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Dataset results
679 results for “Gut microbiome”
HiPR-FISH Mouse Gut Microbiome Experiments 6
<p>This dataset contains images of a mouse gut microbiome.</p>
HiPR-FISH Mouse Gut Microbiome Experiments 7
<p>This dataset contains images of a mouse gut microbiome.</p>
HiPR-FISH Mouse Gut Microbiome Experiments 3
<p>This dataset contains z-stacks of a mouse gut microbiome.</p>
HiPR-FISH Mouse Gut Microbiome Experiments 8
<p>This dataset contains images of a mouse gut microbiome.</p>
HiPR-FISH Mouse Gut Microbiome Experiments 9
<p>This dataset contains images of a mouse gut microbiome.</p>
HiPR-FISH Mouse Gut Microbiome Experiments 10
<p>This dataset contains images of a mouse gut microbiome.</p>
HiPR-FISH Mouse Gut Microbiome Experiments 2
<p>This dataset contains z-stacks of a mouse gut microbiome.</p>
HiPR-FISH Mouse Gut Microbiome Experiments 5
<p>This dataset contains a z-stack of a mouse gut microbiome.</p>
HiPR-FISH Mouse Gut Microbiome Experiments 4
<p>This dataset contains a z-stack of a mouse gut microbiome.</p>
Emergent Ecological Patterns and Modelling of Gut Microbiomes in Health and in Disease
<p><strong><em>Data associated with the paper "Emergent Ecological Patterns and Modelling of Gut Microbiomes in Health and in Disease".</em></strong></p> <p><strong>Content:</strong></p> <ul> <li><strong>Metagenomic curated data considering healthy and diseased state of the human individuals. Aligned against RefSeq with Kaiju.</strong></li> <li><strong>Curated metadata with anonymised physiological and medical information</strong></li> </ul> <p><strong>Paper authors</strong>: Jacopo Pasqualini, Sonia Facchin, Andrea Rinaldo, Amos Maritan, Edoardo Vincenzo Savarino, Samir Suweis</p> <p><strong>Paper preprint</strong>: https://www.biorxiv.org/content/10.1101/2023.10.19.563037v2</p> <p><strong>Data Curator</strong>: Jacopo Pasqualini.</p> <p><strong>Pipeline used to generate the data</strong>: https://github.com/jacopopasqualini/MetaGym</p> <p><strong>Complete description of data generation</strong>: https://www.biorxiv.org/content/10.1101/2023.10.19.563037v2</p>
Experiences of Discrimination are Associated with Microbiome and Transcriptome Alterations in the Gut
<p>Experiences of Discrimination are Associated with Microbiome and Transcriptome Alterations in the Gut. Human stool processed microbiome and transcriptomic data. </p>
Data from: Covariation of diet and gut microbiome in African megafauna
<p>A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of non-human microbiomes have relied on relatively coarse dietary categorizations and have focused either on individual wild populations or on captive animals that are sheltered from environmental pressures, which may obscure the effects of dietary and environmental variation on microbiome composition in diverse natural communities. We analyzed plant and bacterial DNA in fecal samples from an assemblage of 33 sympatric large-herbivore species (27 native, 6 domesticated) in a semi-arid East African savanna, which enabled high-resolution assessment of seasonal variation in both diet and microbiome composition. Phylogenetic relatedness strongly predicted microbiome composition (r = 0.91) and was weakly but significantly correlated with diet composition (r = 0.20). Dietary diversity did not significantly predict microbiome diversity across species or within any species except kudu; however, diet composition was significantly correlated with microbiome composition both across and within most species. We found a spectrum of seasonal sensitivity at the diet-microbiome nexus: seasonal changes in diet composition explained 25% of seasonal variation in microbiome composition across species. Species' positions on (and deviations from) this spectrum were not obviously driven by phylogeny, body size, digestive strategy, or diet composition; however, domesticated species tended to exhibit greater diet-microbiome turnover than wildlife. Our results reveal marked differences in the influence of environment on the degree of diet-microbiome covariation in free-ranging African megafauna, and this variation is not well explained by canonical predictors of nutritional ecology.</p>
Effects of laboratory domestication on the rodent gut microbiome
<p>Metagenome-assembled genomes generated from a collection of public and newly sequenced metagenomes derived from the rodent gut.</p>
Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes
<p>Primates acquire gut microbiota from conspecifics through direct social contact and shared environmental exposures. Host behavior is a prominent force in structuring gut microbial communities, yet the extent to which group or individual-level forces shape the long-term dynamics of gut microbiota is poorly understood. We investigated the effects of three aspects of host sociality (social groupings, dyadic interactions, and individual dispersal between groups) on gut microbiome composition and plasticity in 58 wild Verreaux's sifaka (<i>Propithecus verreauxi</i>) from six social groups. Over the course of three dry seasons in a five-year period, the six social groups maintained distinct gut microbial signatures, with the taxonomic composition of individual communities changing in tandem among co-residing group members. Samples collected from group members during each season were more similar than samples collected from single individuals across different years. In addition, new immigrants and individuals with less stable social ties exhibited elevated rates of microbiome turnover across seasons. Our results suggest that permanent social groupings shape the changing composition of commensal and mutualistic gut microbial communities and thus may be important drivers of health and resilience in wild primate populations.</p>
Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms
<p><strong>Abstract:</strong> Parkinson's disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using uniform standardized methods from start to end. We enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association at species and genus level, followed by network analysis to identify polymicrobial clusters, and functional profiling based on microbial genes and pathways. Here we show that over 30% of species, genes and pathways tested have altered abundances in PD, depicting a widespread dysbiosis. PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. PD microbiome is disease permissive, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. We validate, in human PD, findings that were observed in experimental models; reconcile and resolve human PD microbiome literature, and provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD. </p> <p><strong>Zenodo contents:</strong> In this Zenodo archive we provide (1) post sequence QC and post taxonomic and functional profiling "Source Data" used to generate tables and figures in the manuscript and (2) "Supplementary Code" that contains the workflow and code used to perform bioinformatic processing of shotgun sequences and statistical analyses of microbial profiles and subject metadata. The code provided here is the same "Supplementary Code" that is provided in the supplement of the manuscript. Individual level raw shotgun sequences and metadata are available on NCBI Sequence Read Archive (SRA) under BioProject ID <a href="https://www.ncbi.nlm.nih.gov/bioproject/834801">PRJNA834801</a>.</p>
