The human intestine is home to trillions of bacteria of hundreds of different types, which are collectively referred to as the gut microbiota. Ideally, these microbes exist in a balanced state, where both microbe and man benefit from their presence. However, imbalances in the microbiota, which are referred to as ‘dysbiosis’, have been suggested to underlie the development of a variety of inflammatory diseases, including IBD. While there is broad consensus that microbiota composition in patients with IBD differs from healthy controls, it remains unknown whether this dysbiosis is a cause or effect of the imbalanced immune responses that underlie IBD development. Here, we propose to use a new model system to experimentally examine the effect of dysbiosis in patients with IBD on the gut immune system. These studies will reveal whether imbalances in the gut microbiota play a causal role in the immunological imbalances that trigger IBD development, and will reveal potential mechanisms by which we can correct dysbiosis to prevent or cure IBD in the future.