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Metagenome-assembled genome: ERR2198686_bin.40_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14083995; SRA: ERS11687128
Organism
uncultured Oscillibacter sp.
cellular organisms; Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales; Oscillospiraceae; Oscillibacter; environmental samples
Attributes
collection date2015-01-01
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationUSA
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project nameThe metadata for this study is available on Dropbox:dropbox [DOT] com/sh/kfiu4wb53oemn6j/AAB13sgaKS7MV4lVqXLCxTuMa?dl=0Abstract: 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 nameERR2198686_bin.40_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14083995
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:33:17Z
INSDC last update2023-01-03T00:33:17Z
INSDC statuspublic
Submitter IdERR2198686_bin.40_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaSPAdes v3.12.0
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score91.28
completeness softwareCheckM
contamination score0.67
geographic location (latitude)42.0
geographic location (longitude)71.0
metagenomic sourcehuman gut metagenome
sample derived fromSAMEA104393761
scientific_nameuncultured Oscillibacter sp.
sequencing methodIllumina Genome Analyzer IIx
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2198686 of study ERP105282.

BioProject
PRJEB51075 Large-scale analysis of novel cellular microbes from the human gut biome
Retrieve all samples from this project

Submission
EBI; 2023-01-04
Accession:
SAMEA14083995
ID:
32560623

BioProject Nucleotide

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