Abstract
Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridioides difficile infection (rCDI) and it’s also considered for treating other indications. Metagenomic studies have indicated that commensal donor bacteria may colonize FMT recipients, but cultivation has not been employed to verify strain-level colonization. We combined molecular profiling of Bifidobacterium populations with cultivation, molecular typing, and whole genome sequencing (WGS) to isolate and identify strains that were transferred from donors to recipients. Several Bifidobacterium strains from two donors were recovered from 13 recipients during the 1-year follow-up period after FMT. The strain identities were confirmed by WGS and comparative genomics. Our results show that specific donor-derived bifidobacteria can colonize rCDI patients for at least 1 year, and thus FMT may have long-term consequences for the recipient‘s microbiota and health. Conceptually, we demonstrate that FMT trials combined with microbial profiling can be used as a platform for discovering and isolating commensal strains with proven colonization capacity for potential therapeutic use.
Highlights
In fecal microbiota transplantation (FMT), feces from a healthy donor is transplanted into a recipient in order to re-establish a healthy or normally functioning gut microbiota and to correct microbiota dysbiosis associated with the recipient’s condition
The profile of donor DY consisted of two bands that were in the same positions as those obtained from the donor’s B. longum and B. pseudocatenulatum isolates
Donorrecipient pairing influenced the clustering of the bifidobacterial PCR-denaturing gradient gel electrophoresis (DGGE) profiles substantially, and the appearance of bands corresponding to the donor B. longum isolates contributed to the clustering the most
Summary
In fecal microbiota transplantation (FMT), feces from a healthy donor is transplanted into a recipient in order to re-establish a healthy or normally functioning gut microbiota and to correct microbiota dysbiosis associated with the recipient’s condition. Several studies have demonstrated that microbiota of an FMT-treated rCDI patient is very similar to that of the donor, and there have been efforts to identify the commonly colonizing taxa along with specific set of bacteria that might be crucial for the success of such treatment (Jalanka et al, 2016; Staley et al, 2016). In indications such as IBD, the identity of specific bacteria may be even more important as early reports indicate that success may depend on the microbial profile of the donor (Moayyedi et al, 2015; Browne and Kelly, 2017). Donor strains that are able to colonize recipients in long-term are of special interest, as they might show potential for being so-called next-generation probiotics, i.e., therapeutic bacteria for the treatment of diseases in which dysbiosis is considered to play a role
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