Project Summary/Abstract Celiac Disease (CD) is an autoimmune digestive disease triggered by the consumption of gluten-containing grains (the environmental trigger) in genetically predisposed individuals. The exact cause of CD is unknown as research shows that genetic predisposition and exposure to gluten are necessary but not sufficient to trigger the development of CD. A growing body of research supports the critical role of the gut microbiota in CD pathogenesis as alterations in the gut microbiota composition (“gut dysbiosis”) have been associated with the clinical manifestation and severity of CD. However, it is unclear whether the gut dysbiosis is the cause or the consequence of intestinal inflammation in CD. This is because there are critical gaps in our knowledge about molecular mechanisms and biochemical pathways through which the gut microbiota interacts with the host and environment, and how precisely specific microbial species/strains contribute to a disrupted gut homeostasis and the loss of gluten tolerance in CD. This proposal aims to build a mechanistic understanding of the functional role of individual gut microbes and the gut microbiota as a whole in CD pathogenesis. To this end, we will leverage multi-omics data and specimens collected before and at disease onset from at-risk subjects to construct mechanistic in silico and ex vivo models of the gut microbiota and host. Our in silico models are based on computational genome-scale models of metabolism and integrate diet (as an environmental risk factor), the gut microbiota (at metagenome scale), and the host’s intestinal epithelial cells and macrophage into one inclusive model. Our ex vivo models are based on patient-derived organoid co-cultures and integrate the host’s intestinal epithelial cells and macrophages with microbial cues. By modeling germ-free and non-germ- free human gut conditions using these in silico and ex vivo models, we aim to address two key objectives. First, we will uncover specific gut microbial species/strains that are mechanistically linked to the production of modulatory metabolites previously implicated in CD under different dietary regimens. Second, we will parse the metabolic crosstalk between the gut microbiota and the host’s intestinal epithelial cells and macrophages before and at disease onset. This integrative approach will allow us to uncover key microbial players in the gut that individually or collectively trigger aberrant metabolic and immunometabolic responses by the host in the early stages of disease development. Overall, this study paves the way for designing early intervention and therapeutic strategies for CD that target specific gut microbial strains to re-establish the host’s immune and metabolic homeostasis.