The mechanism to maintain homeostasis of the gut microbiota remains largely unknown despite its critical role in the body defense. In the intestines of mice with deficiency of activationinduced cytidine deaminase (AID), the absence of hypermutated IgA is partially compensated for by the presence of large amounts of unmutated IgM and normal expression levels of defensins and angiogenins. We show here a predominant and persistent expansion of segmented filamentous bacteria throughout the small intestine of AID ؊/؊ mice. Reconstitution of lamina propria IgA production in AID ؊/؊ mice recovered the normal composition of gut flora and abolished the local and systemic activation of the immune system. The results indicate that secretions of IgAs rather than innate defense peptides are critical to regulation of commensal bacterial flora and that the segmented filamentous bacteria antigens are strong stimuli of the mucosal immune system. M ucosal epithelial surfaces represent points of continuous and intimate interactions between the immune system and the outside environment. Under a constant antigenic pressure from Ͼ400 species of commensal bacteria, the gut immune system has developed highly sophisticated and efficient defensive as well as symbiotic mechanisms (1, 2). Secretion of antibiotic peptides by epithelial cells represents an important component of the innate immune system in the gut. Bacteria or bacterial antigens are capable of stimulating secretion of large amounts of antimicrobial peptides by crypt Paneth cells (3, 4). Also, transgenic (Tg) mice expressing a human intestinal defensin are protected against enteric salmonellosis (5), whereas mice deficient in the metalloproteinase matrilysin MMP-7 and thus lacking mature cryptdins show decreased resistance to some intestinal infections (6). Therefore, antimicrobial peptides appear to be involved in the maintenance of the symbiotic environment in the gut and protection of crypt stem cells from infections.Another front line body defense mechanism that provides protection against microbial agents at mucosal surfaces is production and secretion of IgA (7). Indeed, IgA is the most abundant Ig isotype in mucosal secretions, and at least 80% of all plasma cells in mice are located in the intestinal lamina propria (LP) (8). The gut IgA responses are initiated primarily in organized lymphoid structures present in the intestine, namely Peyer's patches (PP) (9) and the isolated lymphoid follicles (ILFs), which have architecture similar to PP (10, 11). These structures contain a large number of conventional B2 cells, which are derived from precursor cells generated in the bone marrow (BM) (9, 10). In addition, peritoneal cavity B1 cells contribute to intestinal IgA plasma cells. B1 cells are shown to generate large amounts of IgAs independent of T cells and germinal centers (GC) (12, 13). Both B1 and conventional B2 cells are most likely to switch in situ from IgM to IgA in the LP with the help of dendritic cells and factors secreted by stromal cells (14). However, it is...