Disturbance During Biofilm Community Succession Promotes Cooperation and Diversity

AbstractDiversity-disturbance relationships have found widespread application in ecology, conservation and biodiversity management. In spite of their explanatory power, these conceptual frameworks have yet to be systematically applied to understanding succession in diverse microbial biofilms. Here we investigate community assembly in biofilms formed in replicate microbial bioelectrochemical systems using time-course sequencing of community 16S rRNA genes, corresponding to hundreds of operational taxonomic units (OTUs). For the first time we present a statistical model showing that a simple diversity-disturbance relationship can be used to explain dynamic changes in high diversity biofilm communities. This simple model reveals that succession in these systems is guided towards either a low diversity, generalist-dominated biofilm or a high diversity, cooperative-specialist biofilm, depending on the level of endogenous disturbance measured within the community. The pattern observed shows remarkable symmetry with findings from macro-scale communities such as grasslands, forests and coral reefs.

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Treatment nonresponse in children receiving silver diamine fluoride for caries: A pilot study

10.1101/2020.10.02.20204743 ◽

2020 ◽

Author(s):

Ryan Richard Ruff ◽

Bidisha Paul ◽

Maria A Sierra ◽

Fangxi Xu ◽

Yasmi Crystal ◽

...

Keyword(s):

Pilot Study ◽

Bacterial Species ◽

Illumina Miseq ◽

16S Rrna Genes ◽

Rrna Genes ◽

Lasso Regression ◽

Silver Diamine Fluoride ◽

Operational Taxonomic Units ◽

Acid Tolerant ◽

Nonsurgical Therapy

AbstractObjectives: Silver diamine fluoride (SDF) is a nonsurgical therapy for the arrest and prevention of dental caries with demonstrated clinical efficacy. Approximately 20% of children receiving SDF fail to respond to treatment. The objective of this study was to develop a predictive model of treatment nonresponse using machine learning. Methods: An observational pilot study (N=20) consisting of children with and without active decay and who did and did not respond to silver diamine fluoride provided salivary samples and plaque from infected and contralateral sites. 16S rRNA genes from samples were amplified and sequenced on an Illumina Miseq and analyzed using QIIME. The association between operational taxonomic units and treatment nonresponse was assessed using lasso regression and artificial neural networks. Results: Bivariate group comparisons of bacterial abundance indicate a number of genera were significantly different between nonresponders and those who responded to SDF therapy. No differences were found between nonresponders and caries-active subjects. Prevotella pallens and Veillonella denticariosi were retained in full lasso models and combined with clinical variables in a six-input multilayer perceptron. Discussion: The acidogenic and acid-tolerant nature of retained bacterial species may overcome the antimicrobial effects of SDF. Further research to validate the model in larger external samples is needed.

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Investigation of Sources, Diversity, and Variability of Bacterial Aerosols in Athens, Greece: A Pilot Study

Atmosphere ◽

10.3390/atmos13010045 ◽

2021 ◽

Vol 13 (1) ◽

pp. 45

Author(s):

Angelina Metaxatos ◽

Sydonia Manibusan ◽

Gediminas Mainelis

Keyword(s):

Field Application ◽

16S Rrna Genes ◽

Rrna Genes ◽

Airborne Bacteria ◽

Urban Air ◽

Operational Taxonomic Units ◽

Bacterial Aerosol ◽

Bacterial Aerosols ◽

Taxonomic Categories

We characterized the composition, diversity, and potential bacterial aerosol sources in Athens’ urban air by DNA barcoding (analysis of 16S rRNA genes) during three seasons in 2019. Air samples were collected using the recently developed Rutgers Electrostatic Passive Sampler (REPS). It is the first field application of REPS to study bacterial aerosol diversity. REPS samplers captured a sufficient amount of biological material to demonstrate the diversity of airborne bacteria and their variability over time. Overall, in the air of Athens, we detected 793 operational taxonomic units (OTUs), which were fully classified into the six distinct taxonomic categories (Phylum, Class, Order, etc.). These OTUs belonged to Phyla Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Fusobacteria. We found a complex community of bacterial aerosols with several opportunistic or potential pathogens in Athens’ urban air. Referring to the available literature, we discuss the likely sources of observed airborne bacteria, including soil, plants, animals, and humans. Our results on bacterial diversity are comparable to earlier studies, even though the sampling sites are different or geographically distant. However, the exact functional and ecological role of bioaerosols and, even more importantly, their impact on public health and the ecosystem requires further air monitoring and analysis.

