Microbiota signatures and genetic risk in pediatric celiac disease

Celiac disease (CD) is a chronic, immune-mediated enteropathy triggered by dietary gluten in genetically susceptible individuals, most commonly those carrying human leukocyte antigen-DQ2 or human leukocyte antigen-DQ8 haplotypes. However, because these haplotypes are prevalent in the general population while only a minority of carriers develop disease, additional factors are likely to contribute to disease onset and progression. In recent years, the gut microbiota has emerged as a potential mediator between host genetic susceptibility and environmental triggers, particularly in pediatric CD. Current evidence suggests that children with CD exhibit reduced microbial diversity, depletion of beneficial commensals, enrichment of proinflammatory taxa, and broader alterations extending to fungal and viral communities. However, these findings remain heterogeneous, largely due to variability in study design, sampling sites, diet, age, and analytical methods. This review examines the interplay between host genetic risk and the intestinal microbiota in pediatric CD, with emphasis on bacterial, fungal, and viral components. Moreover, it highlights the importance of longitudinal, functionally oriented, and multi-omics approaches, particularly in genetically at-risk yet clinically unaffected children, to better clarify causality and identify early microbial markers of disease susceptibility.