High-resolution analysis of the treated coeliac disease microbiome reveals increased inter-individual variability

Background : Coeliac disease (CeD) is a prevalent immune-mediated disorder primarily affecting the small intestine, characterised by a breakdown of tolerance to dietary gluten. Its onset results from the multifaceted interplay of genetic and environmental factors. Recent data show that alterations in gut microbiome composition could play an important role in CeD. However, many current studies have been constrained by small sample sizes and limited resolution. Methods : To address these limitations, faecal gut microbiota from two Dutch patient cohorts, CeDNN (129 treated CeD patients; tCeD and 106 non-CeD controls) and the Lifelines Dutch Microbiome Project (24 self-reported treated CeD and 659 non-CeD controls), was analyzed using shotgun metagenomic sequencing. Controls were matched by age, sex, and sequencing depth. Self-reported IBS and IBD were used as comparative conditions of the gastrointestinal tract. Inter-individual variation among cases and controls was calculated for the whole microbiome and on the strain-level. Finally, species-specific gene repertoires were analysed in tCeD patients and controls. Results : Alpha diversity was decreased in patients with self-reported IBS and IBD, but not in tCeD. Each condition displayed a unique microbial pattern, with minimal overlap in differentially abundant species. In addition to confirming existing studies, we identified an increase in the abundance of previously unreported species, including Clostridium sp. CAG:253 , Roseburia hominis , and Clostridium lavalense . We demonstrate that changes in tCeD gut microbiome can be, at least partly, explained by adherence to a GFD and report an increased inter-individual variation in gut microbiome composition among tCeD patients. More detailed analyses revealed that a higher bacterial mutation frequency in CeD also leads to a higher inter-individual variation on the strain-level. In line with this, we found that the immotile European subspecies of Eubacterium rectale , with distinct carbohydrate metabolism potential, was nearly absent in tCeD patients. Conclusion : Our study sheds light on the complex interplay between the gut microbiome and CeD, revealing unique microbial patterns and increased inter-individual variation among tCeD patients. These findings expand our understanding of the role of the microbiome in intestinal health and disease. Highlights : Shotgun metagenomic sequencing of the largest coeliac disease (CeD) patient cohort to date provides insights into gut microbiome composition down to the strain level. Novel associations between tCeD (treated CeD; adhering to a gluten-free diet) were identified. tCeD patients have a less uniform microbiome structure. Bacteria display higher mutation frequency in tCeD, compared to controls. The European subspecies of Eubacterium rectale is almost absent in tCeD patients. ### Competing Interest Statement The authors have declared no competing interest.