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1,065 results for “gut microbiota”
Comparative seagulls of gut microbiota by using metagenomics and 16S rDNA sequencing
<p><span>Shotgun</span><span> metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. </span><span>We compared the metagenome and 16S rDNA amplicon results to demonstrate the features of this animal. </span><span>In general, </span><span>relatively </span><span>consistent patterns and reliability could be identified by both sequencing methods, but the results varied </span><span>following </span><span>the refinement of taxonomic levels. </span><span>Metagenomic </span><span>sequencing was more suitable for the discovery and detection of pathogenic bacteria of gut microbiota in seagulls.</span><span> Although there were large differences in the numbers and abundance of </span><span>bacterial </span><span>species of</span><span> the</span><span> two methods in terms of taxonomic levels, the patterns and reliability results of </span><span>the </span><span>samples were consistent.</span></p>
Data from: Effects of high dose aspartame-based sweetener on the gut microbiota and bone strength in young and aged mice
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Individual variation in the avian gut microbiota: The influence of host state and environmental heterogeneity
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Data from: Seasonal restructuring facilitates compositional convergence of gut microbiota in free-ranging rodents
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Bespoke plant glycoconjugates for gut microbiota-mediated drug targeting
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Comparative seagulls of gut microbiota by using metagenomics and 16S rDNA sequencing
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Gut Microbiota from Multiple Sclerosis patients triggers spontaneous autoimmune encephalomyelitis in mice --shotgun data--
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Gut Microbiota from Multiple Sclerosis patients triggers spontaneous autoimmune encephalomyelitis in mice --16S data--
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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>
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: 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.
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>
Something in the water: Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior
<p>Microorganisms colonize the gastrointestinal tract of animals and establish symbiotic host-associated microbial communities that influence vertebrate physiology. More specifically, these gut microbial communities influence neurodevelopment through the microbiota-gut-brain (MGB) axis. We tested the hypothesis that larval amphibian neurodevelopment is affected by the aquatic microbial community present in their housing water. Newly hatched Northern Leopard Frog (<em>Lithobates pipiens</em>) tadpoles were raised in pond water that was unmanipulated (natural) or autoclaved. Tadpoles raised in autoclaved pond water had a gut microbiota with reduced bacterial diversity and altered community composition, had decreased behavioral responses to sensory stimuli, were larger in overall body mass, had relatively heavier brains, and had altered brain shape when compared with tadpoles raised in natural pond water. Further, the diversity and composition of the gut microbiota was associated with tadpole behavioral responses and brain measurements. Our results suggest that aquatic microbial communities shape tadpole behavior and brain development, providing strong support for the occurrence of the MGB axis in amphibians. Lastly, the dramatic role played by aquatic microbial communities on vertebrate neurodevelopment and behavior should be considered in future wildlife conservation efforts.</p>
Data from: Gut microbiota composition and functionality are associated with REM sleep duration and continuous glucose levels
<p><span><strong>Context</strong>:</span><span> Sleep disruption is associated with poorer glucose metabolic control and altered gut microbiota in animal models.</span></p> <p><span><strong>Objective</strong>:</span><span> We aimed to evaluate the possible links among REM sleep duration, continuous glucose levels, and gut microbiota composition.</span></p> <p><strong><span>Design</span></strong><span>: This is an observational, prospective, real-life, cross-sectional case-control study. </span></p> <p><span><strong>Setting</strong>: </span><span>Tertiary Hospital recruiting healthy volunteers.</span></p> <p><span><strong>Patients or Other Participants</strong>:</span><span> One-hundred and eighteen (60 with obesity), middle-aged (39.1-54.8) subjects.</span></p> <p><span><strong>Intervention(s)</strong>:</span><span> Glucose variability and REM sleep duration were assessed by 10-day continuous glucose monitoring (CGM) (Dexcom G6®) and wrist-actigraphy (Fitbit Charge 3®), respectively</span></p> <p><span><strong>Main Outcome Measure(s)</strong>:</span><span>. Glucose variability was evaluated through standard deviation (SD), coefficient of variation (CV), and interquartile range (IQR). The percentage of time in range (% TIR), 126-139 mg/dL (TIR2), and 140-199 mg/dL (TIR3) were calculated. Shotgun metagenomics sequencing was applied to study gut microbiota taxonomy and functionality. </span></p> <p><span><strong>Results</strong>:</span><span> Increased glycemic variability (SD, CV, and IQR) was observed among subjects with obesity in parallel to increased % TIR2 and % TIR3. REM sleep duration was independently associated with the % TIR3 (β=-0.339; p<0.001) and glucose variability (SD, β=-0.350; p<0.001). Microbial taxa from Christensenellaceae family (Firmicutes phylum) were positively associated with REM sleep and negatively with glucose continuous monitoring levels, while bacteria from Enterobacteriacea family and bacterial functions involved in iron metabolism showed opposite associations. </span></p> <p><span><strong>Conclusions</strong>:</span><span> Decreased REM sleep duration was independently associated with a worse glucose profile. The associations of species from Christensenellaceae and Enterobacteriaceae families with REM sleep duration and continuous glucose values suggest an integrated picture of metabolic health.</span></p>
