Fecal microbiome separates pediatric Crohn disease from other GI disorders

Distinct gut bacteria have been observed in children with Crohn disease (CD) vs those with other gastrointestinal conditions, with findings published in Physiological Reports.¹

The data highlighted more proinflammatory bacteria and less protective bacteria in CD patients, with differences also reported based on CD symptoms and severity. According to investigators, this indicates a potential for gut bacteria to be assessed alongside current tools to diagnose and manage the condition.¹

“Microbes that colonize the gastrointestinal tract provide support for digestion and other functions to keep us healthy. But when there is a disturbance, this microbiome changes, which can cause inflammation,” Deepak Saxena, MS, PhD, senior author and professor at New York University.¹

Exctracting CD and non-CD samples

Participants included children recently diagnosed with CD and those recently diagnosed with functional abdominal disorders not currently on medications.² These patients were defined as cases and controls, respectively. Experts used established criteria to determine CD cases and the Pediatric Crohn's Disease Activity Index (PCDAI) to determine severity.²

Cases were often matched to controls by sex, race and ethnicity, age, and insurance status. Participants provided fecal samples using the OMNIgene•GUT|OM-200 kit (DNA Genotek; Cat. No. OM-200).²

QIAmp PowerFecal DNA extraction kits (Qiagen, Hilden, Germany; Cat. No. 12830-50) were used to extract microbial DNA from these samples. Investigators targeted the 16S rRNA gene for amplification and subsequent sequencing.²

Differences in microbial diversity and composition

There were 43 patients with CD matched to 139 controls with disorders of brain–gut interaction (DGBI) included in the analysis. These participants were aged 5 to 20 years, and significantly reduced body mass indexes were observed in the former group vs the latter. However, no other traits significantly differed between groups.²

Significant differences in the richness and diversity of fecal samples were observed between DGBI and CD groups during the alpha and beta diversity analyses. This included a significant decline in alpha diversity measures among the CD group vs the DGBI group.²

More than 80% of bacteria communities in both groups were composed of the phyla Firmicutes and Bacteroidota. However, proinflammatory phyla, including Fusobacteria and Proteobacteria, were significantly enriched in the CD cohort, while phyla such as Firmicutes, Verrucomicrobia, and Actinobacteria were significantly reduced vs DGBI patients.²

The CD group also presented with significantly enriched Haemophilus, Eikenella, and Klebsiella, in the Proteobacteria phylum. For the Fusobacteria phylum, the CD group had enriched Fusobacterium.²

Negative correlations were reported between microbial alpha diversity measures and disease phenotype. These measures included the Shannon Diversity Index, observed amplicon sequence variant, and phylogenetic diversity.²

Associations with disease severity

An association was reported between increased PCDAI scores and greater Veillonella and and Hungatella abundance. According to investigators, this indicates a potential role in disease activity. Decreased Lachnospiraceae abundance was also reported in patients with greater PCDAI scores.²

Overall, these results indicated significant differences in fecal microbiomes in patients with CD vs DGBI. Investigators concluded fecal microbiome could serve as a biomarker for disease prognosis, severity, and treatment response among children with CD.²

“Our study underscores the potential of fecal microbiome profiling as an effective tool for understanding Crohn’s disease pathogenesis, identifying microbial biomarkers, and predicting disease activity for treatment response,” said Ryan Zanganeh, study author and dental student at New York University.¹

References

1. Children with Crohn’s have distinct gut bacteria from kids with other digestive disorders. News release. New York University. February 12, 2026. Accessed February 20, 2026. https://www.eurekalert.org/news-releases/1116423
2. Levine J, Thomas SC, Isbiroglu A, 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