1a). gut, and that these responses are correlated with the establishment of unique microbial communities. Transplantation experiments in germfree mice indicate that MHC-mediated differences in microbiota composition are sufficient to explain susceptibility to enteric infection. Our findings indicate that MHC polymorphisms contribute to defining an individual’s unique microbial fingerprint that influences health. Classical major histocompatibility complex (genes are also some of the most polymorphic loci found in vertebrates6, and alleles have been linked to most known infectious and autoimmune diseases of man7. The central role MHC molecules play in vertebrate adaptive immunity has led to intense research spanning several THBS-1 decades on the functional significance of their extreme diversity. The physiological relevance of MHC polymorphisms has classically been appreciated from the perspective of host-pathogen interactions, where certain MHC alleles bias susceptibility to infection by virtue of their ability to present different pathogenic epitopes. However, in contrast to the transient nature of most infections, individuals are colonized from birth with their microbiota, which is known to have a pervasive influence on host physiology8. Studies in knockout mouse models have shown that immune-mediated dysregulation of microbiota composition is a predisposing factor for multiple diseases9,10,11,12,13,14,15. In addition, multiple studies in mice16, rats17, fish18 and humans19,20,21 have demonstrated correlations between MHC variation and microbiota composition, though the physiologic relevance of these relationships were not determined. Together, these observations suggest that an individual’s MHC genotype might exert its most profound effect on host fitness by influencing the relationship between hosts and their symbiotic microbiota. Whether MHC genotype impacts host health by functioning to sculpt an individual’s microbiota has not been tested. Antibody-mediated (that is, humoral) immunity is facilitated in the gut by interactions between MHC class II restricted CD4+ T-follicular (TFH) helper cells and naive B cells that instigate germinal centre formation and the production of high-affinity immunoglobulin A (IgA). IgA controls the abundance of extracellular PLX8394 microbes by tagging organisms for destruction by the immune system, by regulating bacterial epitope expression22, and by aggregating and eliminating them from the gut via peristalsis. Thus, antibody-mediated selection is a key means by which hosts are capable of controlling microbial community composition in the gut. In support of this, activation-induced PLX8394 cytidine deaminase (AID)-deficient animals (whose B cells do not undergo somatic hypermutation and affinity maturation) have severe alterations to their gut microbiota23. In addition, defects in the interaction between TFH cells and germinal centre B cells alters the host IgA antibody repertoire, which is associated with differences in the community of organisms that develop within these animals15,24. Given the role of MHC class II molecules in driving humoral immune responses, this is a likely mechanism through which MHC polymorphisms could shape microbiota composition. Previous research has demonstrated differential patterns of susceptibility among MHC congenic mouse strains against a wide variety of enteric pathogens25,26. This is generally assumed to reflect variability in an individuals’ suite of MHC molecules that differentially stimulate the immune system to clear infection and limit disease. However, differences in the composition of resident microbial communities can influence disease susceptibility associated with pathogenic infection. Colonization resistance is a phenomenon that occurs when members of the microbiota inhibit the establishment of environmentally acquired pathogens, thus limiting their potential to infect and cause disease. Moreover, PLX8394 specific members of a microbiota are more important than others in conferring colonization resistance27,28. Based on this, we tested the hypothesis that MHC polymorphisms could dictate susceptibility to enteric infection and its associated disease by influencing microbial community architecture. Results from our experiments demonstrate that MHC polymorphisms influence gut mucosal immunity by driving differential IgA responses that develop against commensal microbes. MHC-mediated differences in gut immunity were correlated with the establishment of unique microbiota communities among individuals. Importantly, microbiota transplant experiments in germfree mice demonstrated that the unique microbiotas formed in mice of different MHC PLX8394 genotypes impacted host health by controlling susceptibility to enteric infection independent of the immune response. In addition, microbiota from an MHC heterozygous genotype conferred resistance to infection similarly to the microbiota derived from the most resistant MHC homozygous genotype. Thus, results from our experiments indicate that MHC-mediated patterns of disease susceptibility, including heterozygote advantage, may partially be explained by how MHC sculpts microbiota composition in the gut. This study also establishes genes as primary PLX8394 host immunogenetic factors driving the high degree of individuality in microbiota composition observed among humans. Results MHC polymorphisms control.