Durable coexistence of donor and recipient strains after fecal microbiota transplantation

TLDR

FMT has proven effective for recurrent Clostridium difficile infection and is increasingly used for other gastrointestinal disorders, yet the fate of native and introduced microbial strains remains largely unknown. To quantify donor microbiota colonization, we monitored strain populations in fecal samples from a recent FMT study on metabolic syndrome patients using single‑nucleotide variant analysis of metagenomes. We assessed strain dynamics by sequencing metagenomes and tracking single‑nucleotide variants to determine donor‑recipient strain persistence. We observed extensive coexistence of donor and recipient strains 3 months post‑treatment, with conspecific strains colonizing more successfully than new species, and variable microbiota transfer among same‑donor recipients reflecting individual microbiome resistance and donor‑recipient compatibility.

Abstract

Fecal microbiota transplantation (FMT) has shown efficacy in treating recurrent Clostridium difficile infection and is increasingly being applied to other gastrointestinal disorders, yet the fate of native and introduced microbial strains remains largely unknown. To quantify the extent of donor microbiota colonization, we monitored strain populations in fecal samples from a recent FMT study on metabolic syndrome patients using single-nucleotide variants in metagenomes. We found extensive coexistence of donor and recipient strains, persisting 3 months after treatment. Colonization success was greater for conspecific strains than for new species, the latter falling within fluctuation levels observed in healthy individuals over a similar time frame. Furthermore, same-donor recipients displayed varying degrees of microbiota transfer, indicating individual patterns of microbiome resistance and donor-recipient compatibilities.