Crohn’s disease (CD) is a chronic relapsing intestinal inflammatory disorder that results from an abnormal mucosal immune response against intestinal bacteria in genetically susceptible individuals. Several susceptibility genes have been linked to CD, most of which are involved in host responses to bacteria. Although associated with CD, it is unclear whether dysbiosis is a consequence of intestinal inflammation or plays a causal role in disease. It is also uncertain whether overall dysbiosis or specific bacteria trigger disease in genetically susceptible individuals.