Inflammatory bowel diseases
Inflammatory bowel disease (IBD) is a chronic intestinal inflammation of the gut, consisting of two closely related diseases, Crohn’s Disease (CD) and Ulcerative Colitis (UC). Both diseases are partly driven by pathogenic T-cell responses to components of commensal bacteria, with evidence that flagellin is a key antigen driving IBD pathogenesis. Chronic inflammation in IBD leads to microbial imbalance in the gut, resulting in a loss of key beneficial bacteria, further perpetuating the disease. Using stool and peripheral blood samples from IBD patients and healthy controls, we investigated the relationship between the gut microbiome composition and adaptive immune responses to Lachnospiraceae-derived A4-Fla2 and E. coli H18 FliC flagellin antigens. We used a flow cytometry-based assay to detect circulating flagellin-specific CD4+ T-cells following antigen-stimulated upregulation of CD25 and OX40, and detected anti-flagellin IgG and IgA by ELISA. We observed that, compared to healthy controls, IBD patients had enriched proportions of Fla2-specific CD4+ T-cells and anti-Fla2 antibodies. Microbiome analysis utilized 16s rDNA sequencing, with IBD patients and healthy controls clustering significantly separately by β-diversity analysis. As expected, we observed a reduced Shannon’s diversity in IBD patients, with lower diversity correlating with greater disease severity and higher proportions of circulating flagellin-specific CD4+ T-cells. Differential abundance analyses confirmed enrichment of previously reported bacterial species in IBD patients. Importantly, we show that the relative abundance of these enriched bacteria positively correlated with immune responses to flagellin antigen. These data are the first report of relationships between gut bacteria and flagellin-specific immune responses in IBD patients.