Abstract Background Altered gut microbiota have been implicated during biologics combined with exclusive enteral nutrition (BioEEN) therapy in pediatric Crohn’s Disease (CD). This study aimed to characterize gut microbiota modifications in adult CD patients during and after BioEEN treatment over a 2-year follow-up and evaluate the predictive value of gut microbiota across various treatment stages and for treatment response. Methods This retrospective study analyzed fecal samples from 207 healthy controls (HCs) and 961 patients with diagnosed CD who received 16-week BioEEN treatment followed by biologics treatment. Fecal samples were collected at week 0 (pre-BioEEN), week 8 and 16 (during BioEEN), week 32, 52 and 104 (post-BioEEN). 16S rRNA gene sequencing profiled the gut microbiota composition. Machine learning models were trained to analyze gut microbiota composition and define microbial signatures associated with treatment stages and future non-remission. Results Characteristics of fecal microbiota in active CD patients before BioEEN treatment included significant enrichment of Bacteroides and Streptococcus, and depletion of Faecalibacterium and Prevotella₉. BioEEN therapy increased gut microbiota biodiversity and significantly enriched multiple beneficial bacteria and short-chain fatty acid-producing bacteria. Furthermore, specific bacterial taxa (Parabacteroides, Faecalitalea and Lactobacillus, etc. ) demonstrated significant alterations between week 8 and week 16. Classification models achieved an area under the curve of 0. 807 for predicting future non-remission. The most important taxa contributing to the models included Parabacteroides, Enterococcus and Escherichia-Shigella. Conclusion This study demonstrated that the effects of BioEEN are partially mediated by enriching beneficial bacterial taxa. Gut microbiota composition is reliable predictor of future non-remission in CD. Conflict of interest: Wang, Jing: No conflict of interest An, Ping: No conflict of interest
Wang et al. (Thu,) studied this question.