We have a mutually beneficial relationship with the trillions of microorganisms inhabiting our gastrointestinal tract. However, maintaining this relationship requires recognizing these organisms as affable and restraining inflammatory responses to these organisms when encountered in hostile settings. How and when the immune system develops tolerance to our gut microbial members is not well understood. We identify a specific preweaning interval in which gut microbial antigens are encountered by the immune system to induce antigen-specific tolerance to gut bacteria. For some bacterial taxa, physiologic encounters with the immune system are restricted to this interval, despite abundance of these taxa in the gut lumen at later times outside this interval. Antigen-specific tolerance to gut bacteria induced during this preweaning interval is stable and maintained even if these taxa are encountered later in life in an inflammatory setting. However, inhibiting microbial antigen encounter during this interval or extending these encounters beyond the normal interval results in a failure to induce tolerance and robust antigen-specific effector responses to gut bacteria upon reencounter in an inflammatory setting. Thus, we have identified a defined preweaning interval critical for developing tolerance to gut bacteria and maintaining the mutually beneficial relationship with our gut microbiota.

Abstract The delivery of antigens across the intestinal epithelium is an early and critical event in homeostatic responses to innocuous antigens and inflammatory responses to potential pathogens. The factors and mechanisms regulating antigen delivery to the lamina propria (LP) immune system are largely unknown. We recently demonstrated when small intestinal goblet cells (GCs) secrete, they form goblet cell-associated antigen passages (GAPs) and deliver luminal antigens to LP dendritic cells (DCs). Here we report in the basal state, GAP formation is driven by acetylcholine (Ach) signaling via the muscarinic ACh receptor 4 (mAChR4) expressed by GCs. In contrast to conventionally housed mice, GAPs were present in the colon of mice with a reduced microbiota or altered microbial sensing. Formation of colonic GAPs in these mice was dependent upon mAChR4 signaling. Moreover, in mice with a reduced microbial load, luminal microbial stimuli inhibited GAP formation within minutes. In vitro studies revealed GC intrinsic sensing of the microbiota rapidly inhibited ACh induced GC secretion, and conditional deletion of Myd88 in GCs in conventionally housed mice resulted in the spontaneous formation of colonic GAPs, and the delivery of luminal antigen to colonic LP DCs. These findings identify a role for microbial sensing by colonic GCs to rapidly regulate antigen delivery to the LP immune system, and preventing delivery of luminal antigens when the luminal microbial load is abundant and complex.