Gut microbiota and its diet-related activity in children with intestinal failure receiving long-term parenteral nutrition

Background: This study characterized gut microbiota and its diet-related activity in children with intestinal failure (IF) receiving parenteral nutrition (PN) compared with those of healthy controls (HC) and in relation to disease characteristics. Methods: The fecal microbiota and short-chain fatty acids (SCFAs) were measured in 15 IF patients (n = 68) and 25 HC (n = 25). Results: Patients with IF had a lower bacterial load (P =.003), diversity (P <.001), evenness (P <.001) and richness (P = 0.006) than HC. Patients with surgical IF had lower diversity (P <.039) than those with functional IF. Propionic acid and butyric acid (p <.001) were lower and d-lactate and l-lactate were higher (p < 0.001) in IF patients than in HC. The energy supplied by PN (%PN) was negatively associated with microbiota diversity and SCFA profile. IF patients had more Escherichia-Shigella (P =.006), Cronobacter (P =.001), and Staphylococcus (Operational Taxonomic Unit 14, P <.001) and less Faecalibacterium (P < 0.001) and Ruminococcus 1 and 2 (P <.001). Duration of PN (P =.005), %PN (P =.005), and fiber intake (P =.011) were predictive of microbiota structure. Higher intake of enteral nutrition was associated with microbiota structure and function closer to those of HC. Conclusions: Microbiota composition and its diet-related function are altered in IF, with depletion of beneficial SCFAs and species and supraphysiological increase of potentially harmful pathobionts. The influence of this compositional and functional microbial dysbiosis on patients’ outcomes and management warrants further exploration.