Donor strain engraftment varied substantially across cohorts, and such variability was explained best by mixed FMT administration routes (combining upper and lower gastrointestinal (GI) tract), by the administration in the recipient of antibiotics before FMT (therapeutically or as preconditioning), and by the recipient being affected by infectious diseases.
patients who received antibiotics before FMT—as part of their therapy for underlying diseases or as pretreatment before FMT—had a significantly higher fraction of donor strains compared with the fraction of retained strains
Previous studies suggest that strain engraftment might be associated with clinical success of FMT, but consolidated evidence is still lacking. When considering single studies, we found that recipients experiencing clinical success showed significantly higher engraftment only in the VaughnB_2016 cohort. When analyzing all cohorts together, we found an overall positive association between strain engraftment rate and clinical response to FMT.
The limited total sample size, the binary categorization of success of clinical treatments, and the heterogeneity of conditions tested represent limitations in our analyses, but the results overall suggest that both higher microbial engraftment and, partially, the overall convergence of microbial species abundances between recipient and donor might improve clinical success of FMT.
Post-FMT strain engraftment rates are phylum- and species-dependent
suggests that ability to engraft is linked to the microbes’ capability of surviving in diverse environments
we found no association between the engraftment of individual species and clinical success
Machine learning can predict post-FMT microbial composition
ML models can pinpoint suitable FMT donors
The choice of donor has a higher influence on the post-FMT microbiome in patients with infectious disease and/or those that were treated with antibiotics
We also found that the donors with higher richness were predicted to induce higher richness in the recipient post-FMT
Our results provide further support for administering FMT by combined routes and including antibiotic preconditioning in FMT working protocols to increase donor microbiome engraftment, even though the potential side effects of antibiotic treatments for noninfectious diseases should be considered.
the link we observed between engraftment and clinical success of the FMT treatment needs to be substantiated in appropriately sized studies with higher number of patients in both outcome arms (for example, clinical failures for rCDI are relatively rare) and with more fine-grained evaluation of clinical success. Dedicated studies and randomized controlled trials are also needed to clarify the influence of protocol-related variables, such as antibiotic preconditioning or combined routes of delivery, on strain engraftment.