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Analysis of the Salivary Microbiome in the Periodontal Disease patients with hypertension and non-hypertension

Current Bioinformatics ◽

10.2174/1574893615999200728201624 ◽

2020 ◽

Vol 15 ◽

Author(s):

Suhua Li ◽

Rexidan Zaker ◽

Xueqian Chu ◽

Reyida Asihati ◽

Chong Li ◽

...

Keyword(s):

Periodontal Disease ◽

Anaerobic Bacteria ◽

16S Rrna Genes ◽

Rrna Genes ◽

Oral Microbiota ◽

Periodontal Health ◽

Differential Abundance ◽

Operational Taxonomic Units ◽

Hypervariable Regions ◽

Microbiota Diversity

Background: An improved comprehension of the oral microbiota function in the pathogenesis of disease will contribute to diagnosis and treatment for both hypertension and periodontal disease. In our study, a comparison of the salivary microbiome between hypertension and Non-hypertension cohorts was designed to reveal microbial signatures. <P> Methods: Patients were divided into four sub-groups: Gingivitis, Periodontitis (stage 2, 3 and 4). Then the hypertension and Non-hypertension cohorts were split into periodontal health and periodontitis subgroups. The salivary samples were processed for DNA extraction (n=246). The V3-V4 hypervariable regions of microbiome 16S rRNA genes were amplified. Finally, sequencing libraries was constructed and subjected them to bioinformatics and statistical analyses. <P> Results: The oral microbial diversity decreased in both hypertension and periodontal disease groups compared to the healthy. At the genus level, the diversity showed 100 different operational taxonomic units (OTUs) for differential abundance testing. The first trend showed OTUs decreased in relative abundance with increasing periodontal disease, and as well as hypertension groups and non-hypertensive. For this trend OTUs comprised a mix of primarily anaerobic commensals and potential acute diarrhea pathogens. The second trend was that the diversity of genera was decreased in hypertension relative to non-hypertension, including other anaerobic bacteria related with periodontal disease. <P> Conclusions: Microbiota diversity decreased in both hypertension and different stages of periodontal disease groups, however, Neisseria and Solobacterium genera increased in co-existing hypertension and periodontal disease. Obviously, these findings indicate that the abundance of genera continues to change due to additional stresses caused by co-existing conditions

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Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis

BMC Veterinary Research ◽

10.1186/1746-6148-8-231 ◽

2012 ◽

Vol 8 (1) ◽

pp. 231 ◽

Cited By ~ 83

Author(s):

Samantha M Steelman ◽

Bhanu P Chowdhary ◽

Scot Dowd ◽

Jan Suchodolski ◽

Jan E Janečka

Keyword(s):

16S Rrna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Fecal Samples ◽

High Diversity

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Identification of differential duodenal gene expression levels and microbiota abundance correlated with differences in energy utilisation in chickens

Animal Production Science ◽

10.1071/an12426 ◽

2013 ◽

Vol 53 (12) ◽

pp. 1269 ◽

Cited By ~ 15

Author(s):

Barbara M. Konsak ◽

Dragana Stanley ◽

Volker R. Haring ◽

Mark S. Geier ◽

Robert J. Hughes ◽

...

Keyword(s):

Gene Expression ◽

High Throughput Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Lactobacillus Species ◽

Operational Taxonomic Units ◽

Similar Genetic Background ◽

The Difference ◽

Production Animals ◽

Utilisation Efficiency

Among the terrestrial production animals, chickens are the most efficient users of energy. Apparent metabolisable energy (AME) is a measure of energy utilisation efficiency representing the difference between energy consumed and energy lost via the excreta. There are significant differences in the energy utilisation capability of individual birds that have a similar genetic background and are raised under identical conditions. It would be of benefit to poultry producers if the basis of these differences could be understood and the differences minimised. We analysed duodenal gene expression and microbiota differences in birds with different energy utilisation efficiencies. Using microarray analysis, significant differences were found in duodenal gene expression between high- and low-AME birds, indicating that level of cell turnover may distinguish different groups of birds. High-throughput sequencing of bacterial 16S rRNA genes indicated that duodenal microbiota was dominated by Lactobacillus species and two operational taxonomic units, identified as lactobacilli species, were found to be more abundant (P < 0.05) in low-AME birds. The present study has identified gene expression and microbiota properties that correlate with differences in AME; further studies will be required to investigate the causal relationships.

