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2,708 results for “microbiota”
Gut Microbiota from Multiple Sclerosis patients triggers spontaneous autoimmune encephalomyelitis in mice --16S data--
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Microbiota of sows and their offspring
<p>Microbiota composition was determined of sow feces, sow vaginal swabs and piglet jejunal digesta. Samples were frozen on dry-ice and stored at -80°C. To isolate DNA, samples were mixed in a 1:1 ratio with phosphate buffered saline (PBS) and centrifuged for 5 min at 4°C at 300<em>xg</em>. Supernatant was collected and centrifuged for 10 min at 4°C at 9000<em>xg</em>. DNA was extracted from the pellet using the “QIAamp DNA stool minikit” (Qiagen, Valencia, CA, USA) according to manufacturers’ instructions, after mechanical shearing of the bacteria in Lysing Matrix B tubes using the FastPrep-24 (MP Biomedicals, Solon, OH, USA). Quality and quantity of DNA were checked using the NANOdrop (Agilent Technologies, Santa Clara, CA, USA). PCR was used to amplify (20 cycles) the 16S rRNA gene V3 fragment using forward primer V3_F (CCTACGGGAGGCAGCAG) and reverse primer V3_R (ATTACCGCGGCTGCTGG). PCR efficiency was checked on agarose gel. Amplicons were sequenced using paired-end, excluding one sample that did not pass the quality control, 150bp technology on a MiSeq sequencer (Illumina, San Diego, CA, USA) at a sequencing depth in the range of 196K-1.2M read-pairs per sample (median 670,647 read-pairs per sample).</p> <p> </p>
Raw Fast5 data for "Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon" - PART I
<p>Raw Fast5 data for "Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon". See Supplementary Table 2 for associating each sample to its barcode.</p> <p>- FC1_1 includes data for the HM mock community from BEI resources and skin microbiome of the chin in dogs.</p> <p>- FC1_2 includes data for the dorsal skin samples</p> <p>- FC2 includes data for the Zymobiomics mock community and Staphylococcus pseudintermedius isolate</p> <p> </p> <p> </p>
Microbiota data analysis lesson datasets
<p>Datasets to be used in the Carpentry-style lesson on [microbiota data analysis](https://scienceparkstudygroup.github.io/microbiome-lesson/).</p> <p>Datasets from the paper: Zancarini, A., Echenique-Subiabre, I., Debroas, D. <em>et al.</em> Deciphering biodiversity and interactions between bacteria and microeukaryotes within epilithic biofilms from the Loue River, France. <em>Sci Rep</em> <strong>7, </strong>4344 (2017). https://doi.org/10.1038/s41598-017-04016-w. <a href="https://rdcu.be/b3CZh">https://rdcu.be/b3CZh</a></p>
Divergent microbiota of echinoid eggs separated by the Isthmus of Panama
<p>Relationships between animals and their associated microbiota are dependent on the evolutionary history of the host and on the environment. The majority of studies tend to focus on one of these factors and rarely consider how both determine the community composition of the associated bacteria. One "natural experiment" to test how evolutionary history, shared environments, and the interaction between these factors drive community composition is to compare geminate species pairs. Echinoids separated by the Isthmus of Panama are suitable for this comparison due to the known evolutionary history and differences in oceanographic characteristics of the Caribbean Sea and Pacific Ocean. By comparing the egg-associated microbiota of the <i>Echinometra</i> and <i>Diadema</i> geminate species pairs, we show that each pair of geminate species associates with a distinct bacterial community in a pattern consistent with phylosymbiosis, and that the interaction between the evolutionary history of the host and the environment best explain differences in these communities. Moreover, we found that particular microbial taxa differed considerably between, but not within, oceans and that the microbiota of the two Caribbean <i>Echinometra</i> species were dominated by the phototrophic Oxyphotobacteria. Taken together, data presented here support the hypothesis that the microbiota associated with geminate species are another characteristic of these taxa that diverged in ~2.8 million years of isolation.</p>
Data from: Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris muris infection
<p>Studies of controlled lab animals and natural populations represent two insightful extremes of microbiota research. We bridged these two approaches by transferring lab-bred female C57BL/6 mice from a conventional mouse facility to an acclimation room and then to an outdoor enclosure, to investigate how the gut microbiota changes with environment. Mice residing under constant conditions served as controls. Using 16S rRNA sequencing of fecal samples, we found that the shift in temperature and humidity, as well as exposure to a natural environment, increased microbiota diversity and altered community composition. Community composition in mice exposed to high temperatures and humidity diverged as much from the microbiota of mice housed outdoors as from the microbiota of control mice. Additionally, infection with the nematode <i>Trichuris muris</i> modulated how the microbiota responded to environmental transitions: The dynamics of several families were buffered by the nematodes, while invasion rates of two taxa acquired outdoors were magnified. These findings suggest that gut bacterial communities respond dynamically and simultaneously to changes within the host's body (e.g., the presence of nematodes) and to changes in the wider environment of the host.</p>