Data from: Association between gut health and gut microbiota in a polluted environment
<p>Animals host complex bacterial communities in their gastrointestinal tracts, with which they share a mutualistic interaction. The numerous effects these interactions grant to the host include regulation of the immune system, defense against pathogen invasion, aid in digestion of otherwise indigestible foodstuffs, and even changing host behaviour. Stress, such as environmental pollution, parasites, predators, and intraspecies competition, can alter the composition of the gut microbiome, which in turn can change host-microbiome interactions in ways that are detrimental to the host such as causing metabolic dysfunction and inflammation. While host-microbiome interactions have been extensively studied in humans and captive animals, studies into wild animal microbiomes have been scarce. We assessed the effects of disturbed environment on gut health of bank voles exposed to radionuclides in natural habitat using a combined approach of transcriptomics, microbial community analysis by 16S amplicon sequencing, histological staining analyses of colon tissue, and quantification of gut microbiota -produced short-chain fatty acids in faecal matter and blood that act as mediators of host-microbiome interactions. We found signs of weakened mucus layer and related changes in <em>Clca1</em> and <em>Agr2</em> gene expression and microbiome composition in animals exposed to radionuclides. These results imply that disturbed environment can have widely reaching effects through gut health.</p>
With or without you: Gut microbiota does not predict aggregation behavior in European earwig females
<p>The reasons why some individuals are solitary and others gregarious are the subject of ongoing debate as we seek to understand the emergence of sociality. Recent studies suggest that the expression of aggregation behaviors may be linked to the gut microbiota of the host. Here, we tested this hypothesis in females of the European earwig. This insect is ideal for addressing this question, as adults both naturally vary in the degree to which they live in groups and show inter-individual variation in their gut microbial communities. We video-tracked 320 field-sampled females to quantify their natural variation in aggregation and then tested whether the most and least gregarious females had different gut microbiota. We also compared the general activity, boldness, body size, and body condition of these females and examined the association between each of these traits and the gut microbiota. Contrary to our predictions, we found no difference in the gut microbiota between the most and least gregarious females. There was also no difference in activity, boldness, and body condition between these two types of females. Independent of aggregation, gut microbiota was overall associated with female body condition, but not with any of our other measurements. Overall, these results demonstrate that a host's gut microbiota is not necessarily a major driver or a consequence of aggregation behavior in species with inter-individual variation in group living and call for future studies to investigate the determinants and role of gut microbiota in earwigs.</p>
Supplemental Data for "Embryonic Exposure to Tryptophan Yields Bullying Victimization via Reprogramming the Microbiota-Gut-Brain Axis in a Chicken Model"
<p>This is data set associated with an article "Embryonic Exposure to Tryptophan Yields Bullying Victimization via Reprogramming the Microbiota-Gut-Brain Axis in a Chicken Model" by Xiaohong Huang, Jiaying Hu, Haining Peng, and Heng-wei Cheng, including Supplemental Table S1, S2, S3, S4, S5, S6.</p>
HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota.
<p>We reported 102 complete metagenome assembled genomes (cMAGs) from five human fecal HiFi sequencing samples.</p> <p>102_cMAGs_fna.tar.gz: Fasta sequence files of 102 cMAGs.</p> <p>gc_skew_figures.tar.gz: GC-skew pattern figures of 102 cMAGs. (SVG format)</p> <p>coverage_plots.tar.gz: Genome coverage plot of 102 cMAGs.</p>
structure of microbiota in gut of fish 1992-2021
<p>You don’t need to provide an elaborate abstract for the moment. However, keep in mind that, together with the title, the abstract is one of the fields that a potential user will check in order to decide whether the dataset is useful for him/her or not. Have a look at the checklist in this page to get a feeling of what a good abstract should include.</p>
Sexual dimorphism of the gut microbiota in the Chinese alligator and its convergence in the wild environment
<p>The gut microbiota forms a complex microecosystem in vertebrates and is affected by various factors. As a key intrinsic factor, sex has a persistent impact on the formation and development of gut microbiota. Few studies have analysed sexual dimorphism of gut microbiota, particularly in wild animals. We used 16S rRNA sequencing to analyse the gut microbiota of juvenile and adult Chinese alligators, and untargeted metabolomics to study serum metabolomes of adult alligators. We observed significant sex-biased differences in the community diversity in juvenile, but not adult, alligators. In terms of taxonomic composition, the phylum Fusobacteriota and genus <em>Cetobacterium</em> were highly abundant in adult alligators, similar to that in carnivorous fishes, whereas the gut microbiota composition in juvenile alligators resembled that in terrestrial reptiles, indicating that adults are affected by their wild aquatic environment and lack sex dimorphism in gut microbiota. The correlation analysis revealed that the gut microbiota of adults was also affected by cyanobacteria in the external environment, and this effect was sex-biased and mediated by sex hormones. Overall, this study reveals sexual differences in the gut microbiota of crocodilians and their convergence in the external environment. It also provides insights into host-microbiota interactions in the wild.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.