Genetic loci associated with inflammatory bowel disease (IBD) include pathways affecting alterations in the delicately balanced homeostatic relationship between the gut microbiota and susceptible hosts, which can lead to sustained inflammation of IBD. Thus, the interaction between host genetics and intestinal microbiota in the development of IBD has led to the notion that the rapidly increasing incidence of IBD over the past few decades is caused by an alternation in the microbial environment. Alternation of the microbiota composition associated with IBD is known as dysbiosis. However, the mechanism by which IBD-associated dysbiosis develops is not well understood because it remains unclear whether the dysbiosis could be a cause or consequence of IBD. To elucidate the role of dysbiosis in IBD pathogenesis is very important for the development of microbial-based therapeutic approaches for IBD patients. In this regard, this workshop focuses on the recent findings in host-microbial interaction in IBD, and also we hope that the therapeutic approach targeting microbiota is discussed.