Metagenome-assembled genome: ERR732777_bin.103_CON... - BioSample

Metagenome-assembled genome: ERR732777_bin.103_CONCOCT_v1.1_MAG

Identifiers: BioSample: SAMEA14085107; SRA: ERS11688239

Organism: uncultured Clostridia bacterium
cellular organisms; Bacteria; Terrabacteria group; Bacillota; Clostridia; environmental samples

Attributes

collection date	2012-01-01
broad-scale environmental context	Host-associated
local-scale environmental context	Human
environmental medium	Digestive system
geographic location	Sweden
investigation type	metagenome-assembled genome
isolation 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 name	ERR732777_bin.103_CONCOCT_v1.1_MAG
ENA-CHECKLIST	ERC000047
ENA-FIRST-PUBLIC	2023-01-03
ENA-LAST-UPDATE	2023-01-03
External Id	SAMEA14085107
INSDC center alias	EBI
INSDC center name	European Bioinformatics Institute
INSDC first public	2023-01-03T00:33:48Z
INSDC last update	2023-01-03T00:33:48Z
INSDC status	public
Submitter Id	ERR732777_bin.103_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
completeness score	99.33
completeness software	CheckM
contamination score	0.36
geographic location (latitude)	55.7
geographic location (longitude)	13.2
metagenomic source	human gut metagenome
sample derived from	SAMEA3212658
scientific_name	uncultured Clostridia bacterium
sequencing method	Illumina HiSeq 2000
taxonomic identity marker	multi-marker approach

Description: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR732777 of study ERP009306.

BioProject: PRJEB51075 Large-scale analysis of novel cellular microbes from the human gut biome
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Submission: EBI; 2023-01-04

Accession:: SAMEA14085107
ID:: 32561734

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Metagenome-assembled genome: ERR732777_bin.103_CONCOCT_v1.1_MAG

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