IBD Basic Science

Background and Aims:We aimed to assess and compare the biogeography of the mucosa associated microbiome (MAM) in patients with inflammatory bowel disease (IBD) and controls in different segments of the gastrointestinal tract, and explore the links between the MAM, gastrointestinal symptoms and use of proton pump inhibitors (PPI).Methods: We recruited 59 controls (without structural abnormalities and gastrointestinal symptoms),44 patients with ulcerative colitis (UC) and 31 with Crohn's disease (CD).Biopsies from various segments of the upper and lower gastrointestinal tract were collected.Microbial composition was assessed via 16S rRNA gene amplicon analysis and the bacterial load of the mucosal biopsies were assessed via qPCR.The MAM was examined in the context of disease status, PPI usage, the severity of gastrointestinal symptoms, and the symptom response to a standardized nutrient challenge (SNC).Results: Microbial communities of the MAM in the upper and lower gastrointestinal tract are different.Compared to controls, IBD patients were characterised by relative and absolute depletion of numerous butyrate and/or propionate producing genera, with the largest differentiation being the depletion of Faecalibacterium in the lower GI tract of CD patients.PPI users had enrichment of Faecalibacteriumin the lower GI tract.The severity of gastrointestinal symptoms, as well as the symptom response to the SNC, were significantly associated with MAM composition in the GI tract. Conclusion:The absolute and relative composition of the MAM is variable across different segments of the GI tract and is different in patients with IBD and controls.Gastrointestinal symptoms are associated with quantitative changes of bacterial taxa along the GI tract.