Deepak Saxena, MS, PhD, highlights a distinct microbiome of Crohn disease

In a discussion with Contemporary Pediatrics, Deepak Saxena, MS, PhD, a professor at New York University, explores the evolving role of fecal microbiome profiling as a diagnostic and monitoring tool for pediatric Crohn disease (CD).

While the field is progressing rapidly, identifying the exact moment when microbial imbalances begin remains a challenge due to a lack of longitudinal studies following high-risk cohorts before symptom onset. Currently, most data stem from patients already diagnosed, making it difficult to pinpoint the earliest reliable age for detection.

Saxena explains that the gut microbiome shifts from a healthy state to a “dysbiotic” one when exposed to environmental toxins, physical trauma, or pathophysiological changes. His research highlights a significant reduction in microbial diversity among pediatric CD patients compared with healthy, treatment-naïve populations.

Specifically, the study identified an enrichment of proinflammatory bacteria, such as Fusobacterium and Proteobacteria, which correlate with higher Pediatric Crohn’s Disease Activity Index scores. Conversely, beneficial bacteria that produce short-chain fatty acids and maintain the gut barrier—essential for reducing inflammation—are notably depleted in these patients.

A critical hurdle for pediatricians is differentiating early-onset Crohn disease from other common infantile gastrointestinal disorders. Saxena suggests that microbiome signatures can serve as noninvasive biomarkers to provide this diagnostic clarity. By identifying these specific microbial shifts, clinicians can initiate earlier interventions. While still in early stages, potential strategies include the following:

• Fecal microbial transplant: using healthy donor microbiomes to restore balance
• Targeted therapies: using probiotics and dietary interventions to suppress proinflammatory taxa
• Disease monitoring: using baseline profiling to predict disease severity and tailor personalized treatment plans

While the current findings are based on a smaller cohort of 35 patients and 100 controls, Saxena’s team is currently analyzing a much larger study involving 600 to 700 patients. This expanded data set is expected to validate the use of microbiome signatures as a robust, noninvasive diagnostic tool.

If successful, this approach will open new doors for early diagnosis and microbiome-based therapies, significantly improving the management of Crohn disease in the pediatric population before significant symptoms or permanent intestinal damage occur.

No relevant disclosures.

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