Evidence supporting the microbiota-gut-brain axis in a songbird
<p>Recent research in mammals supports a link between cognitive ability and the gut microbiome, but little is known about this relationship in other taxa. In a captive population of 38 Zebra Finches <em>(Taeniopygia guttata)</em>, we quantified performance on cognitive tasks measuring learning and memory. We sampled the gut microbiome via cloacal swab and quantified bacterial alpha and beta diversity. Performance on cognitive tasks related to beta diversity but not alpha diversity. We then identified differentially abundant genera influential in the beta diversity differences among cognitive performance categories. Though correlational, this study provides some of the first evidence of an avian microbiota-gut-brain axis, building foundations for future microbiome research in wild populations and during host development.</p>
Description of the microbiota in epidermal mucus and skin of sharks (Ginglymostoma cirratum and Negaprion brevirostris) and one stingray (Hypanus americanus)
<p>Skin mucus in fish is the first barrier between the organism and the environment but the role of skin mucus in protecting fish against pathogens is not well understood. During copulation in sharks, the male bites the female generating wounds, which are then highly likely to become infected by opportunistic bacteria from the water or from the male shark's mouth. Describing the microbial component of epithelial mucus may allow future understanding of this first line of defense in sharks. In this study, we analyzed mucus and skin samples obtained from 19 individuals of two shark species and a stingray: the nurse shark (<i>Ginglymostoma cirratum</i>), the lemon shark (<i>Negaprion brevirostris</i>) and the southern stingray (<i>Hypanus americanus</i>). Total DNA was extracted from all samples, and the bacterial 16S rRNA gene (region V3-V4) was amplified and sequenced on the Ion Torrent Platform. Bacterial diversity (order) was higher in skin and mucus than in water. Order composition was more similar between the two shark species. Alpha-diversities (Shannon and Simpson) for OTUs (clusters of sequences defined by a 97% identity threshold for the16S rRNA gene) were high and there were non-significant differences between elasmobranch species or types of samples. We found orders of potentially pathogenic bacteria in water samples collected from the area where the animals were found, such as Pasteurellales (i.e. genus <i>Pasteurella</i> spp. and <i>Haemophilus</i> spp.) and Oceanospirillales (i.e. genus <i>Halomonas</i> spp.) but these were not found in the skin or mucus samples from any species. Some bacterial orders, such as Flavobacteriales, Vibrionales (i.e. genus <i>Pseudoalteromonas</i>), Lactobacillales and Bacillales were found only in mucus and skin samples. However, in a co-occurrence analyses, no significant relationship was found among these orders (strength less than 0.6, p-value > 0.01) but significant relationships were found among the order Trembayales, Fusobacteriales, and some previously described marine environmental Bacteria and Archaea, including Elusimicrobiales, Thermoproteales, Deinococcales and Desulfarculales. This is the first study focusing on elasmobranch microbial communities. The functional role and the benefits of these bacteria still needs understanding as well as the potential changes to microbial communities as a result of changing environmental conditions.</p>
Data from: Anthelmintic drugs modulate the acute phase immune response but not the microbiota in wild Song Sparrows
<p>Co-infection with microparasites (e.g., bacteria) and macroparasites (e.g., helminths) is often the natural state for wild animals. Despite evidence that gut helminths can bias immune responses away from inflammatory processes, few field studies have examined the role that helminths, or their potential interactions with internal microbial communities, play in modulating immunity in free-living, wild birds. Here, we used anthelmintic drugs to treat wild Song Sparrows (<em>Melospiza melodia</em>) for helminth infections and measured markers of systemic inflammation (heterothermia and locomotor activity) in response to an immune challenge with lipopolysaccharide (LPS), a cell wall component of gram-negative bacteria. Using birds from a population that previously showed high helminth prevalence, we monitored skin temperature and activity remotely using automated radio telemetry. We also collected cloacal swabs to determine whether drug treatment was associated with changes in the cloacal microbiota, and