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3,415 results for “Gut”
Data from: Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka
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Co-development of gut microbial metabolism and visual neural circuitry over human infancy
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Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre’s leaf monkeys
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Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification
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Comparative seagulls of gut microbiota by using metagenomics and 16S rDNA sequencing
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Gut microbiome composition associated with Plasmodium infection in the Eurasian tree sparrow
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Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course
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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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Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models
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Investigating Host Feeding Strategy as a Determinant of Insect Gut Microbial Community Profile at the Sevilleta National Wildlife Refuge, New Mexico
Diverse microbial communities live in the gut regions of animals. The precise ecological and evolutionary circumstances that govern relationships between hosts and their gut communities is unclear. In this study, we hypothesize that host feeding strategy shapes the microbial communities within the gut systems of insects. We collected five insect species from the Sevilleta National Wildlife Refuge that exhibited herbivorous, detritovorous and carnivorous diets. Using gut samples from the insects we measured if and how microbial communities are shaped based on any effect host feeding strategy might have. Preliminary analysis of bacterial communities using 16S rDNA sequences has thus far revealed that the sampled community profiles initially appear to show signs of being determined by host feeding type. Analysis has also shown that sequences from the phyla Firmicutes and Proteobacteria appear to contribute most significantly to the differences between communities of different feeding types. We expect that upon further data recovery, the extent of the effect host feeding type has on the communities will be clarified. Additionally we intend to incorporate bacterial community data from previous studies to further broaden our sample set. We expect our results to further define the ecological circumstances that shape the microbial populations within living systems.
Biobox YAML file for the CAMI 2 Mouse Gut Toy data set, samples 0-63
<p>Biobox YAML file for the CAMI 2 Mouse Gut Toy data set, samples 0-63</p>
Average genome coverage of the CAMI 2 Mouse Gut Toy data set
<p>Genome coverage (short reads) averaged over the 64 samples of the CAMI 2 Mouse Gut Toy data set</p>
Data from: Gut microbiome critically impacts PCB-induced changes in metabolic fingerprints and the hepatic transcriptome in mice
<p class="western"><span><span><span>Polychlorinated biphenyls (PCBs) are ubiquitously detected in the environment and have been linked to metabolic diseases. The liver serves as a central hub for the metabolism of xenobiotics and endogenous metabolites. Gut dysbiosis is recognized as a critical regulator of disease susceptibility, however, little is known regarding how PCBs and gut microbiome interact to modulate the interface between xenobiotic and intermediary metabolism. We hypothesized that the gut microbiome regulates PCBs-mediated changes in the metabolic fingerprints and hepatic transcriptome. Ninety-day-old female conventional (CV) and germ-free (GF) C57BL/6 mice were orally exposed to the PCB Fox River Mixture (synthetic PCB mixture, 6 or 30 mg/kg) or corn oil (vehicle control, 10 ml/kg), once daily for 3 consecutive days. Organs were collected 24 hours after the final dose. RNA-Seq was conducted on liver, and endogenous aqueous metabolites (amino acids, carbohydrates, and nucleotides) were measured in liver and serum by LC-MS. The primary factor in clustering the transcriptomic and metabolomic signatures within the same exposure was by enterotype. The numbers of PCB-regulated genes were higher in CV than in GF conditions. The prototypical target genes of the major xenobiotic-sensing transcription factors AhR, PXR, and CAR were more readily up-regulated by PCBs in CV than in GF conditions, indicating the effect of PCBs on the hepatic transcriptome act partly through the gut microbiome. Xenobiotic and steroid metabolism pathways were up-regulated, whereas response to incorrect proteins pathway was down-regulated by PCBs in a gut microbiome-dependent manner. At the high PCB dose, NADP and arginine appear to interact with drug-metabolizing enzymes (Cyp1-3 family, DhcR7, and Nqo1), which are highly correlated with <i>Anaerotruncus</i> and <i>Roseburia</i> in CV mice, providing a novel explanation of gut-liver interaction in toxicant exposures. In GF exposure groups, hepatic glucose was down-regulated, whereas fructose 6-phosphate and glucose 6-phosphate were up-regulated, indicating increased glucose utilization potentiated by lack of gut microbiota. Through querying the LINCS L1000 chemical database, Enrichr predicted that therapeutic drugs targeting the anti-inflammatory and ER stress pathways are potential remedies to mitigate PCB toxicity. In conclusion, our findings demonstrate that habitation of the gut microbiota drives PCBs-mediated hepatic responses, possibly due to crosstalk between gut and liver. </span></span></span></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>
