SAMEA14083986 ERS11687119 uncultured Clostridium sp. This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2198663 of study ERP105282. EBI Generic Generic.1.0 ERC000047 2023-01-03 2023-01-03 SAMEA14083986 EBI European Bioinformatics Institute 2023-01-03T00:33:12Z 2023-01-03T00:33:12Z public ERR2198663_bin.37_CONCOCT_v1.1_MAG Many fragments with little to no review of assembly other than reporting of standard assembly statistics metaSPAdes v3.12.0 Default CONCOCT v1.1 EMG broker account, EMBL-EBI 2015-01-01 97.58 CheckM 0.0 Host-associated Human Digestive system USA 42.0 71.0 metagenome-assembled genome human gut metagenome human gut metagenome The 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. SAMEA104393738 ERR2198663_bin.37_CONCOCT_v1.1_MAG uncultured Clostridium sp. Illumina Genome Analyzer IIx multi-marker approach