Huang JG, Tay CJ, Aw MM, Lee YS, Ooi DS. World Journal of Clinical Pediatrics. 2026.
Background & Rationale
Paediatric inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, is linked to altered gut microbial composition and function compared with healthy children. Dysbiosis is known to accompany active disease, but longitudinal, within-patient comparisons across flare and remission remain limited in paediatric populations, with most existing data drawn from cross-sectional IBD-versus-healthy-control comparisons. This study aimed to characterise within-subject microbial and functional differences in a single-centre paediatric cohort, seeking features that track with disease activity rather than diagnosis alone, to inform understanding of pathophysiology and monitoring.
Study Design
This single-centre cohort study compared stool-derived microbial profiles from children with established IBD during clinical flare versus clinical remission. Faecal samples underwent sequencing-based taxonomic profiling to assess composition and diversity, alongside predicted functional pathway analysis of metabolic capacity. The primary aim was to characterise differences in microbial diversity, taxonomic abundance, and predicted functional pathways between states; a secondary aim compared findings across disease subtypes where represented. Non-parametric statistical methods suited to compositional microbiome data were used, with correction for multiple comparisons at taxonomic and pathway levels.
Patient Population
The cohort comprised children with confirmed Crohn’s disease or ulcerative colitis recruited from a single paediatric gastroenterology centre. Samples were collected at differing points in each child’s course, allowing comparison of flare and remission states within the same population. Baseline characteristics reported include disease subtype distribution, age at sampling, and activity scores used to classify flare versus remission, along with any imbalance in sample numbers between states.
Key Findings
Microbial diversity was reduced during flare relative to remission, consistent with dysbiosis accompanying active inflammation. Certain commensal taxa associated with a healthy gut ecosystem were less abundant during flare, while taxa with pro-inflammatory potential were relatively enriched. Predicted functional pathways, including those related to short-chain fatty acid metabolism, showed reduced representation during flare compared with remission. These shifts were consistent across the cohort, though magnitude varied by taxon and pathway. Subgroup analyses suggested the direction of change was broadly similar between Crohn’s disease and ulcerative colitis, with some taxon-level differences noted between subtypes. Overall diversity metrics consistently separated the two disease states.
Discussion
The authors interpret these findings as evidence that microbial structure and functional capacity track with disease activity within individual children rather than remaining static. The reduced representation of short-chain fatty acid-related taxa and pathways during flare fits a broader pattern of functional impairment in the dysbiotic gut during active inflammation. The authors suggest relevance for disease monitoring and understanding of flare biology, without proposing specific interventions. As an observational, stool-based cohort study, no intervention was administered and no adverse events or procedural complications are reported.
Authors’ Conclusions
The authors conclude that microbial composition and predicted functional pathways differ meaningfully between flare and remission in children with IBD, supporting activity-associated dysbiosis within individual patients over time. Limitations include the single-centre design, sample size constraints, and reliance on functional pathway prediction rather than direct metabolomic or shotgun metagenomic confirmation throughout. Larger, multi-centre, longitudinal studies are called for to validate these findings and clarify whether microbial and functional shifts precede, accompany, or follow changes in clinical disease activity.
Reference
Huang JG, Tay CJ, Aw MM, Lee YS, Ooi DS. Microbial and functional shifts between flare and remission in a single-center cohort of children with inflammatory bowel disease. World J Clin Pediatr. 2026. doi:10.5409/wjcp.120066
This Scientific Publication Summary is an objective summary of the published trial for personal and educational use. It does not constitute clinical advice, endorsement of the intervention, or a recommendation to alter clinical practice.