Metagenome-assembled genome: SRR769527_bin.58_CONCOCT_v1.1_MAG
uncultured Collinsella sp.
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR769527 of study SRP019038.
ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14086050
INSDC center alias
EBI
INSDC center name
European Bioinformatics Institute
INSDC first public
2023-01-03T00:33:24Z
INSDC last update
2023-01-03T00:33:24Z
INSDC status
public
Submitter Id
SRR769527_bin.58_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 version 3.10.139
binning parameters
Default
binning software
CONCOCT v1.1
broker name
EMG broker account, EMBL-EBI
collection date
not provided
completeness score
56.64
completeness software
CheckM
contamination score
0.62
environment (biome)
Host-associated
environment (feature)
Human
environment (material)
Digestive system
geographic location (country and/or sea)
USA
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
Associating the biomolecular and metabolic activities of human-associated microbial communities with environment, diet, and conditions such as inflammatory bowel disease remains a significant challenge despite an ever-improving understanding of the human microbiome. This project aims to pilot detection of taxonomic and functional shifts with respect to diet and gastrointestinal disease status in a large prospective cohort: 1. We will establish a reliable and scalable collection method for the oral and gut microbiota. This will determine whether shippable collection kits are comparable to fresh frozen stool and/or saliva samples. 2. We will test the hypothesis that a Western dietary pattern correlates with microbiome community structures or functions enriched in inflammatory bowel disease in either the oral (saliva) or gut (stool) microbiota. By providing methodology to understand the human microbiome from the molecular to the population level, we hope to enable its future use as a diagnostic indicator and as a point of intervention to improve outcomes in IBD and other chronic diseases.
sample derived from
SAMN01915225
sample name
SRR769527_bin.58_CONCOCT_v1.1_MAG
scientific_name
uncultured Collinsella sp.
sequencing method
Illumina HiSeq 2000
taxonomic identity marker
multi-marker approach