Metagenome-Assembled Genome: SRR13061492_bin.12_Me... - BioSample

Metagenome-Assembled Genome: SRR13061492_bin.12_MetaWRAP_v1.3_MAG

Identifiers: BioSample: SAMEA114448902; SRA: ERS16435546

Organism: Colibacter massiliensis
cellular organisms; Bacteria; Bacillati; Bacillota; Negativicutes; Veillonellales; Veillonellaceae; Colibacter

Attributes

broad-scale environmental context	human digestive system
collection date	2018-01
environmental medium	saliva
geographic location	Denmark
investigation type	metagenome-assembled genome
isolation source	oral metagenome
project name	The purpose of the present investigation was to use the oral cavity as an in-vivo model to study the impact of internal and external perturbations on bacterial biofilm communities. We tested the hypotheses that bacterial gene expression of the healthy microbiota reflects habituation to site-specific ecological perturbations, and that the perturbation effect of chronic inflammation, periodontitis, impacts bacterial gene expression not only locally, but also at other sites of the oral cavity. Oral microbial samples were collected from three oral sites plaque, tongue and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterisation of taxonomic composition and to determine species specific bacterial activity as expressed by the ratio of messenger RNA to the corresponding genomic DNA.
sample name	SRR13061492_bin.12_MetaWRAP_v1.3_MAG
ENA-CHECKLIST	ERC000047
INSDC center name	EMG
Submitter Id	SRR13061492_bin.12_MetaWRAP_v1.3_MAG
assembly quality	Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software	metaspades v3.15.3
binning parameters	MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning software	MetaWRAP v1.3
broker name	EBI-EMG
completeness score	74.17
completeness software	CheckM
contamination score	0.75
geographic location (latitude)	55.67
geographic location (longitude)	12.57
local environmental context	oral cavity
metagenomic source	oral metagenome
sample derived from	SAMN16796830
scientific_name	Colibacter massiliensis
sequencing method	Illumina HiSeq 2500
taxonomic classification	The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Colibacter;s__Colibacter massiliensis
taxonomic identity marker	multi-marker approach

Description: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR13061492 of study SRP292586.

BioProject: PRJEB65451
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Submission: EBI; 2023-09-29

Accession:: SAMEA114448902
ID:: 37604360

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Metagenome-Assembled Genome: SRR13061492_bin.12_MetaWRAP_v1.3_MAG

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