Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn's disease

Crohn's Disease (CD) is a chronic gastrointestinal disease resulting from the dysfunctional interplay between the immune system and commensal intestinal microbiota. Emerging evidence suggests that concurrent treatment of both suppression of the immune response and replacement of the microbiota through Fecal Microbiota Transplantation (FMT) is a promising approach for the treatment of CD. Here, we analyze metagenomic data from CD patients receiving FMT while in remission, and assess gut microbiome composition before and after FMT at the species and strain levels. These allowed us to identify the gain, loss, and strain replacement of specific species in the context of remission or relapse. We found that FMT had a long-term effect on patient microbial compositions, though this was primarily driven by the engraftment of donor species which remained at low abundance in the patient. Engraftment of some Actinobacteria, and engraftment or loss of Proteobacteria, were related to better disease outcomes in FMT patients, while transmission of Bacteroidetes was found to be deleterious. Our results suggest clades that may be beneficial to transmit/eliminate through FMT, and thus provide criteria that my help identify personalized FMT donors to more effectively maintain remission in CD patients.