Combining site-specific gut microbiome and mycobiome profiling with clinical indicators for effective management of pediatric Crohn's disease.

Pediatric-onset Crohn's disease (pCD) is characterized by frequent relapses and long-term impacts on growth, requiring targeted strategies for disease monitoring and treatment. To characterize gut microbiome and mycobiome changes in pCD, we profiled bacterial and fungal communities across multiple gastrointestinal (stool, colon, and terminal ileum) in 30 pre- and post-treatment patients and 36 healthy controls. Microbial shifts in mucosal biopsies lagged behind those in stool, indicating site-specific responsiveness to treatment. Notably, erythrocyte sedimentation rate (ESR) and the simple endoscopic score for CD (SES-CD) were strongly associated with bacterial composition, while platelet count (PLT) and body mass index (BMI) correlated with fungal compositional changes. Twelve key genera were linked to clinical indices across different sample types, with emerging as a relapse-associated biomarker. These findings highlight the importance of spatial sampling in pCD and delineate microbiota-associated genera and clinical indicators that may guide future precision diagnostics and therapeutic monitoring strategies.