whether cloacal microbial community structure was associated with the severity of birds' immune responses. Because helminths can reduce the severity of inflammatory immune responses in other species, we predicted that in comparison with untreated control birds, anthelmintic-treated birds would be more lethargic and display higher fevers when challenged with LPS. Consistent with these predictions, anthelmintic-treated birds expressed higher fevers in response to immune challenge. However, all LPS-challenged birds decreased locomotor activity to a similar degree, regardless of anthelmintic treatment. Although several individual indicator bacterial taxa were strongly associated with anthelmintic treatment, this treatment did not alter overall bacterial alpha- and beta- diversity. Similarly, we did not find evidence that bacterial community diversity influenced the severity of immune responses to LPS. These results suggest that under field conditions, natural helminth infection can reduce the severity of songbirds' thermoregulatory responses (fever) during an immune challenge, without major impacts on internal microbial communities or behavioral responses to infection.</p>
The airway microbiota and exacerbations of COPD
<p><span><span><span><span><span><span><span><span><span><span><span>Aim: To investigate whether the compositionality of the lower airway microbiota predicts later exacerbation risk in persons with COPD in a cohort study.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Materials and methods: We collected lower airways microbiota samples by bronchoalveolar lavage and protected specimen brushes, and oral wash samples from 122 participants with COPD. Bacterial DNA was extracted from all samples, before we sequenced the V3-V4 region of the 16S RNA gene. The frequency of moderate and severe COPD exacerbations was surveyed in telephone interviews and in a follow-up visit. Compositional taxonomy and alpha and beta diversity were compared between participants with and without later exacerbations. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Results: The four most abundant phyla were <i>Firmicutes</i>, <i>Bacteroidetes</i>, <i>Proteobacteria</i> and <i>Fusobacteria</i> in both groups, and the four most abundant genera were <i>Streptococcus</i>, <i>Veillonella</i>, <i>Prevotella</i> and <i>Gemella</i>. The relative abundances of different taxa showed a large variation between samples and individuals, and no statistically significant difference of either compositional taxonomy, or alpha or beta diversity could be found between participants with and without COPD exacerbations within follow-up. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Conclusion: The findings from the current study, indicate that individual differences in the lower airway microbiota in persons with COPD far outweigh group differences between frequent and non-frequent COPD exacerbators, and that the compositionality of the microbiota is so complex as to present large challenges for use as a biomarker of later exacerbations. </span></span></span></span></span></span></span></span></span></span></span></p>
Link to dataset related to article "Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth "
<p>This record contains raw data related to article “ Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth"</p> <p>The microbiota has been shown to promote intestinal tumourigenesis, but a possible anti-tumourigenic effect has also been postulated. Here, we demonstrate that changes in the microbiota and mucus composition are concomitant with tumourigenesis. We identified two anti-tumourigenic strains of the microbiota-Faecalibaculum rodentium and its human homologue, Holdemanella biformis-that are strongly under-represented during tumourigenesis. Reconstitution of Apc<sup>Min/+</sup> or azoxymethane- and dextran sulfate sodium-treated mice with an isolate of F. rodentium (F. PB1) or its metabolic products reduced tumour growth. Both F. PB1 and H. biformis produced short-chain fatty acids that contributed to control protein acetylation and tumour cell proliferation by inhibiting calcineurin and NFATc3 activation in mouse and human settings. We have thus identified endogenous anti-tumourigenic bacterial strains with strong diagnostic, therapeutic and translational potential.</p>
Data from: Characterization of gut microbiota composition in hemodialysis patients with normal weight obesity
