Engraftment of donor phageome via fecal microbiota transplantation in recurrent C. difficile infection

Many attribute the 90% efficacy rate of fecal microbiota transplantation (FMT) in treating recurrent Clostridioides difficile infection (rCDi) to the restoration of the bacterial community. However, factors beyond bacteria, such as bacteriophages (phages), may also play a critical role in FMT's success. We hence aimed to evaluate the preservation of the phage community (phageome) along the production process following Good Manufacturing Practices (GMP) at the Lausanne University Hospital (CHUV), and its engraftment in patients receiving FMT to treat rCDi. Sixteen samples, from four donations of one healthy donor, were collected at various production stages – fresh, frozen, homogenized, and encapsulated – for phageome analysis. The phage community profiles of three patients before, at 14, and 60 days after FMT were examined to evaluate donor phage engraftment. During protocol development, magnetic bead purification without further amplification yielded more viral reads and longer contigs of better quality compared to spin column purification followed by amplification. Phages were detected in all sample types, and samples clustered by donation, indicating that the pre-processing steps did not alter significantly the phage profile. The recipients' phageome prior to FMT was characterized by low diversity, each recipient being dominated by a different phage. In contrast, the profile 14 days post-FMT demonstrated the engraftment of donor-derived phages which persisted at 60 days. Most were predicted to be temperate phages of the Caudoviricetes class infecting members of the Clostridia bacterial class, and Lachnospiraceae and Oscillospiraceae bacterial families. Our findings suggest that the CHUV production process for oral FMT capsules preserves the phage community and that donor phages successfully engraft in recipients. Further larger-scale studies and intervention trials will help elucidate the mechanisms underlying the potential of phages in FMT's efficacy.