Selective Bacteroidota Depletion but Not Global Microbiome Differences in Short Bowel Syndrome on Fiber-Free Enteral Nutrition

Intestinal dysbiosis in pediatric short bowel syndrome (SBS) is associated with poor growth, but the factors that are driving this dysbiosis remain unclear. Prior studies suggest that parenteral nutrition (PN) dependence and remnant intestinal anatomy are correlated with dysbiosis. However, these studies often compared SBS patients to healthy controls, making it difficult to distinguish SBS-specific factors from alterations due to differences in diet, namely the consumption of enteral nutrition with complex composition and exposure to dietary fiber. In this preliminary report from the GREENBEANS study, we examined baseline stool shotgun metagenomic profiles from 10 SBS patients and 13 non-SBS controls receiving fiber-free enteral nutrition. Alpha diversity did not differ significantly between groups by richness or Shannon diversity. Beta diversity showed minimal separation by Bray-Curtis distance and modest separation in Jaccard distance. Differential abundance analysis identified depletion of Bacteroidota in SBS. Compared to control patients also receiving fiber-free enteral nutrition, SBS was associated with only a small global difference in the gut microbiome, suggesting that diet, and not anatomy as previously assumed, is the predominant determinant of gut microbiome structure. This suggests that the inclusion of complex substrates, such as dietary fiber, in enteral nutrition, may be a modality to prevent the development of a dysbiotic microbiome in patients with SBS.