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Metagenome-assembled genome: ERR732781_bin.96_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14085113; SRA: ERS11688245
Organism
uncultured Actinomyces sp.
cellular organisms; Bacteria; Bacillati; Actinomycetota; Actinomycetes; Actinomycetales; Actinomycetaceae; Actinomyces; environmental samples
Attributes
collection date2012-01-01
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationSweden
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project nameMicroscopic 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 nameERR732781_bin.96_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14085113
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:33:08Z
INSDC last update2023-01-03T00:33:08Z
INSDC statuspublic
Submitter IdERR732781_bin.96_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaspadesv3.12.0
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score96.96
completeness softwareCheckM
contamination score2.06
geographic location (latitude)55.7
geographic location (longitude)13.2
metagenomic sourcehuman gut metagenome
sample derived fromSAMEA3212662
scientific_nameuncultured Actinomyces sp.
sequencing methodIllumina HiSeq 2000
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR732781 of study ERP009306.

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:
SAMEA14085113
ID:
32561740

BioProject Nucleotide

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