Bacteroides uniformis
ENA first public
2024-09-21
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_01416810
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
2015
completeness score
94.76
completeness software
checkm2 0.1.3
contamination score
0.5
environmental medium
stool
geographic location (country and/or sea)
USA
geographic location (latitude)
42.00000000
geographic location (longitude)
71.00000000
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
The metadata for this study is available on Dropbox: dropbox [DOT] com/sh/kfiu4wb53oemn6j/AAB13sgaKS7MV4lVqXLCxTuMa?dl=0 Abstract: Fecal microbiota transplantation (FMT) is a treatment for microbiome-associated diseases in which gut microbiota are transferred from a healthy donor to a patient. Although the success of FMT requires donor bacteria to engraft in the patient's gut, the forces governing bacterial engraftment in humans are unknown. Here, we use a vast, ongoing clinical experiment - the treatment of recurrent Clostridium difficile infection with FMT - to uncover the rules of engraftment in humans. First, we built a machine learning model that accurately predicts which bacterial species will engraft in a given host. We then developed a maximum-likelihood strain inference method, Strain Finder, allowing us to infer the genotypes of donor strains and to track them through patients' guts over time. Surprisingly, engraftment could be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient. We also found that donor strains within a species engraft in an all-or-nothing manner and that previously undetected strains frequently colonize the patient after FMT. We validated these findings in another disease context, metabolic syndrome, suggesting that the same principles of engraftment extend to other indications. These findings may guide the design of bacterial therapeutics that target diseases ranging from ulcerative colitis to cancer.
sample derived from
SAMEA104393711
sample name
spire_mag_01416810
scientific_name
Bacteroides uniformis
sequencing method
Illumina Genome Analyzer IIx
taxonomic identity marker
multi-marker approach