<p><b>Background:</b> Normal weight obesity (NWO), defined by a normal body mass index (BMI) but increased body fat percentage (BF%), is associated with an increased risk of cardiovascular disease and mortality. NWO is characterized by inflammation and muscle wasting in chronic kidney disease (CKD), but the underlying mechanisms remain largely unknown. Gut microbiota has been implicated in the regulation of host metabolism and may play important roles in the development of NWO in CKD.</p> <p><b>Methods:</b> In this case-control study, we examined the gut microbial diversity and taxonomy in 96 hemodialysis patients with normal weight (BMI <25 kg/m<sup>2</sup> and BF% ≤25% for men or ≤35% for women, n = 32), NWO (BMI <25 kg/m<sup>2</sup> and BF% >25% for men or >35% for women, n = 32), and overweight/obesity (BMI ≥25 kg/m<sup>2</sup>, n = 32), matched for age, gender, and diabetes. BF% was measured using bioimpedance spectroscopy device. Gut microbiota was determined by 16S rRNA sequencing.</p> <p><b>Results:</b> We found that α-diversity was significantly different among the 3 adiposity phenotypes, with NWO being the least diverse. α-diversity was positively correlated with BMI, subjective global assessment score, and physical activity, but negatively correlated with interleukin-6 and tumor necrosis factor-α. Patients with or without NWO were distinguished with respect to principal coordinate analysis of β-diversity. Notably, the relative abundance of butyrate-producing bacteria, such as <i>Faecalibacterium </i><i>prausnitzii</i> and<i> Coprococcus</i>, was markedly reduced in patients with NWO.</p> <p><b>Conclusion:</b> Our findings support associations between gut dysbiosis and a proinflammatory and catabolic state in hemodialysis patients with NWO.</p>
Data from: Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons
Background: The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of any other mammal studied to date, raising key questions about the forces that shape the vaginal microbiome in non-human mammals. Results: We used Illumina sequencing of the bacterial 16S rRNA gene to investigate variation in the taxonomic composition of the vaginal microbiota in 48 baboons (Papio cynocephalus), members of a well-studied wild population in Kenya. Similar to prior studies, we found that the baboon vaginal microbiota was not dominated by lactobacilli. Despite this difference, and similar to humans, reproductive state was the dominant predictor of baboon vaginal microbiota, with pregnancy, postpartum amenorrhea, and ovarian cycling explaining 18% of the variance in community composition. Furthermore, among cycling females, a striking 39% of variance in community composition was explained by ovarian cycle phase, with an especially distinctive microbial community around ovulation. Peri-ovulatory females exhibited the highest relative abundance of lactic acid-producing bacteria compared to any other phase, with a mean relative abundance of 44%. To a lesser extent, sexual behavior, especially a history of shared sexual partners, also predicted vaginal microbial similarity between baboons. Conclusions: Despite striking differences in their dominant microbes, both human and baboon vaginal microbiota exhibit profound changes in composition in response to reproductive state, ovarian cycle phase, and sexual behavior. We found major shifts in composition during ovulation, which may have implications for disease risk and conception success. These findings highlight the need for future studies to account for fine-scale differences in reproductive state, particularly differences between the various phases of the ovarian cycle. Overall, our work contributes to an emerging understanding of the forces that explain intra- and inter-individual variation in the mammalian vaginal microbiome, with particular emphasis on its role in host health and disease risk.
Data from: No evidence that gut microbiota impose a net cost on their butterfly host
Gut microbes are believed to play a critical role in most animal life, yet fitness effects and cost benefit-tradeoffs incurred by the host are poorly understood. Unlike most hosts studied to date, butterflies largely acquire their nutrients from larval feeding, leaving relatively little opportunity for nutritive contributions by the adult's microbiota. This provides an opportunity to measure whether hosting gut microbiota comes at a net nutritional price. Since host and bacteria may compete for sugars, we hypothesized that gut flora would be nutritionally neutral to adult butterflies with plentiful food, but detrimental to semi-starved hosts, especially when at high density. We held field-caught adult Speyeria mormonia under abundant or restricted food conditions. Since antibiotic treatments did not generate consistent variation in their gut microbiota, we leveraged inter-individual variability in bacterial loads and OTU abundances to examine correlations between host fitness and the abdominal microbiota present upon natural death. We detected strikingly few relationships between microbial flora and host fitness. Neither total bacterial load nor the abundances of dominant bacterial taxa were related to butterflies' fecundity, egg mass, or egg chemical content. Increased abundance of a Commensalibacter species did correlate with longer host lifespan, while increased abundance of a Rhodococcus species correlated with shorter lifespan. Contrary to our expectations, these relationships were unchanged by food availability to the host and were unrelated to reproductive output. Our results suggest the butterfly microbiota comprise parasitic, commensal, and beneficial taxa that together do not impose a net reproductive cost, even under caloric stress.