Indirect maternal effects via nest microbiome composition drives gut colonization in altricial chicks
<p>The new version of the dataset includes the raw data and R scripts necessary to reproduce the analyses and figures explained in the manuscript "Indirect maternal effects via nest microbiome composition drives gut colonization in altricial chicks"<strong>. </strong></p> <p>The manuscript linked to this data has undergone a first round of peer-reviewed, which explains the differences between the first and second (current) version of the dataset.</p> <p>Notice that the manuscript has a new title and consequently the dataset title has been updated.</p> <p>This dataset includes:</p> <p>- ASV.xlxs: Complete ASV table of the field experiment. We collected cloacal swabs from parents and chicks in ten nests of Great tits (<em>Parus major</em>) and ten nests of Blue tis (<em>Cyanistes caeruleus</em>) together with nest and water microbiome. The Genbank accession numbers of the samples are given in each column (Bioproject: PRJNA800248). This file has been placed out of the folder "project data & code" for easy access.</p> <p>- README.docx: Complete explanation of the different raw data used for the statistical analyses, together with the link to the R script where data is analyzed. We recommend to read this document before diving into the data and scripts.</p> <p>- Project data & code: Two separate folders for raw data and code.</p>
Data from: Gut microbiome dysbiosis is associated with host genetics in the Norwegian Lundehund
<p class="MsoNormal"><span>A group of diseases have been shown to correlate with a phenomenon called microbiome dysbiosis, where the bacterial species composition of the gut becomes abnormal. The gut microbiome of an animal is influenced by many factors including diet, exposures to bacteria during post-gestational growth, lifestyle, and disease status. Studies also show that host genetics can affect microbiome composition. We sought to test whether host genetic background is associated with gut microbiome composition in the Norwegian Lundehund dog, a highly inbred breed with an effective population size of 13 individuals. The Lundehund has a high rate of a protein-losing enteropathy in the small intestine that is often reported as Lundehund syndrome, which negatively affects longevity and life-quality. An outcrossing project with the Buhund, Norrbottenspets and Icelandic sheepdog was recently established to reintroduce genetic diversity to the Lundehund and improve its health. To assess whether there was an association between host genetic diversity and the microbiome composition, we sampled the fecal microbiomes of 75 dogs of the parental (Lundehund), F1 (Lundehund x Buhund), and F2 (F1 x Lundehund) generations. We found significant variation in microbiome composition from the parental Lundehund generation compared to the outcross progeny. The variation observed in purebred Lundehunds corresponded to dysbiosis as seen by a highly variable microbiome composition with an elevated Firmicutes to Bacteroidetes ratio and an increase in the prevalence of <em>Streptococcus bovis/Streptococcus equinus </em>complex, a known pathobiont that can cause several diseases. We tracked several other environmental factors including diet, the presence of a cat in the household, living on a farm and the use of probiotics, but we did not find evidence of an effect of these on microbiome composition and alpha diversity. In conclusion, we found an association between host genetics and gut microbiome composition, which in turn may be associated with the high incidence of Lundehund syndrome in the purebred parental dogs.</span></p>
Data from: Host phylogeny and functional traits differentiate gut microbiomes in a diverse natural community of small mammals
<p>Differences in the bacteria inhabiting mammalian gut microbiomes tend to reflect the phylogenetic relatedness of their hosts, a pattern dubbed phylosymbiosis. Although most research on this pattern has compared the gut microbiomes of host species across biomes, understanding the evolutionary and ecological processes that generate phylosymbiosis requires comparisons across phylogenetic scales and under similar ecological conditions. We analyzed the gut microbiomes of 14 sympatric small-mammal species in a semi-arid African savanna, hypothesizing that there would be a strong phylosymbiosis pattern associated with the different body sizes and diets of the mammalian lineages present. Consistent with phylosymbiosis, microbiome dissimilarity increased with phylogenetic distance among hosts, ranging from congeneric sets of mice and hares that did not differ significantly in microbiome composition to species from different taxonomic orders that had almost no gut bacteria in common. While phylosymbiosis was detected among just the 11 species of rodents, it was substantially weaker than comparisons involving all 14 species together. In contrast, microbiome diversity and composition were generally more strongly correlated with body size, dietary breadth, and dietary overlap in comparisons restricted to rodents than in those including all lineages. The starkest divides in microbiome composition thus reflected the broad evolutionary divergence of hosts, regardless of body size or dietary composition, while subtler microbiome differences reflected variation in ecologically important traits between closely related hosts. Strong phylosymbiotic patterns arose deep in the phylogeny, and ecological filters that promote functional differentiation of cooccurring host species may disrupt or obscure this pattern near the tips.</p>
Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population
<p><span>Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health</span><span>. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. </span><span>Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is </span><span>critical. </span><span>We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances, and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding </span><span>which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform </span><span>targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes. </span></p>
Multi-omics Dissection of Gut Microbiome Engraftment During FMT
ClinicalTrials.gov study NCT06992453. IPD Sharing: YES. Countries: 1. Publications: 45.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.