Abstract:A large number of commensal microorganisms inhabit the human and animal guts. These commensals participate in host life activities throughout the whole life course. Revealing the dynamic changes of the commensals, and the mutual dependency and competitive relationships between microorganisms and host will give us a comprehensive view on the life's essence of higher organisms. This special issue present domestic researchers' new progress and opinions in the field of gut microbes form the following five aspects:gut microbes and disease, gut microbial community structure, interaction between gut microbes and host, gut microbial resource and methods to study gut microbes.