Crohn’s disease (CD) is a chronic inflammatory gastrointestinal disorder characterized by dysregulation in immune response and changes in the gut microbiome. Pediatric CD is rising rapidly and frequently causing more severe symptoms. It can affect body development, growth, and psychological health. Multiple risk factors contribute to pediatric CD, including impaired mucosal immunity, diet, and environmental influences. The pediatric Crohn’s disease activity index (PCDAI) determines the severity of the disease. Appropriate control groups are essential, as CD symptoms can overlap with disorders of gut–brain interaction (DGBIs). Characterization of microbiomes has been limited, despite their potential for detecting biomarkers that predict the treatment response, disease activity, and course. A recent study published in Physiological Reports aimed to compare the fecal microbiomes in treatment-naïve pediatric CD patients and DGBI patients. This study also examines the association between CD severity and microbial diversity.
In this cross-sectional study, patients with gastrointestinal complaints were recruited from NYU Langone’s Laurence D & Lori Weider Fink Children’s Ambulatory Care Center. Two groups were included in this study: newly diagnosed CD pediatrics (n = 43, mean age = 11.977±3.342 years, female = 41.9%) and patients with DGBIs (n = 139, mean age = 11.957±3.453 years, female = 41.7%). The diagnoses were based on standard endoscopic, laboratory, clinical, and imaging techniques. The disease severity in CD was estimated by using the PCDAI. CD cases and DGBIs controls were matched through demographic characteristics of patients. Stool samples (182 total) were collected at home within 1–2 weeks of diagnosis. Microbial DNA was extracted, and the V3-V4 region of the 16S rRNA was sequenced. Data were analyzed by using standard QIMME2 v2021.11.0, with quality assessment performed using MultiQC and FastQC.
Alpha diversity was determined through Faith’s phylogenetic diversity (PD), amplicon sequence variants (ASVs), and Shannon index. Beta diversity used Bray-Curtis distances and UniFrac. The difference between the two groups was tested with linear discriminant analysis effective size (LEfSe), Wilcoxon, and permutational multivariate analysis of variance (PERMANOVA). The Spearman correlation analysis was used to assess the associations with PCDAI scores.
Results demonstrated that alpha diversity was significantly lower in CD cases compared to control groups, including the Shannon index with p <0.0001, both ASVs and Faith’s diversity with p <0.01. Beta diversity differed significantly between both groups using Bray-Curtis with p = 0.001 and UniFrac with p = 0.01.
Bacteroidota and Firmicutes comprised more than 80% of the taxa. CD showed enrichment of fusobacteria with p <0.01 and proteobacteria with p <0.0001. Actinobacteria, Firmicutes, and Verrucomicrobia were depleted, each with p <0.05, in cases compared to controls. Fusobacterium, Eikenella, Haemophilus, and Klebsiella were enriched among CD patients.
A significant negative association was observed between the disease phenotype and ASVs (p <0.001), Faith’s PD (p <0.01), and Shannon diversity index (p <0.01). There were higher PCDAI scores associated with increased Hungatella (p <0.05) and Veillonella (p <0.01), with lower alpha diversity, whereas decreased Lachinospiraceae groups NK4A136 (p <0.01) and FCS020 (p <0.001).
Limitations of the study include its cross-sectional design, which prevents causal or longitudinal conclusions, a relatively small sample size, clinically heterogeneous controls, and limited taxonomic resolution due to 16S sequencing.
In conclusion, this study highlights clear differences in the fecal microbiome between pediatric CD and DGBI patients. Reduced alpha diversity was associated with greater disease severity. Pro-inflammatory genera like Hungatella and Veillonella were enriched, whereas protective Lachnospiraceae taxa were depleted. These findings suggest that the fecal microbiome may serve as a biomarker for treatment response, severity, and prognosis in pediatric CD.
Reference: Levine J, Thomas SC, Xu F, et al. Microbial signature of pediatric Crohn’s disease: Differentiation from functional gastrointestinal disorders and relationship with increased disease activity. Physiol Rep. 2026;14(1):e70665. doi:10.14814/phy2.70665
