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Metagenome-assembled genome: SRR341702_bin.43_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14085697; SRA: ERS11688828
Organism
uncultured Clostridia bacterium
cellular organisms; Bacteria; Terrabacteria group; Bacillota; Clostridia; environmental samples
Attributes
collection datenot provided
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationnot provided
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project nameAssessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.
sample nameSRR341702_bin.43_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14085697
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:33:32Z
INSDC last update2023-01-03T00:33:32Z
INSDC statuspublic
Submitter IdSRR341702_bin.43_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwarespades_v3.11.1
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score79.58
completeness softwareCheckM
contamination score4.57
geographic location (latitude)not provided
geographic location (longitude)not provided
metagenomic sourcehuman gut metagenome
sample derived fromSAMN00715252
scientific_nameuncultured Clostridia bacterium
sequencing methodIllumina Genome Analyzer II
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR341702 of study SRP008047.

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:
SAMEA14085697
ID:
32562323

BioProject Nucleotide

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