In nature, symbiotic associations with microorganisms are ubiquitously found, which often play pivotal biological roles in animals, in plants and even in human. Now “symbiosis” and “microbiome” are among the important keywords not only in basic biology but also in agriculture and medical science. However, highly intimate symbiotic associations are difficult to investigate experimentally, because the symbiotic partners are usually non-model organisms that are integrated into an almost inseparable biological entity. Thus, the symbiotic microorganisms cannot survive outside the host and are mostly uncultivable. For a long time, these conditions have severely hindered our understanding of symbiosis. This project aims at bringing about breakthroughs to overcome these difficulties, on the basis of the establishment of novel insect-E. coli and mammal-E. coli experimental symbiotic systems and the development of recent genome engineering technologies, thereby drastically promoting our understanding of symbiosis.