from 10 caries children and 9 caries-free children. Plaque DNA was extracted, used to generate DNA amplicons of the V1-V3 hypervariable region of the bacterial 16S rRNA gene, and subjected to 454-pyrosequencing. On average, over 22,000 sequences per sample were generated. High bacterial diversity was noted in the plaque of children with caries [170 operational taxonomical units (OTU) at 3% divergence] and caries-free children (201 OTU at 3% divergence) with no significant difference. A total of 8 phyla, 15 classes, 21 orders, 30 families, 41 genera and 99 species were represented. In addition, five predominant phyla (Firmicute, Fusobacteria, Proteobacteria, Bacteroidetes and Actinobacteria) and seven genera (Leptotrichia, Streptococcus, Actinomyces, Prevotella, Porphyromonas, Neisseria, and Veillonella) constituted a majority of contents of the total microbiota, independent of the presence or absence of caries. Principal Component Analysis (PCA) presented that caries-related genera included Streptococcus and Veillonella; while Leptotrichia, Selenomonas, Fusobacterium, Capnocytophaga and Porphyromonas were more related to the caries-free samples. Neisseria and Prevotella presented approximately in between. In both groups, the degree of shared organism lineages (as defined by species-level OTUs) among individual supragingival plaque microbiomes was minimal. Our study represented for the first time using pyrosequencing to elucidate and monitor supragingival plaque bacterial diversity at such young age with second primary molar unerrupted. Distinctions were revealed between caries and caries-free microbiomes in terms of microbial community structure. We observed differences in abundance for several microbial groups between the caries and caries-free host populations, which were consistent with the ecological plaque hypothesis. Our approach and findings could be extended to correlating microbiomic changes after occlusion establishment and caries treatment.

Bioconservation of deteriorated monumental calcarenite stone and identification of bacteria with carbonatogenic activity.

PubMed

Jroundi, Fadwa; Fernández-Vivas, Antonia; Rodriguez-Navarro, Carlos; Bedmar, Eulogio J; González-Muñoz, María Teresa

2010-07-01

The deterioration of the stone built and sculptural heritage has prompted the search and development of novel consolidation/protection treatments that can overcome the limitations of traditional ones. Attention has been drawn to bioconservation, particularly bacterial carbonatogenesis (i.e. bacterially induced calcium carbonate precipitation), as a new environmentally friendly effective conservation strategy, especially suitable for carbonate stones. Here, we study the effects of an in situ bacterial bioconsolidation treatment applied on porous limestone (calcarenite) in the sixteenth century San Jeronimo Monastery in Granada, Spain. The treatment consisted in the application of a nutritional solution (with and without Myxococcus xanthus inoculation) on decayed calcarenite stone blocks. The treatment promoted the development of heterotrophic bacteria able to induce carbonatogenesis. Both the consolidation effect of the treatment and the response of the culturable bacterial community present in the decayed stone were evaluated. A significant surface strengthening (consolidation) of the stone, without altering its surface appearance or inducing any detrimental side effect, was achieved upon application of the nutritional solution. The treatment efficacy was independent of the presence of M. xanthus (which is known as an effective carbonatogenic bacterium). The genetic diversity of 116 bacterial strains isolated from the stone, of which 113 strains showed carbonatogenic activity, was analysed by repetitive extragenic palindromic-polymerase chain reaction (REP-PCR) and 16S rRNA gene sequencing. The strains were distributed into 31 groups on the basis of their REP-PCR patterns, and a representative strain of each group was subjected to 16S rRNA gene sequencing. Analysis of these sequences showed that isolates belong to a wide variety of phylogenetic groups being closely related to species of 15 genera within the Proteobacteria, Firmicutes and the Actinobacteria. This study shows that the abundant carbonatogenic bacteria present in the decayed stone are able to effectively consolidate the degraded stone by producing new calcite (and vaterite) cement if an adequate nutritional solution is used. The implications of these results for the conservation of cultural heritage are discussed.

Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill▿ †

PubMed Central

Alonso-Gutiérrez, Jorge; Figueras, Antonio; Albaigés, Joan; Jiménez, Núria; Viñas, Marc; Solanas, Anna M.; Novoa, Beatriz

2009-01-01

The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution-affected areas with similar characteristics. PMID:19376924

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review

PubMed Central

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using four factors: temperature, relative humidity (RH), air exchange rate, and occupant density, as a minimum requirement. We also summarize the relevant legislation by country. Choice of factors to measure remain controversial are discussed. PMID:29238327

Bacteriological profiling of diphenylureas as a novel class of antibiotics against methicillin-resistant Staphylococcus aureus

PubMed Central

Younis, Waleed; Ezzat, Hany G.; Peters, Christine E.; AbdelKhalek, Ahmed; Cooper, Bruce; Pogliano, Kit; Pogliano, Joe; Mayhoub, Abdelrahman S.; Seleem, Mohamed N.

2017-01-01

Bacterial resistance to antibiotics remains an imposing global public health challenge. Of the most serious pathogens, methicillin-resistant Staphylococcus aureus (MRSA) is problematic given strains have emerged that exhibit resistance to several antibiotic classes including β-lactams and agents of last resort such as vancomycin. New antibacterial agents composed of unique chemical scaffolds are needed to counter this public health challenge. The present study examines two synthetic diphenylurea compounds 1 and 2 that inhibit growth of clinically-relevant isolates of MRSA at concentrations as low as 4 µg/mL and are non-toxic to human colorectal cells at concentrations up to 128 μg/mL. Both compounds exhibit rapid bactericidal activity, completely eliminating a high inoculum of MRSA within four hours. MRSA mutants exhibiting resistance to 1 and 2 could not be isolated, indicating a low likelihood of rapid resistance emerging to these compounds. Bacterial cytological profiling revealed the diphenylureas exert their antibacterial activity by targeting bacterial cell wall synthesis. Both compounds demonstrate the ability to resensitize vancomycin-resistant Staphylococcus aureus to the effect of vancomycin. The present study lays the foundation for further investigation and development of diphenylurea compounds as a new class of antibacterial agents. PMID:28797064

Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed

PubMed Central

Wüst, Pia K.; Nacke, Heiko; Kaiser, Kristin; Marhan, Sven; Sikorski, Johannes; Kandeler, Ellen; Daniel, Rolf

2016-01-01

Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actinobacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms. PMID:26896137

Bacterial infective arthritis of the coxofemoral joint in dogs with hip dysplasia.

PubMed

Benzioni, H; Shahar, R; Yudelevitch, S; Milgram, J

2008-01-01

The objective of this study was to describe seven cases of unilateral bacterial infective coxarthritis from a total of 19 cases of bacterial infective arthritis (BIA), presenting over a two year period. We recorded the history, clinical signs, diagnostic process, treatment and clinical outcome in these cases. The data were obtained from medical records, review of the radiographs, and telephone follow-up with the owners. All of the dogs in this study had severe chronic osteoarthritis secondary to hip dysplasia, which caused periodic hind limb lameness. They were all admitted with severe acute hind-limb lameness. Pelvic radiographs were performed under general anaesthesia shortly after presentation, followed immediately by arthrocentesis of the affected joint. The synovial fluid was evaluated microscopically by direct smear and a sample was sent for culture and sensitivity. An attempt was not made to drain or lavage the affected joint during the course of treatment. The initial choice of antibiotics was empiric and subsequently modified, as required, based on the sensitivity results. Four of the dogs showed a rapid return to weight-bearing after the initiation of antibiotic treatment, and all of the patients returned to their pre-BIA level of function. Neither recurrent infections nor any adverse sequela requiring further intervention were reported by the owners on telephone follow-up.