2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21062495
SRA accession
spire_mag_01627540
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
megahit 1.2.9
assembly software
default
binning parameters
metabat 2.12.1
binning software
human digestive system
broad-scale environmental context
EBI-EMG
broker name
2015
collection date
99.96
%
completeness score
checkm2 0.1.3
completeness software
8.37
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic runs ERR2738753,ERR2738755,ERR2738752,ERR2738754 of study ERP110418.
description
stool
environmental medium
Canada
geographic location (country and/or sea)
46.7687302
DD
geographic location (latitude)
-71.283642
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Phocaeicola vulgatus
organism
In this study, we used culture enrichment of stools to reveal lower abundance bacteria by high-throughput sequencing. We sequenced fecal bacteria growing under four culture conditions from 24 individuals, before and after use of antibiotics (day 0 and day 7). Overall, 187 species of bacteria had an assembly size greater than 1 million nucleotides, 67 species achieved it only under culture conditions and 22 only in culture-independent fecal microbiomes.The four culture conditions are : (i) MCDA maximum enrichment broth anaerobic culture (MEB-ANA)(ii) MCDA maximum enrichment broth aerobic culture (air enriched with 5% CO2) (MEB-CO2), (iii) MCDA anaerobic culture in presence of 32µg/ml cefoxitin (FOX-ANA)(iv) MCDA aerobic (with 5% CO2) culture in presence of 32µg/ml cefoxitin (FOX-CO2)
project name
SAMEA4833070
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 1000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01627540
title