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Metagenome-assembled genome: ERR906885_bin.24_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14085138; SRA: ERS11688270
Organism
uncultured Clostridia bacterium
cellular organisms; Bacteria; Terrabacteria group; Bacillota; Clostridia; environmental samples
Attributes
collection date2011-01-01
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationUganda
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project nameThe effect of HIV on the enteric DNA virome and bacterial microbiome is incompletely characterized. Here we sequenced virus-like particles and bacterial 16S ribosomal RNA genes in stool from 40 HIV-negative subjects, 42 HIV-infected subjects and 40 HIV-infected subjects on anti-retroviral therapy (ART) living in Uganda. CD4 T cell counts inversely correlated with plasma soluble CD14 (sCD14) levels, suggesting increased translocation of pro-inflammatory microbial products across the enteric mucosa with worsening immunodeficiency. Low CD4 T cell counts were associated with expansion of the eukaryotic DNA virome including adenoviruses and Anelloviruses and changes in the bacterial microbiome including increases in Enterobacteriaceae members and decreases in Ruminococci. Thus immunodeficiency in progressive HIV infection is associated with significant alterations in the human enteric virome and bacterial microbiome. These changes may contribute to acquired immunodeficiency syndrome (AIDS) enteropathy, translocation of pro-inflammatory materials across the intestinal mucosa and systemic inflammation associated with progression to AIDS.
sample nameERR906885_bin.24_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14085138
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:33:23Z
INSDC last update2023-01-03T00:33:23Z
INSDC statuspublic
Submitter IdERR906885_bin.24_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaspadesv3.12.0
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score79.88
completeness softwareCheckM
contamination score0.0
geographic location (latitude)-0.617
geographic location (longitude)30.6565
metagenomic sourcehuman gut metagenome
sample derived fromSAMEA3444260
scientific_nameuncultured Clostridia bacterium
sequencing methodIllumina MiSeq
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR906885 of study ERP010635.

BioProject
PRJEB51075 Large-scale analysis of novel cellular microbes from the human gut biome
Retrieve all samples from this project

Submission
EBI; 2023-01-04
Accession:
SAMEA14085138
ID:
32561765

BioProject Nucleotide

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