Changes in Microbial Ecology after Fecal Microbiota Transplantation for recurrent C. difficile Infection Depends on Underlying Inflammatory Bowel Disease

Gut microbiota play a key role in maintaining homeostasis in the human gut and alterations in the gut microbial ecosystem predispose to Clostridium difficile infection (CDI) and gut inflammatory disorders such as inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) from a healthy donor can restore gut microbial diversity and pathogen colonization resistance and is being investigated for its ability to improve inflammatory gut conditions such as IBD. In this study, we investigated changes in gut microbiota following FMT in 38 patients with CDI with or without underlying IBD. Following FMT that successfully treated CDI, there was a significant change in gut microbial composition towards the donor microbiota and an overall increase in microbial diversity consistent with previous studies. FMT was successful in treating CDI using a diverse set of donors and varying degrees of donor stool engraftment suggesting donor type and degree of engraftment were not key for successful FMT treatment of CDI. However, in patients with underlying IBD, there was significantly lower expansion of new taxa and higher proportion of original community and more CDI relapses after FMT during a 24-month follow up. Moreover, the need for therapy for IBD did not change following FMT. These results suggest that changes in gut microbial landscape may be important for long term success of CDI treatment in patients with underlying IBD and potentially for improvement of underlying pathophysiology in IBD.