Metagenome-assembled genome: ERR906885_bin.24_CONC... - BioSample

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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; Bacillati; Bacillota; Clostridia; environmental samples

Attributes

collection date	2011-01-01
broad-scale environmental context	Host-associated
local-scale environmental context	Human
environmental medium	Digestive system
geographic location	Uganda
investigation type	metagenome-assembled genome
isolation source	human gut metagenome
project name	The 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 name	ERR906885_bin.24_CONCOCT_v1.1_MAG
ENA-CHECKLIST	ERC000047
ENA-FIRST-PUBLIC	2023-01-03
ENA-LAST-UPDATE	2023-01-03
External Id	SAMEA14085138
INSDC center alias	EBI
INSDC center name	European Bioinformatics Institute
INSDC first public	2023-01-03T00:33:23Z
INSDC last update	2023-01-03T00:33:23Z
INSDC status	public
Submitter Id	ERR906885_bin.24_CONCOCT_v1.1_MAG
assembly quality	Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software	metaspadesv3.12.0
binning parameters	Default
binning software	CONCOCT v1.1
broker name	EMG broker account, EMBL-EBI
completeness score	79.88
completeness software	CheckM
contamination score	0.0
geographic location (latitude)	-0.617
geographic location (longitude)	30.6565
metagenomic source	human gut metagenome
sample derived from	SAMEA3444260
scientific_name	uncultured Clostridia bacterium
sequencing method	Illumina MiSeq
taxonomic identity marker	multi-marker approach

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