2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21058218
SRA accession
spire_mag_00820510
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
2012-01-24
collection date
100
%
completeness score
checkm2 0.1.3
completeness software
0.91
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic runs ERR720093,ERR720081,ERR720087,ERR720078,ERR720091,ERR720077,ERR720082,ERR720088,ERR720094,ERR720083,ERR720090,ERR720092,ERR720095,ERR720085,ERR720086,ERR720089,ERR720080,ERR720084,ERR720096,ERR720079 of study ERP009131.
description
stool
environmental medium
Canada
geographic location (country and/or sea)
46.8032826
DD
geographic location (latitude)
-71.242796
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
The human gut microbiota is affected by antibiotics, but the heterogeneous response between individuals remains unexplored. To specifically address this question and examine the effect of antibiotics on selection of resistance genes, we administered the second-generation cephalosporin cefprozil to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and three months later were analyzed using shotgun metagenomic sequencing. We show that normal antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable fashion. Strikingly, we identified a subgroup of participants that were enriched in opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to the Bacteroides enterotype. Resistance genes that were not detectable before the treatment were observed after a 7-day course of antibiotic. Knowledge of the initial composition of the microbiome could assist in the prevention of the adverse effects of antibiotics.
project name
SAMEA3182048
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 1000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_00820510
title