The Effects of the Crohn's Disease Exclusion Diet (CDED) Alone Versus CDED Plus Partial Enteral Nutrition (PEN) on Gut Microbiome Composition in Pediatric CD Patients

Crohn's disease (CD) is a chronic inflammatory bowel condition characterized by relapsing inflammation and microbial dysbiosis. Diet-based therapies have emerged as promising adjuncts in pediatric CD management. To our knowledge, this is the first randomized trial to directly compare Crohn's Disease Exclusion Diet (CDED) with and without Partial Enteral Nutrition (PEN) in pediatric Crohn's patients from a microbiome perspective, highlighting the potential clinical relevance of dietary strategies that are more feasible than exclusive enteral nutrition. In this randomized controlled trial, 60 children with mild-to-moderate CD were assigned to either a CDED-only group or a CDED + PEN group. Gut microbiota composition was assessed using quantitative PCR before and after the 8-week intervention. After 8 weeks, both groups exhibited significant increases in Faecalibacterium prausnitzii, with the CDED + PEN group demonstrating a significantly greater increase compared to the CDED group alone (+8.94 vs. +5.00 log CFU, p < 0.001). In the CDED + PEN group, levels of Bifidobacterium and Lactobacillus also rose significantly, whereas in the CDED-only group, Bifidobacterium slightly decreased and Lactobacillus showed only a modest increase. Moreover, a significant reductions in Escherichia coli and Fusobacterium were observed in the CDED + PEN group compared to CDED alone (E. coli, -1.44 log CFU, p < 0.001; Fusobacterium, -1.08 log CFU, p < 0.001). Changes in Clostridium leptum and Ruminococcus were minimal and not statistically significant between or within groups. These findings suggest a synergistic effect of CDED when combined with PEN in modulating the gut microbiome toward a more anti-inflammatory profile. These findings suggest that CDED + PEN may enhance microbiome modulation compared to CDED alone; however, given the modest sample size and 8-week follow-up, these results should be interpreted cautiously.