Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics

Fecal microbiota transplantation (FMT) is a promising therapeutic approach for microbiota-associated pa-thologies, but our understanding of the post-FMT microbiome assembly process and its ecological and clin-ical determinants is incomplete. Here we perform a comprehensive fecal metagenome analysis of 14 FMT tri-als, involving five pathologies and >250 individuals, and determine the origins of strains in patients after FMT. Independently of the underlying clinical condition, conspecific coexistence of donor and recipient strains af-ter FMT is uncommon and donor strain engraftment is strongly positively correlated with pre-FMT recipient microbiota dysbiosis. Donor strain engraftment was enhanced through antibiotic pretreatment and bowel lavage and dependent on donor and recipient alpha-diversity; strains from relatively abundant species were more likely and from predicted oral, oxygen-tolerant, and gram-positive species less likely to engraft. We introduce a general mechanistic framework for post-FMT microbiome assembly in alignment with ecological theory, which can guide development of optimized, more targeted, and personalized FMT therapies.

Automated summary

The study reveals that the coexistence of donor and recipient strains after fecal microbiota transplantation is rare, and the engraftment of donor strains is strongly positively correlated with recipient microbiota dysbiosis. Engraftment of donor strains can be enhanced through antibiotic pretreatment and bowel lavage, and is dependent on the diversity of donor and recipient microbiota.