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Metagenome-assembled genome: SRR413623_bin.1_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14085746; SRA: ERS11688877
Organism
Bacteroides ilei
cellular organisms; Bacteria; FCB group; Bacteroidota/Chlorobiota group; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides
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 nameSRR413623_bin.1_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14085746
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:33:18Z
INSDC last update2023-01-03T00:33:18Z
INSDC statuspublic
Submitter IdSRR413623_bin.1_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaspades_v3.12.0
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score96.67
completeness softwareCheckM
contamination score0.93
geographic location (latitude)not provided
geographic location (longitude)not provided
metagenomic sourcehuman gut metagenome
sample derived fromSAMN00791968
scientific_nameBacteroides ilei
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 SRR413623 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:
SAMEA14085746
ID:
32562372

BioProject Nucleotide

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