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Metagenome-assembled genome: ERR3519525_bin.44_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14036478; SRA: ERS11639760
Organism
uncultured Lactobacillus sp.
cellular organisms; Bacteria; Bacillati; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus; environmental samples
Attributes
collection date2017-01-01
broad-scale environmental contextEngineered
local-scale environmental contextWastewater
environmental mediumWastewater
geographic locationUnited Kingdom
investigation typemetagenome-assembled genome
isolation sourcewastewater metagenome
project nameHospitals are nodal points for antimicrobial consumption and identification of resistant pathogens and therefore hospital wastewater is a potential major source of AMR. This study uses metagenomics to study how the abundances of resistance genes in hospital wastewater are related to clinical activity within different buildings of the hospital. Sewage was collected over a 24-hour period from multiple wastewater collection points representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. Sequence reads were assigned taxonomically and to the AMR genes in the ResFinder database. The measured AMR gene abundances were then correlated to hospital antimicrobial usage (AMU), other data on clinical activity such as patient/ward characteristics and resistance prevalence in clinical isolates.
sample nameERR3519525_bin.44_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14036478
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:32:00Z
INSDC last update2023-01-03T00:32:00Z
INSDC statuspublic
Submitter IdERR3519525_bin.44_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaSPAdes v3.13.1
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score98.37
completeness softwareCheckM
contamination score0.14
geographic location (latitude)not provided
geographic location (longitude)not provided
metagenomic sourcewastewater metagenome
sample derived fromSAMEA5953998
scientific_nameuncultured Lactobacillus sp.
sequencing methodIllumina HiSeq 4000
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR3519525 of study ERP117308.

BioProject
PRJEB51080 Large-scale analysis of novel cellular microbes from the wastewater biome
Retrieve all samples from this project

Submission
EBI; 2023-01-04
Accession:
SAMEA14036478
ID:
32555791

BioProject Nucleotide

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