2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21065378
SRA accession
spire_mag_02964670
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
2018-01-23
collection date
85.4
%
completeness score
checkm2 0.1.3
completeness software
0.73
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR4320052 of study ERP118932.
description
stool
environmental medium
Switzerland
geographic location (country and/or sea)
46.20000000
DD
geographic location (latitude)
6.10000000
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
Objective Fecal microbiota transplantation (FMT) has been recently suggested for decolonization of extended-spectrum beta-lactamase (ESBL-E) or carbapenemase-producing (CPE) Enterobacteriaceae from the gut. We aimed to explore which microbiota signatures of the donor and recipient influence successful decolonization by analyzing a cohort of FMT-treated carriers and corresponding donors. Design We used whole-metagenome shotgun sequencing to characterize fecal microbiota obtained from a nested cohort of 16 ESBL-E/CPE carriers having received oral colistin/neomycin followed by FMT and their corresponding 7 donors in the context of a randomized trial (NCT02472600). Ten treatment-naïve controls from the same trial were also included. Fecal samples were collected at baseline (V0), after antibiotics but before FMT (V2) and three times after FMT (a median of 3.7 weeks [V3], 6.7 weeks [V4] and 24.1 weeks [V5] from V0). Decolonization was defined as stool culture negative for ESBL-E/CPE at V4.Results Antibiotic treatment resulted in transient changes characterized by decreased species richness and diversity and increased abundance of antibiotic resistance determinants. Plasmid-borne resistance to colistin was not detected. After FMT, propionate and butyrate producers were increased in successfully decolonized carriers. Conclusions Our findings provide a basis for future studies that should explore whether the microbiota profiles identified in this study might potentially allow targeted selection of ESBL-E carriers with a higher likelihood of successful ESBL-E/CPE decolonization through FMT.
project name
SAMEA7041086
sample derived from
Phocaeicola vulgatus
scientific_name
NextSeq 500
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_02964670
title