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Metagenome-Assembled Genome: SRR5535761_bin.9_MetaWRAP_v1.3_MAG

Identifiers
BioSample: SAMEA114402903; SRA: ERS16391593
Organism
Gardnerella vaginalis
cellular organisms; Bacteria; Bacillati; Actinomycetota; Actinomycetes; Bifidobacteriales; Bifidobacteriaceae; Gardnerella
Attributes
broad-scale environmental contexthuman excretory system
collection date2013-05-13
environmental mediumurine
geographic locationnot provided
investigation typemetagenome-assembled genome
isolation sourceurine metagenome
project nameUrinary tract infection is thought to result from the growth of a limited number of uropathogenic organisms in an otherwise sterile environment. We revisited this concept by analyzing clean-catch urine samples representing a spectrum of clinical laboratory profiles. Whole genome shotgun sequencing was served to described the microbial metagenome. Infection was associated with dominant organisms in the metagenome as well as novel potential pathogens that are difficult to grow in routine cultures.
sample nameSRR5535761_bin.9_MetaWRAP_v1.3_MAG
ENA-CHECKLISTERC000047
INSDC center nameEMG
Submitter IdSRR5535761_bin.9_MetaWRAP_v1.3_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaspades v3.15.3
binning parametersMaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning softwareMetaWRAP v1.3
broker nameEBI-EMG
completeness score86.6
completeness softwareCheckM
contamination score0.0
geographic location (latitude)not provided
geographic location (longitude)not provided
local environmental contexturethra
metagenomic sourceurine metagenome
sample derived fromSAMN06899212
scientific_nameGardnerella vaginalis
sequencing methodIllumina HiSeq 2500
taxonomic classificationThe taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Gardnerella;s__Gardnerella vaginalis
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR5535761 of study SRP107013.

BioProject
PRJEB65453
Retrieve all samples from this project

Submission
EBI; 2023-09-21
Accession:
SAMEA114402903
ID:
37496597

BioProject Nucleotide

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