Metagenome-assembled genome: SRR413623_bin.4_CONCOCT_v1.1_MAG
uncultured Bacillota bacterium
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR413623 of study SRP008047.
ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14085747
INSDC center alias
EBI
INSDC center name
European Bioinformatics Institute
INSDC first public
2023-01-03T00:33:18Z
INSDC last update
2023-01-03T00:33:18Z
INSDC status
public
Submitter Id
SRR413623_bin.4_CONCOCT_v1.1_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaspades_v3.12.0
binning parameters
Default
binning software
CONCOCT v1.1
broker name
EMG broker account, EMBL-EBI
collection date
not provided
completeness score
91.49
completeness software
CheckM
contamination score
4.03
environment (biome)
Host-associated
environment (feature)
Human
environment (material)
Digestive system
geographic location (country and/or sea)
not provided
geographic location (latitude)
not provided
geographic location (longitude)
not provided
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
metagenomic source
human gut metagenome
project name
Assessment 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 derived from
SAMN00791968
sample name
SRR413623_bin.4_CONCOCT_v1.1_MAG
scientific_name
uncultured Firmicutes bacterium
sequencing method
Illumina Genome Analyzer II
taxonomic identity marker
multi-marker approach