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Bacteria Associated with Mucus and Tissues of the Coral Oculina patagonica in Summer and Winter

Applied and Environmental Microbiology ◽

10.1128/aem.00554-06 ◽

2006 ◽

Vol 72 (8) ◽

pp. 5254-5259 ◽

Cited By ~ 185

Author(s):

Omry Koren ◽

Eugene Rosenberg

Keyword(s):

16S Rrna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Culturable Bacteria ◽

Vibrio Splendidus ◽

Marine Agar ◽

Tissue Samples ◽

Operational Taxonomic Units ◽

Sybr Gold ◽

16S Rrna Clone Library

ABSTRACT The relative abundance of bacteria in the mucus and crushed tissue of the Mediterranean coral Oculina patagonica was determined by analyses of the 16S rRNA genes of isolated colonies and from a 16S rRNA clone library of extracted DNA. By SYBR gold staining, the numbers of bacteria in mucus and tissue samples were 6.2 × 107 and 8.3 × 108/cm2 of coral surface, respectively, 99.8% of which failed to produce colonies on Marine Agar. From analysis of mucus DNA, the most-abundant bacterium was Vibrio splendidus, representing 68% and 50% of the clones from the winter and summer, respectively. After removal of mucus from coral by centrifugation, analyses of DNA from the crushed tissue revealed a large diversity of bacteria, with Vibrio species representing less than 5% of the clones. The most-abundant culturable bacteria were a Pseudomonas sp. (8 to 14%) and two different α-proteobacteria (6 to 18%). Out of a total 1,088 16S rRNA genes sequenced, 400 different operational taxonomic units were identified (>99.5% identity). Of these, 295 were novel (<99% identical to any sequences in the GenBank database). This study provides a comprehensive database for future examinations of changes in the bacterial community during bleaching events.

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Bacterial Composition, Community Structure, and Diversity in Apis nigrocincta Gut

International Journal of Microbiology ◽

10.1155/2020/6906921 ◽

2020 ◽

Vol 2020 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

Christian Apolinaris Lombogia ◽

Max Tulung ◽

Jimmy Posangi ◽

Trina Ekawati Tallei

Keyword(s):

Community Structure ◽

Illumina Miseq ◽

Gut Bacteria ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Adult Worker ◽

Gut Microbial Community ◽

Apis Nigrocincta

Understanding the honeybee gut bacteria is an essential aspect as honeybees are the primary pollinators of many crops. In this study, the honeybee-associated gut bacteria were investigated by targeting the V3-V4 region of 16S rRNA genes using the Illumina MiSeq. The adult worker was captured in an urban area in a dense settlement. In total, 83,018 reads were obtained, revealing six phyla from 749 bacterial operational taxonomic units (OTUs). The gut was dominated by Proteobacteria (58% of the total reads, including Enterobacteriaceae 28.2%, Erwinia 6.43%, and Klebsiella 4.90%), Firmicutes (29% of the total reads, including Lactococcus garvieae 13.45%, Lactobacillus spp. 8.19%, and Enterococcus spp. 4.47%), and Actinobacteria (8% of the total reads, including Bifidobacterium spp. 7.96%). Many of these bacteria belong to the group of lactic acid bacteria (LAB), which was claimed to be composed of beneficial bacteria involved in maintaining a healthy host. The honeybee was identified as Apis nigrocincta based on an identity BLAST search of its COI region. This study is the first report on the gut microbial community structure and composition of A. nigrocincta from Indonesia.

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A Metagenomic-Based Approach for the Characterization of Bacterial Diversity Associated with Spontaneous Malolactic Fermentations in Wine

International Journal of Molecular Sciences ◽

10.3390/ijms20163980 ◽

2019 ◽

Vol 20 (16) ◽

pp. 3980 ◽

Cited By ~ 16

Author(s):

Carmen Berbegal ◽

Luigimaria Borruso ◽

Mariagiovanna Fragasso ◽

Maria Tufariello ◽

Pasquale Russo ◽

...

Keyword(s):

