Gut Microbiota Composition Changes following Discontinuation of Exclusive Enteral Nutrition in Children with Crohn’s Disease

Abstract

This study aims to determine changes in the intestinal microbiota of children with Crohn’s disease (CD) before and during exclusive enteral nutrition (EEN) and after its discontinuation. A total of 14 newly diagnosed children with CD (median age 16.0 years; 43% female) were included in this study. Patients were initially treated with EEN and were followed for one year after EEN discontinuation. Stool samples were taken at the time of diagnosis (before EEN introduction), the second day of EEN, the last day of EEN, and every two months for one year after the discontinuation of EEN. A molecular approach targeting 16S ribosomal RNA was used for analysing the gut microbiota. No change was found in the Shannon diversity index before, during, and after EEN cessation (HhaI-digestion p = 0.82; MspI-digestion p = 0.87). According to the PCO, on the basis of the dissimilarity matrices of OTUs, a clear separation of patients at different time points, forming two clusters (before and during EEN as opposed to after EEN), was evident. No clear separation was noted between patients who achieved sustained remission as opposed to those who did not achieve sustained remission during EEN and at the follow-up. In conclusion, a distinct change in the microbiota composition already occurred after two months of EEN discontinuation and remained mostly unchanged over a year of follow-up.