Metagenome-assembled genome: ERR209569_bin.10_CONC... - BioSample

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Metagenome-assembled genome: ERR209569_bin.10_CONCOCT_v1.1_MAG

Identifiers: BioSample: SAMEA14083908; SRA: ERS11687042

Organism: Helicobacter winghamensis
cellular organisms; Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae; Helicobacter

Attributes

collection date	2008-01-01
broad-scale environmental context	Host-associated
local-scale environmental context	Human
environmental medium	Digestive system
geographic location	Spain
investigation type	metagenome-assembled genome
isolation source	human gut metagenome
project name	The microbial diversity of environments like the human gut extends far beyond what is covered by reference genomes. Here we present a method for exhaustive and unsupervised co-abundance gene binning across a series of highly complex metagenomic samples. As the method does not rely on previously sequenced reference genomes it allows for discovery of new species, viruses and clonal heterogeneity. We demonstrate the method on human gut microbiome data and identify 7,381 co-abundance gene groups (CAGs) ranging in size from 3 to 6,319 genes. The CAGs represent a wide variety of biological entities including microbial genomes, phages and clonal differences. We name the 741 largest of these metagenomic species (MGS), because they correspond to microbial species. In addition, we establish microbial host affiliations by dependency-associations for many small CAGs. Longitudinal sampling in the same individuals indicates that some of these dependency-associations are important for the persistence of their microbial host
sample name	ERR209569_bin.10_CONCOCT_v1.1_MAG
ENA-CHECKLIST	ERC000047
ENA-FIRST-PUBLIC	2023-01-03
ENA-LAST-UPDATE	2023-01-03
External Id	SAMEA14083908
INSDC center alias	EBI
INSDC center name	European Bioinformatics Institute
INSDC first public	2023-01-03T00:33:07Z
INSDC last update	2023-01-03T00:33:07Z
INSDC status	public
Submitter Id	ERR209569_bin.10_CONCOCT_v1.1_MAG
assembly quality	Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software	metaspadesv3.11.1
binning parameters	Default
binning software	CONCOCT v1.1
broker name	EMG broker account, EMBL-EBI
completeness score	99.24
completeness software	CheckM
contamination score	1.08
geographic location (latitude)	40.416634
geographic location (longitude)	-3.7037659
metagenomic source	human gut metagenome
sample derived from	SAMEA2042841
scientific_name	Helicobacter winghamensis
sequencing method	Illumina Genome Analyzer IIx
taxonomic identity marker	multi-marker approach

Description: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR209569 of study ERP002061.