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24 results for “human metagenome”
Evaluation of an adapted semi-automated DNA extraction for human salivary shotgun metagenomics
<p>This deposit contains :</p> <p>- a RMarkdown filte containing the codes for the mcirobial analysis of saliva samples</p> <p>- the html report with codes, results and figures</p> <p>- a RData containing microbial datasets (MSp species abundance table, genus, family and phylum abundance tables, matrix of genes correlations, taxonomy)</p> <p>- a RData containing associated metadata </p>
Metagenomic assembly and bin3C clustering result for a healthy human faecal microbiome transplant donor
<p>Metagenomic WGS assembly and Hi-C deconvolution of a healthy human faecal microbiome transplant donor.</p> <p>Metagenomic assembly was produced using Spades (v3.13.1).</p> <p>Extracted MAGs were produced using bin3C (v0.3.3) and QC'd using CheckM (v1.0.18).</p>
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more
<p>S1 Data</p> <p>Dataset including the discovered CRISPR spacers, direct repeats, protospacers, co-occurrence-based spacer clustering results, predicted protein sequences, built HMMs, database comparison results, phylogenetic analysis results, predicted targeting hosts, and CRISPR-targeted TR sequences.</p>
Metagenome assembled genome database of a human cohort and fecal reactors
<p><strong>HumanCohort_annotations.tsv.zip:</strong> This is the custom MAG database (n=2447 MAGs) and corresponding annotations that were used in Borton 2022: "Targeted curation of the gut microbial gene content modulating human cardiovascular disease". The citation will be updated upon publication of the manuscript. Metagenome assembled genomes were generated from fecal metagenomes derived from a 54 person cohort and anoxic methylated amine enrichments. </p> <p><strong>HumanCohortmetabolism_summary.xlsx.zip: </strong> This is the annotation summary for 2447 MAGs in the cohort database. </p> <p><strong>Quality_Abundance_CohortMAGs.xlsx: </strong>This is a genome inventory of the 2447 MAGs in the cohort database including genome statistics and relative abundance. </p> <p><strong>orig_1D_NMR_fids.zip: </strong>NMR data derived from anoxic methylated amine enrichments. </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>
Early-life human gut metagenome-assembled genomes and proteins catalogs
<p>The description of the files:</p> <p>(1) The 32,277 genomes include six parts: ELGG_part_1.zip, ELGG_part_2.zip, ELGG_part_3.zip, ELGG_part_4.zip, ELGG_part_5.zip, ELGG_part_6.zip.</p> <p>(2) The 2,172 representative species: ELGG_representatives_2172.zip.</p> <p>(3) The ELGP catalog clustered at 95% amino acid identity: ELGP_95.faa.gz.</p> <p> </p>
Data supporting publication "Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome"
<p>Data supporting publication "Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome"</p>
Simulated Human gut metagenomic samples to benchmark mOTUs v2
<p>We simulated ten human gut metagenomic samples to assess the taxonomic quantification accuracy of the mOTUs tool (<a href="http://motu-tool.org/">link</a>). In this directory you can find the metagenomic samples, the gold standard (used to produce them) and the profiles obtained with four metagenomic profiler tools.</p> <p>Check README.txt for more information.</p>
Simulation data for "MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations"
<p>This is the simulation data used in the analysis of microbiome-disease association using MicroPro pipeline. Samples 0-24 and 25-49 are cases and controls respectively.</p>
Metagenome-assembled genomes(MAGs) generated from CRC human gut (PRJEB27928).
<p>MAGs generated from CRC human gut (PRJEB27928) with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(_pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
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>
Updated Metagenomic Species Pan-genomes (MSPs) of the human gastrointestinal microbiota
<p></p><h1>Gene catalog construction</h1><br>The methodology for creating the IGC2 catalog is described in the original papers: Li et al., 2014 and Wen et al., 2017<br><h1>MSP creation</h1><br>Reads from publicly available human gut metagenomes were aligned against the IGC2 catalog with the Meteor to produce a raw gene abundance table (10.4M genes quantified in >2000 samples). Then, co-abundant genes were binned in 1,989 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.<br><h1>MSPs taxonomic annotation</h1><br>MSPs taxonomic annotation was performed by aligning MSP core and accessory genes against representative genomes of the Genome Taxonomy Database (GTDB r207) using blastn (task = megablast, word_size = 16). The 20 best hits for each gene were kept (--max-target-seq 20). Using an in-house pipeline, a species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.<br><h1>Construction of the phylogenetic tree</h1><br>39 universal phylogenetic markers genes were extracted from the MSPs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni). <h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB1786, PRJEB5224, PRJEB6337, PRJNA422434 (cohort used in catalogue assembly) and PRJEB11532, PRJEB33500, PRJEB37249, PRNJNA834801 (independent cohort not used in assembly).<p></p>
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>
Co-assembly of 98TBs of metagenomes from human gut using exascale assembler MetaHipMer
Open the record for dataset details and reuse information.
Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease
<p><b>Background: </b>Viral infections are common complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT<b>)</b>. Allo-HSCT recipients<b> </b>with steroid-refractory/dependent graft-versus-host disease (GvHD) are highly immunosuppressed and are more vulnerable to infections with weakly pathogenic or commensal viruses. Here, twenty-five adult allo-HSCT recipients from 2016 to 2019 with acute or chronic steroid-refractory/dependent GvHD were enrolled in a prospective cohort of patients at Geneva University Hospitals. We performed metagenomics next-generation sequencing (mNGS) analysis using a validated viral pipeline and <i>de novo</i> analysis on pooled stored routine plasma samples collected throughout the period of intensive steroid treatment or second-line GvHD therapy to identify weakly pathogenic, commensal and unexpected viruses.</p> <p><b>Results: </b>Median duration of intensive immunosuppression was 5.1 months (IQR 5.5).<b> </b>GvHD-related mortality rate was 36%.<b> </b>mNGS analysis detected viral nucleotide sequences in 24/25 patients. Sequences of ≥3 distinct viruses were detected in 16/25 patients, <i>Anelloviridae</i> (24/25) and human pegivirus-1 (9/25) were the most prevalent. In 7/25 patients with fatal outcomes, unexpected viral sequences, not assessed by routine investigations, were identified with mNGS and confirmed by RT-PCR. These cases included usutu virus (1), rubella virus (1 vaccine-strain and 1 wild-type), novel human astrovirus (HAstV) MLB2 (1), classic HAstV (1), human polyomavirus 6 and 7 (2), cutavirus (1), and bufavirus (1).</p> <p><b>Conclusions: </b>Unexpected, opportunistic and protracted viral infections were identified in 28% of highly immunocompromised allo-HSCT recipients with steroid refractory/dependent GvHD. These identified viruses have all been previously described in humans, but have poorly understood clinical significance. Rubella virus identification raises the possibility of re-emergence from past infections or vaccinations.</p>
Human genome for contaminant removal of metagenome reads
<p>See http://seqanswers.com/forums/archive/index.php/t-42552.html</p>
Pilot Study of the Human Metagenome in Metabolic Diseases
ClinicalTrials.gov study NCT06363253. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Advanced Metagenomic Analysis of Human Colonic Microbiota in Patients With Chronic GI Disorders
ClinicalTrials.gov study NCT01099111. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease
Open the record for dataset details and reuse information.
Pooled metagenomic sequence from human stool
Open the record for dataset details and reuse information.
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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.