Is Autologous Fecal Microbiota Transfer after Exclusive Enteral Nutrition in Pediatric Crohn’s Disease Patients Rational and Feasible? Data from a Feasibility Test

Abstract

Background: Exclusive enteral nutrition (EEN) is a highly effective therapy for remission induction in pediatric Crohn’s disease (CD), but relapse rates after return to a regular diet are high. Autologous fecal microbiota transfer (FMT) using stool collected during EEN-induced clinical remission might represent a novel approach to maintaining the benefits of EEN. Methods: Pediatric CD patients provided fecal material at home, which was shipped at 4 °C to an FMT laboratory for FMT capsule generation and extensive pathogen safety screening. The microbial community composition of samples taken before and after shipment and after encapsulation was characterized using 16S rRNA amplicon sequencing. Results: Seven pediatric patients provided fecal material for nine test runs after at least three weeks of nutritional therapy. FMT capsules were successfully generated in 6/8 deliveries, but stool weight and consistency varied widely. Transport and processing of fecal material into FMT capsules did not fundamentally change microbial composition, but microbial richness was <30 genera in 3/9 samples. Stool safety screening was positive for potential pathogens or drug resistance genes in 8/9 test runs. Conclusions: A high pathogen burden, low-diversity microbiota, and practical deficiencies of EEN-conditioned fecal material might render autologous capsule-FMT an unsuitable approach as maintenance therapy for pediatric CD patients.

The practice of fecal microbiota transplantation in inflammatory bowel disease

“…A clinical trial administering FMT in active UC has shown enhancement and reduction in specific CAM genera as well as their respective negative and positive correlations with fecal calprotectin levels and clinical/endoscopic disease activity scores, thus highlighting the potential link of CAM with the course of UC and its FMT-mediated restitution [ 39 ]. Perhaps unsurprisingly, autologous FMT has not been found useful in IBD due to the dysbiotic nature of the patient’s microbiome [ 46 ]. The contribution of modulation of the immune system by FMT remains to be explored.…”