binned metagenome: spire_mag_02681311
Phocaeicola vulgatus
ENA first public
2024-09-20
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_02681311
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
megahit 1.2.9
binning parameters
default
binning software
metabat 2.12.1
broad-scale environmental context
human digestive system
broker name
EBI-EMG
collection date
2018-01-23
completeness score
92.28
completeness software
checkm2 0.1.3
contamination score
1.9
environmental medium
stool
geographic location (country and/or sea)
Switzerland
geographic location (latitude)
46.20000000
geographic location (longitude)
6.10000000
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
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.
sample derived from
SAMEA7041076
sample name
spire_mag_02681311
scientific_name
Phocaeicola vulgatus
sequencing method
NextSeq 500
taxonomic identity marker
multi-marker approach