Crohn’s disease is a chronic inflammatory disease of the intestinal tract. It has been increasingly appreciated that two factors are involved beyond the genetic setup of individuals: 1) Intestinal microbial dysbiosis and 2) immune system dysregulation. Intestinal microbial dysbiosis refers to changes in the billions of bacteria that are growing in our gut. In healthy people these bacteria come from a certain core set of species. In Crohn’s disease patients these healthy microbes are perturbed. Immune system dysregulation refers to changes in the body’s capacity to deal with foreign particles (such as bacteria) but also your own body tissues. However, it is incompletely understood why and how the gut microbes and the immune system are perturbed in IBD.