Malic Acid ◽

Alcoholic Fermentation ◽

Oenococcus Oeni ◽

Taxonomic Composition ◽

Starter Cultures ◽

16S Rrna Genes ◽

Rrna Genes ◽

Microbial Resources ◽

Next Generation Sequencing Ngs ◽

First Time

This study reports the first application of a next generation sequencing (NGS) analysis. The analysis was designed to monitor the effect of the management of microbial resources associated with alcoholic fermentation on spontaneous malolactic consortium. Together with the analysis of 16S rRNA genes from the metagenome, we monitored the principal parameters linked to MLF (e.g., malic and lactic acid concentration, pH). We encompass seven dissimilar concrete practices to manage microorganisms associated with alcoholic fermentation: Un-inoculated must (UM), pied-de-cuve (PdC), Saccharomyces cerevisiae (SC), S. cerevisiae and Torulaspora delbrueckii co-inoculated and sequentially inoculated, as well as S. cerevisiae and Metschnikowia pulcherrima co-inoculated and sequentially inoculated. Surprisingly, each experimental modes led to different taxonomic composition of the bacterial communities of the malolactic consortia, in terms of prokaryotic phyla and genera. Our findings indicated that, uncontrolled AF (UM, PdC) led to heterogeneous consortia associated with MLF (with a relevant presence of the genera Acetobacter and Gluconobacter), when compared with controlled AF (SC) (showing a clear dominance of the genus Oenococcus). Effectively, the SC trial malic acid was completely degraded in about two weeks after the end of AF, while, on the contrary, malic acid decarboxylation remained uncomplete after 7 weeks in the case of UM and PdC. In addition, for the first time, we demonstrated that both (i) the inoculation of different non-Saccharomyces (T. delbrueckii and M. pulcherrima) and, (ii) the inoculation time of the non-Saccharomyces with respect to S. cerevisiae resources (co-inoculated and sequentially inoculated) influence the composition of the connected MLF consortia, modulating MLF performance. Finally, we demonstrated the first findings of delayed and inhibited MLF when M. pulcherrima, and T. delbrueckii were inoculated, respectively. In addition, as a further control test, we also assessed the effect of the inoculation with Oenococcus oeni and Lactobacillus plantarum at the end of alcoholic fermentation, as MLF starter cultures. Our study suggests the potential interest in the application of NGS analysis, to monitor the effect of alcoholic fermentation on the spontaneous malolactic consortium, in relation to wine.

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Molecular community analysis of magnesium-rich bittern brine recovered from a Tunisian solar saltern

Canadian Journal of Microbiology ◽

10.1139/w11-088 ◽

2011 ◽

Vol 57 (12) ◽

pp. 975-981 ◽

Cited By ~ 10

Author(s):

Houda Baati ◽

Raja Jarboui ◽

Néji Gharsallah ◽

Abdelghani Sghir ◽

Emna Ammar

Keyword(s):

16S Rrna ◽

Sequence Similarity ◽

Archaeal Community ◽

Community Analysis ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Solar Saltern ◽

16S Rrna Gene Analysis ◽

Operational Taxonomic Units

The microbial community of a magnesium-rich bittern brine saturated with NaCl (380–400 g/L) from a Tunisian solar saltern was investigated using a molecular approach based on 16S rRNA gene analysis and viability tests. The results revealed the existence of microbial flora. Viability test assessment showed that 46.4% of this flora was viable but not detectable by culturability tests. 16S rRNA genes from 49 bacterial clones and 38 archaeal clones were sequenced and phylogenetically analyzed. Eleven operational taxonomic units (OTUs) determined by the DOTUR program with 97% sequence similarity were generated for Bacteria. These OTUs were affiliated with Bacteroidetes and Gammaproteobacteria. The archaeal community composition exhibited more diversity with 38 clones, resulting in 13 OTUs affiliated with the Euryarchaeota phylum. Diversity measurement showed a more diverse archaeal than bacterial community at the saturated pond.

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Characterization of Bioaerosols from Dairy Barns: Reconstructing the Puzzle of Occupational Respiratory Diseases by Using Molecular Approaches

Applied and Environmental Microbiology ◽

10.1128/aem.07661-11 ◽

2012 ◽

Vol 78 (9) ◽

pp. 3242-3248 ◽

Cited By ~ 45

Author(s):

Pascale Blais Lecours ◽

Marc Veillette ◽

David Marsolais ◽

Caroline Duchaine

Keyword(s):

16S Rrna ◽

Respiratory Diseases ◽

16S Rrna Genes ◽

Rrna Genes ◽

Exact Nature ◽

Continuous Exposure ◽

Content Type ◽

Humoral Immune ◽

Molecular Approaches ◽

First Time

ABSTRACTTo understand the etiology of exposure-related diseases and to establish standards for reducing the risks associated with working in contaminated environments, the exact nature of the bioaerosol components must be defined. Molecular biology tools were used to evaluate airborne bacterial and, for the first time, archaeal content of dairy barns. Three air samplers were tested in each of the 13 barns sampled. Up to 106archaeal and 108bacterial 16S rRNA genes per m3of air were detected. Archaeal methanogens, mainlyMethanobrevibacterspecies, were represented.Saccharopolyspora rectivirgula, the causative agent of farmer's lung, was quantified to up to 10716S rRNA genes per m3of air. In addition, a wide variety of bacterial agents were present in our air samples within the high airborne bioaerosol concentration range. Despite recommendations regarding hay preservation and baling conditions, farmers still develop anS. rectivirgula-specific humoral immune response, suggesting intense and continuous exposure. Our results demonstrate the complexity of bioaerosol components in dairy barns which could play a role in occupational respiratory diseases.

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