While disturbances in the gut microbiota have been associated with type 1 diabetes progression, the causes of this dysbiosis and the consequences to the host are largely unknown. Using a unique multi-omic approach, we explore the functional link between the gut, pancreas and microbiota in type 1 diabetes. In complementary genetic studies, we show that immune loci linked to type 1 diabetes susceptibility contribute to shaping the gut microbiota.