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

Background: 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. However, limited evidence exists on how different dietary strategies affect gut microbiome composition. This study aimed to compare 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. Methods: In this randomized controlled trial, ۶۰ 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 ۸-week intervention. Results: After ۸ 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 (p ۰.۰۰۱). 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, Escherichia coli and Fusobacterium were observed exclusively in the CDED+PEN group, leading to marked between-group differences. 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. Conclusion: The CDED+PEN intervention led to more pronounced improvements in gut microbial composition than CDED alone, particularly through increased beneficial bacteria and reduced pro-inflammatory taxa.