Longitudinal Changes in Selected Gut Microorganisms During Gluten-Free Diet in Pediatric Coeliac Disease

Abstract Alterations in gut microbiota have been reported in coeliac disease (CeD). However, longitudinal evidence distinguishing disease-related effects from diet-driven changes after gluten-free diet initiation remains scarce, particularly in pediatric cohorts. The present study aimed to evaluate time-dependent changes in selected intestinal microorganisms in children with CeD before and during adherence to a gluten-free diet and to compare these findings with those of healthy controls. Microbial DNA isolates from stool samples of pediatric patients with CeD (n = 24) and healthy children (n = 24) were analyzed by quantitative real-time PCR. Samples from CeD patients were categorized into four time points: pre-diet, 6-month, 1-year, and 2-year follow-up. The healthy controls were assessed once. The prevalence and microbial load of selected microorganisms were evaluated. Bifidobacterium spp. remained highly prevalent across all time points, although their abundance varied significantly over follow-up, with the lowest levels at one year and higher levels at two years, comparable to those in controls. The prevalence of Candida tropicalis increased significantly during dietary treatment, reaching levels similar to those of healthy children after two years. Saccharomyces cerevisiae showed a gradual rise in prevalence and abundance, whereas Methanobrevibacter smithii remained infrequent with low and fluctuating microbial load. The duration of adherence to a gluten-free diet appears to influence gut microbial profiles in pediatric CeD. The selected gut microbiota microorganisms’ assessment may serve as a complementary tool for understanding intestinal adaptation during dietary treatment, however, its routine clinical application requires further validation.