# Tissue and stool microbiome in pediatric inflammatory bowel disease patients: diversity differs in patients with relapsing and non-relapsing Crohn’s disease

## TL;DR

This study shows that the gut and tissue microbiome can predict relapse in children with Crohn’s disease, offering potential for personalized treatment.

## Contribution

The study identifies specific microbial markers in tissue and stool that predict relapse in pediatric Crohn’s disease.

## Key findings

- Relapsing pCD patients had lower alpha diversity and altered beta diversity in tissue microbiomes.
- Barnesiella was the most depleted genus in tissue samples of relapsing pCD patients.
- Combining Barnesiella with wPCDAI improved relapse prediction accuracy in both tissue and fecal samples.

## Abstract

Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), are chronic conditions characterized by periods of clinical remission and relapse. Pediatric cases (pIBD) often have a more complicated disease course, where approximately 30% will develop a relapse within a year of diagnosis. Identifying prognostic markers for pIBD is important to optimize treatment and improve long-term outcomes. Our aim was to analyze the tissue microbiome, identify microbial prognostic markers, and validate their predictive power in non-invasive fecal samples.

Tissue and fecal microbiome were characterized from a prospective cohort comprising 33 therapeutically naïve pCD and 23 pUC patients, and 26 non-IBD pediatric controls, using amplicon 16S rRNA gene sequencing. Disease relapse was monitored for one year. At diagnosis, relapsing pCD patients exhibited a significantly decreased alpha diversity and altered beta diversity in tissue compared to non-relapsing pCD patients. Specific taxa were differentially abundant in relapsing pCD, with Barnesiella being the most depleted genus in tissue samples. Receiver Operating Characteristic (ROC) analysis identified Barnesiella (AUC = 0.818), Butyricimonas, and Collinsella as individual microbial tissue markers discriminating pCD relapse. Combining Barnesiella with the weighted Pediatric Crohn’s Disease Activity Index (wPCDAI) further enhanced the specificity and sensitivity of the ROC analysis (AUC = 0.872 in tissue, 0.852 in feces), suggesting potential for non-invasive prognostic markers from stool.

Tissue and fecal microbial markers can predict relapse in pCD patients with high prognostic power, providing a basis for precision medicine and personalized treatment strategies in pIBD.

The online version contains supplementary material available at 10.1186/s13099-025-00766-5.