29Objective: Celiac disease (CD) is an immune-mediated disease characterized by small intestinal 30 inflammation. CD is associated with HLA-DQ2 and HLA-DQ8 haplotypes, however, genetics 31 alone cannot explain the increasing incidence rates. The main goal of this study was to determine 32 the role of the gut microbiota in CD pathogenesis in the first five years of life. 33Design: We conducted a longitudinal study focusing on three developmental phases of the gut 34 microbiota (ages 1, 2.5 and 5 years). The fecal samples were obtained from 16 children who 35 developed CD and 16 matched controls. We used 16S sequencing combined with functional 36 analysis, flow cytometry, immunoglobulin A (IgA) sequencing (IgA-seq), and plasma 37 metabolomics to determine a microbial link to CD pathogenesis. 38
Results:We identified a distinct gut microbiota composition in CD progressors (CDP, children 39 who developed CD during or after their gut microbiota were sampled) in each developmental 40 phase. Pathogenesis and inflammation-related microbial pathways were enriched in CDP. 41 Moreover, they had significantly more IgA coated bacteria and the IgA targets were significantly 42 different compared to controls. Proinflammatory and pathogenesis-related metabolic pathways 43 were enriched in CDP. Further, we identified inflammatory metabolites, particularly microbiota-44 derived taurodeoxycholic acid (TDCA) as increased in CDP. 45
Conclusion:Our study defines an inflammatory gut microbiota for the CDP including its 46 composition, function, IgA response and related plasma metabolites. The inflammatory nature of 47 CD gut microbiota during development is potentially related to the onset of the disease. 48Targeting inflammatory bacteria in this critical window could affect the pathogenesis and 49 prognosis of CD. 50 51
Significance of this study 52What is already known on this subject? 53• Celiac Disease (CD) is a gluten induced immune-mediated disease in genetically 54 predisposed individuals. 55• CD incidence is increasing worldwide which genetics alone cannot explain. Previous 56 studies have shown that the gut microbiota of CD patients differ from that of healthy 57 populations. However, the role of the microbiome in CD pathogenesis and its role in 58 chronic inflammation is yet be established. 59What are the new findings? 60• In a prospective longitudinal study in children using samples representing all three phases 61 of gut microbiota development (ages 1, 2.5 and 5), we identified significant differences in 62 the composition and function of gut microbiota at each phase. Pathogenesis and 63 inflammation-related functions are enriched in the gut microbiome of CD progressors. 64• We applied IgA-sequencing to identify inflammatory bacteria in both healthy subjects 65 and CD progressors. Flow Cytometry analysis identified more IgA coated bacteria at ages 66 1 and 5 in CD progressors, indicating an early inflammatory response. CD bacterial IgA 67 targets also differed significantly from healthy controls. 68• We analyzed plasma meta...