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54 results for “gut metagenome”
Gut resistome associations with dyslipidemia using metagenomics
<p>Dataset for the alpha diversity analysis of ARGs and microbial species. "ARG_diversity.txt" is the alpha diversity indices of ARG abundance, and "taxa_div.txt" is the alpha diversity indices of microbial species found in all samples.</p>
Metagenomic & Metabolomic Study: Bifidobacterium Probiotic Effects on Gut Microbiota & SCFA in Preterm NICU Infants
ClinicalTrials.gov study NCT07213414. IPD Sharing: NO. Countries: 1. Publications: 1.
Metagenomic bins and biosynthetic gene clusters in gut bacteria of turtle ants
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Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs
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Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features"
<p>Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" (submitted to Nature Communications)</p>
Integrating Metagenomic and Metabolomic Insights into Host-Microbe Connections for Gut-Lung Axis in Childhood Asthma
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Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more
<p>Supplementary Table 2-1. Samples and assembly summary <br> Supplementary Table 2-2. CRISPR-targeted TR sequence summary</p>
Relative abundance tables for bacterial species, pathways, ARGs, and VFGs in "Gut Microbial Community Structure, Metabolic Signature, and Resistome in Dyslipidemia: Insights from Metagenomic Sequencing"
<p>Dyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. In this study, we analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and resistome in 1384 participants (895 with dyslipidemia cases and 489 controls) using shotgun metagenomic sequencing. Our results revealed that Bacteroides caccae was enriched in dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism, while Coprococcus eutactus and Coprococcus catus, known producers of short-chain fatty acids (SCFAs) in lipid regulation, and Blautia obeum, known to be positively impacted by SCFAs, were more abundant in controls. We also identified an enrichment of the dTDP-beta-D-fucofuranose biosynthesis pathway gene family, which is linked to bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris contributing strongly. Dyslipidemia cases exhibited depleted glycogen and peptidoglycan biosynthesis pathways, potentially impairing energy storage and immune function, alongside distinct metabolic profiles, including decreased pseudouridine, which may affect RNA metabolism. Furthermore, we observed a higher abundance of antibiotic-resistance genes, particularly tetQ, in dyslipidemia cases, suggesting a link between gut resistome and metabolic disorders. These findings provide new insights into how dysbiosis of the gut microbiota may contribute to the pathophysiology of dyslipidemia, offering potential avenues for microbiome-based interventions in personalized medicine.</p>
Twenty-five metagenome assembled genomes recovered from the gut microbiome of the domestic ferret, Mustela putorius
<p>This is metadata provided in a single excel file for 25 unique metagenome assembled genomes (MAGs) recovered from the gut microbiome of three domestic ferrets (<em>Mustela putorius</em>). Details on both MAG and host ferret metadata, as well as information on sample collection, DNA sequencing, and bioinformatic processing can be found here, in association with the American Society for Microbiology Resource Announcement by Amundson et al. (in prep). </p>
Validation of StarinIQ software performance using metagenomic data from the ATCC gut microbiome genomic mix
<p>StrainIQ (Strain Identification and Quantification) is a novel tool that implements a new <em>n</em>-gram based algorithm for predicting and quantifying strain-level taxa from whole genome metagenomic sequencing data. We tested our method using simulated (GI tract reference genomes) and mock metagenomic datasets (from ATCC microbial genomic mix) and compared its performance with existing methods. The gut_even.zip file contains the metagenomic sequence data from the ATCC Gut Microbiome Genomic Mix (MSA-1006). From this original sequencing sequence (nearly 120X), we created additional datasets with 90X, 60X, 30X, 5X, 3X, and 1X coverage and tested StrainIQ performance on those sequencing datasets with varying coverage.</p> <p>Please find the new link for this data at https://zenodo.org/record/8132164</p>
The Role of the Gut Metagenome on the Development of Age Related Macular Degeneration (AMD)
ClinicalTrials.gov study NCT02438111. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Gut Microbiota Metagenomics for Chronic Liver Disease
ClinicalTrials.gov study NCT04339725. IPD Sharing: NO. Countries: 1. Publications: 2.
Metagenomic and Metabolomic Reconstitution of Gut Microbiota After Broad Spectrum Antibiotic Therapy
ClinicalTrials.gov study NCT04171466. IPD Sharing: Not stated. Countries: 1. Publications: 13.
Metagenomic Analysis of Gut Microbiome in Preterm
ClinicalTrials.gov study NCT03235635. IPD Sharing: YES. Countries: 1. Publications: 8.
Co-assembly of 98TBs of metagenomes from human gut using exascale assembler MetaHipMer
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Data from: Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics
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Raw metagenomic data from gut contents of Dallia pectoralis specimens collected in Kenai, Alaska, in 2019
<p>Gut contents were dissected from five Alaska blackfish (<em>Dallia pectoralis</em> T. H. Bean, 1880) specimens from Kenai, Alaska. Specimen data and associated images have been made available via an Arctos project at <a href="http://arctos.database.museum/project/10003367">http://arctos.database.museum/project/10003367</a>.</p> <p>Vials of gut contents were sent to RTL Genomics in Lubbock, Texas (<a href="https://rtlgenomics.com/">https://rtlgenomics.com/</a>) for RTL Genomics' standard microbial diversity assay using the <em>mlCOIint</em>/<em>jgHCO2198</em> (GGWACWGGWTGAACWGTWTAYCCYCC/TAIACYTCIGGRTGICCRAARAAYCA) primer set.</p> <p>This dataset includes specimen data downloaded from Arctos and DNA extraction methods, DNA sequencing methods, resulting raw metagenomic data, and related files from RTL Genomics.</p>
Metagenome assembled genomes from mouse gut microbiota
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Metagenomic sequencing of gut microbiota associated with autism spectrum disorders patients
GEO Series GSE113540. feces metagenome. 60 samples. Type: Other.
A Metagenome-wide Association Study of Gut Microbiota in Gastrointestinal Non-Hodgkin's Lymphoma Patients
ClinicalTrials.gov study NCT03930043. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
Understand access before you commit
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.