Cultivation and genomics prove long-term engraftment of donor-derived bifidobacteria in fecal microbiota transplantation recipients

We assessed bacterial engraftment in FMT at strain level by culturing donor-derived bacteria from the recipients during a year post-FMT and by verifying the strain identities by whole genome sequencing (WGS). We first targeted fecal bifidobacterial populations of two FMT donors and their recipients (n=13) by a genus-specific molecular profiling technique to detect donor-derived bifidobacteria in the recipients. We then cultivated bifidobacteria from both the donors and recipients, screened the isolates by rep-PCR typing and finally subjected 65 isolates for WGS and comparative genomic analysis for definite strain identification. Our results show that donor-derived bifidobacteria can engraft FMT-recipients in long-term up to one year after FMT.