Fecal Microbiota Transplantation Restores Gut Microbial Profiles in Inflammatory Bowel Disease Patients More Effectively than Surgical Resection

Abstract

Inflammatory Bowel Disease (IBD) comprises a group of chronic inflammatory disorders of the gastrointestinal (GI) tract driven by immune dysregulation and complex host-microbiome interactions. Current treatments for IBD aim to mitigate GI inflammation through pharmacological therapies or surgical interventions, both of which can cause adverse effects. Fecal microbiota transplantation (FMT), offers a less invasive alternative and has yielded promising clinical results, demonstrating success in treating Clostridium difficile infections. While studies have explored the effects of FMT and surgical resections on the gut microbiota of IBD patients separately, direct comparisons remain underexplored. Here, we compared microbial diversity and abundance in stool samples collected from IBD patients treated with either FMT or surgical resections at both short- and longer-term time points. We showed that FMT restored microbial richness to levels closer to healthy controls, while surgical resections were associated with a reduction in microbial richness. Differential abundance analysis revealed that following FMT, genera abundance in the gut microbiota remained stable over time, compared to surgical resection, which led to a difference in genera in the short-term, followed by a recovery by the long-term time point. Interestingly, FMT was associated with species-level differences in the microbiome, while surgical resections exhibited greater overlap of core taxa with healthy controls. These findings highlight the potential of FMT as a promising treatment for IBD, offering a less invasive option that promotes microbial recovery, while suggesting that surgical interventions, though effective, result in distinct and prolonged alterations to the gut microbiota.