The health of humans is impacted by the symbiotic relationship with their microbiota, while a dysbiosis of the resident microbiota is associated with various disorders, such as inflammatory bowel diseases [1–3], colorectal cancer [4,5], coeliac disease [6] and obesity [7]. The intestinal mucosa is in intimate contact with commensal microorganisms and food antigens but also faces the constant risk of infection by pathogens from the external environment. The challenging task for the intestinal immune system is to maintain a homeostatic balance between tolerance towards harmless agents and immunity against pathogens. This is achieved through various regulatory adaptations in the cross-talk between the commensal bacteria, intestinal epithelial cells (IECs) and immune cells of the GIT.