Metagenome-assembled genome: ERR732783_bin.91_CONCOCT_v1.1_MAG
uncultured Faecalibacterium sp.
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR732783 of study ERP009306.
ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14085115
INSDC center alias
EBI
INSDC center name
European Bioinformatics Institute
INSDC first public
2023-01-03T00:33:10Z
INSDC last update
2023-01-03T00:33:10Z
INSDC status
public
Submitter Id
ERR732783_bin.91_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
collection date
2012-01-01
completeness score
99.13
completeness software
CheckM
contamination score
2.4
environment (biome)
Host-associated
environment (feature)
Human
environment (material)
Digestive system
geographic location (country and/or sea)
Sweden
geographic location (latitude)
55.7
geographic location (longitude)
13.2
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
metagenomic source
human gut metagenome
project name
Microscopic colitis (MC) is a disorder characterized by chronic non-bloody diarrhea predominantly affecting elderly smoking women. Since an altered microbiota is reported in several immune mediated diseases and since MC affects the gut, our hypothesis was that the microbiota would be altered in patients with MC. The bacterial microbiomes was analysed by DNA sequencing (Illumina Hiseq2000). Patients with MC had a marked reduction of Veruccomicrobia (Akkermansia spp) compared to healthy individuals. Specific Akkermansia spp PCR performed on the 10 patients and 7 controls and on an additional 5 female MC-patients confirmed the decreased levels of Akkermansia in MC patients.
sample derived from
SAMEA3212664
sample name
ERR732783_bin.91_CONCOCT_v1.1_MAG
scientific_name
uncultured Faecalibacterium sp.
sequencing method
Illumina HiSeq 2000
taxonomic identity marker
multi-marker approach