The intestinal flora greatly affect the development of the structure and functions of the intestinal mucosa. In the course of association with whole intestinal flora of germ-free mice, physiological and immunological characteristics changed to those of conventionally reared animals. Studies involving gnotobiotic mice have shown that the presence of limited kinds of intestinal bacteria is responsible for the development of the gut immune system, such as secretory IgA and intraepithelial lymphocytes. On the basis of these studies, we evaluated the effects of residential bacteria on the development of gut inflammation using experimental animals which manifest human inflammatory bowel disease and also established an improved human flora-associated mouse, in which intestinal characteristics are normally developed and their major microbial composition reflects that of humans.