Abstract Inflammatory bowel diseases (IBD) occur when there is an unfortunate combination of microbial dysbiosis and genetic susceptibility. Downregulation of Vitamin D receptor (VDR), a host factor, promotes the severity, extent, and duration of mucosal inflammation and dysbiosis. However, most studies examining gut microbiota have primarily relied on fecal or colonic luminal samples. In contrast, few studies have considered the roles of the small intestinal microbiome. Classically, Paneth cells located in the small intestine are a significant source of antimicrobial peptides (AMPs) and proteins important in host defense. Although Paneth cells are located in the small intestine, AMPs are released to the entire intestine, thus shaping the gut microbiome. VDR regulation of gut bacterial pathogenesis has become an emerging area in IBD, however, the aspect of small intestinal microbiome and metabolites has yet to be explored. Given the challenges in treating patients with Crohn’s disease and the limited studies on the small intestinal microbiome, it is critical to understand how Paneth cell VDR is involved in microbial homeostasis, balanced metabolites, and innate immunity. The objective of our current R01 proposal is to study regulatory mechanisms of Paneth cell VDR and to restore microbiome / metabolites in inflamed states. Our preliminary data showed Paneth cell VDR conditional knockout (VDRΔPC) leads to dysbiosis and susceptibility to Salmonella-induced colitis. We established a method to purify Paneth cells and study their alertness to bacterial pathogens. Furthermore, conditional VDR deletion severely changed the metabolite profile. However, the complex mechanisms in the ileitis through the Paneth cell VDR are still unknown. We hypothesize that VDR deficiency in Paneth cells alters the microbiome/metabolites and makes the host susceptible to chronic intestinal inflammation (e.g., ileitis). We have designed two Aims to rigorously examine the hypotheses at the cellular and microbiome levels: Aim 1. Define the mechanism by which VDR maintains healthy Paneth cells and impacts ileitis inflammation. Aim 2. Investigate the role of Paneth cell VDR in altering the microbiome / metabolites and define the mechanism of VDR in restoring microbial homeostasis, when administering microbiome via fecal transplantation or recolonization in originally germ-free mice. Specifically, we will use novel animal models, organoids from human IBD biopsies, and statistical and bioinformatic tools to understand the host factors and aspects of microbiome / metabolites in chronic intestinal inflammation. Our research team includes experts in the following areas: epithelial biology, animal models, clinical gastroenterology, and microbiome. Our studies are innovative because we provide a unifying hypothesis that can potentially account for defective a host factor in VDR signaling pathway, abnormal Paneth cells, and dysbiosis in IBD. Cutting edge technologies and models will be...