MIcrobiota - different dietary inclusion of rye in broilers
<p>The dataset contains an experiment that was conducted to investigate the effects of dietary inclusion of rye, a model ingredient to increase gut viscosity, between 14 and 28 d of age on immune competence-related parameters and performance of broilers.</p> <p>A total of 960 day-old male Ross 308 chicks were weighed and randomly allocated to 24 pens (40 birds per pen), and the birds in every 8 replicate pens were assigned to 1 of 3 experimental diets including graded levels, 0%, 5%, and 10% of rye.</p> <p>Here, the microbiota of jejunal digesta samples is reported, i.e. the raw fastq data, as well as the metadata.</p> <p>The accompanying (peer-reviewed) scientific article can be found here: </p> <ul> <li>PMID: 28854752</li> <li>DOI: <a href="https://doi.org/10.3382/ps/pex152">10.3382/ps/pex152</a></li> </ul> <p> </p>
Molecular analysis of bacterial microbiota on Brazilian currency note surfaces
<p>MiSeq forward and reverse reads paired reads of the V4 region of the 16S rRNA gene. Data were generated from banknotes involving five denominations (2, 5, 10, 20, and 50), 30 notes each. Currency were randomly collected from three different street markets or "feiras" in the <em>metropolitan</em> region of <em>São Paulo.</em></p>
High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes
<p>This project contains anvi'o profiles and contigs databases that is used and/or referenced from the Lee STM and Khan SA, <em>et al.</em> study titled "<strong>High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes</strong>". The pre-print of this study is available via http://dx.doi.org/10.1101/090993.</p> <p>To be able to work with the data files you will need anvi'o <strong>v2.1.0</strong> to be installed on your system. For installation instructions, or to have access to a Docker image for anvi'o, please visit this URL: http://merenlab.org/software/anvio</p> <p>Public data:</p> <ul> <li><strong>ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION.tar.gz</strong>: Data files for a quick visualization of the 97 MAGs and their distribution across the two FMT recipients. A run script in the archive explains how to use this data.<br> </li> <li><strong>ANVIO-FMT-D-R01-R02-MERGED-PROFILE.tar.gz</strong>: The merged anvi'o profile for the entire data, which also contains a collection of 97 MAGs identified in the donor. The profile database contains no hierarchical clustering of contigs, however, individual MAGs can be displayed via the following notation since the collection 'MAGs' describe the organization of contigs in each MAG referenced from the dataset `ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION`, as well as from the paper: "anvi-refine -c CONTIGS.db -p PROFILE.db -C MAGs -b <em>FMT-Donor_MAG_00054</em>". All MAG names are in the supplementary tables in our paper.<br> </li> <li><strong>ANVIO-FMT-D-R01-R02-MAGs-SUMMARY.tar.gz</strong>: A static HTML website that contains FASTA files for each MAG, and TAB-delimited matrices for coverage and detection values, and others. After unpacking, you can double-click the index.html file. </li> </ul>
Multi-omics reveals the attenuation of metabolic cardiomyopathy in mice by extracts from Clausena0 lansium (Lour.) by transiting gastrointestinal microbiota to an alternative homeostasis
<p>The raw data for MS "<strong>Multi-omics reveals the attenuation of metabolic cardiomyopathy in mice by extracts from </strong><i><strong>Clausena0 lansium</strong></i><strong> (Lour.) by transiting gastrointestinal microbiota to an alternative homeostasis".</strong></p>
Dataset for "Developmental progression of the nasopharyngeal microbiota during childhood and association with the lower airway microbiota"
<p>Data files and R Markdown Notebooks used in "Developmental progression of the nasopharyngeal microbiota during childhood and association with the lower airway microbiota".</p><p>AOJ16S_decontam.Rmd performs decontamination of low abundance sequencing data.</p><p>AOJ16S_exploratory_analysis.Rmd analyzes and produces figures used in the manuscript.</p>
Data and code for: Effects of past and present habitat on the gut microbiota of a wild rodent
<p><strong>Files description:</strong></p> <ul> <li>RT_workflow.qmd (quarto file that shows the R code)</li> <li>RT_workflow.html (online html file created from the quarto file)</li> <li>Input files needed for the R workflow (qza files extracted from QIIME2 and text files)</li> </ul> <p><em>For general queries, unexpected errors and/or inconsistencies, please contact tiffany.scholier@gmail.com.</em></p>
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Annotated Behaviour and Observability Dataset (ABODe)
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