Dataset - Calorie restriction improves metabolic state independently of gut microbiome composition
<p>This dataset contains the supplementary information for the paper: <em>Calorie restriction improves metabolic state independently of gut microbiome composition</em>.</p>
A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits
<ol> <li>Natal body mass is a key predictor of viability and fitness in many animals. While variation in body mass and therefore viability of juveniles may be explained by genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. The gut microbiota is known to change during development, but it remains unclear whether the microbiome predicts fitness, and if it does, at which developmental stage it affects fitness traits.</li> <li>We collected data on two traits associated with fitness in wild nestling great tits (<i>Parus major</i>): weight and survival to fledging. We characterised the gut microbiome using 16S rRNA sequencing from nestling faeces and investigated temporal associations between the gut microbiome and fitness traits across development at day 8 (D8) and day 15 (D15) post-hatching. We also explored whether particular microbial taxa were 'indicator species' that reflected whether nestlings survived or not.</li> <li>There was no link between mass and microbial diversity on D8 or D15. However, we detected a time-lagged relationship whereby the microbial diversity at D8 was negatively associated with weight at D15, while controlling for weight at D8. Indicator species analysis revealed that while several taxa were unique to birds that either survived or did not survive, there were no universal taxa that were consistently found across all birds within either survival group. This suggests that the presence of particular bacterial taxa may be sufficient, but not necessary for determining future survival, perhaps owing to functional overlap in microbiota.</li> <li>We highlight that measuring microbiome-fitness relationships at just one time point may be misleading, especially early in life. Instead, microbial-host fitness effects should be investigated longitudinally as there may be critical development windows in which key microbiota are established and prime host traits associated with nestling weight. Pinpointing which features of the gut microbial community impact on host fitness, and when during development this occurs, will shed light on population level processes and has the potential to support conservation.</li> </ol>
16S rRNA sequences from Mediterranean Sparidae gut microbiome
<p><span>Animals have been developing key associations with micro-organisms through evolutionary processes and ecological diversification. Hence, in some host clades, phylogenetic distance between hosts is correlated to dissimilarity in microbiomes, a pattern called phylosymbiosis. Teleost fishes, despite being the most diverse and ancient group of vertebrate, have received little attention from the microbiome perspective and our understanding of its determinants is currently limited. In this study, we assessed the gut microbiome of 12 co-occurring species of teleost representing a large breadth of ecological diversity and originating from a single family (<i>i.e.</i> the Sparidae). We tested how host evolutionary history, diet composition and morphological traits are related to fish gut microbiome. Despite fish species having different microbiomes, there is no phylosymbiosis signal in this fish family, but gut length and diet had a strong influence on the microbiome. We revealed that the only species with a specialized herbivorous diet, <i>Sarpa salpa</i> had a 3.3 times longer gut than carnivorous species and such a long gut favor the presence of anaerobic bacteria typical of herbivorous gut microbiomes. Hence, dietary uniqueness is paired with both unique gut anatomy and unique microbiome.</span></p>
Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and feces
<p>Microbial diversity and community function are related, and both can be highly specialized in different regions of the gut. The cloacal microbiome of Sceloporus virgatus lizards has low diversity, suggesting a specialized function, and is known to transfer antifungal microbes to eggshells during oviposition. We hypothesize that the cloacal microbiome is distinct from other parts of the digestive and reproductive systems. Here, we compare the microbiome of tissue samples from the cloaca, lower intestine, upper intestine, and oviduct. We further assessed whether common methods of microbial sampling – cloacal swabs and feces – provide accurate representations of these tissues, and whether feces might "seed" the cloacal microbiome. We found that the upper intestine and oviduct had unique microbial communities, while the lower intestine and cloaca had similar communities with lower diversity indicative of regional specialization. The cloacal community, in particular, showed extreme specialization averaging 99% Proteobacteria (Phylum) and 83% Enterobacteriacaea (Family). Cloacal swabs recovered communities similar to that of lower intestine and cloacal tissues, but fecal samples had much higher diversity and a distinct composition (62% Firmicutes and 39% Lachnospiraceae) relative to all gut regions. This result serves as a caution against the frequent assumption that fecal samples provide an accurate representation of the gut. Finally, we found that defecation did not alter the cloacal microbiome, suggesting that community is robust to perturbations from transient microbiota. </p>
GUT MICROBIOME COMPOSITION IN ALZHEIMER'S DEMENTIA PATIENTS: REPORT FROM PILOT STUDY IN KAZAKHSTAN
<p>Sequencing raw data of microbiome in fastq format</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.