The development of microbiome has been promoting the study on the relationship between human microbiota and diseases. However, few researches have been performed in the study of prevention and control of animal diseases. In this study, we review and illustrate the roles of microbiome in the following directions: the impact of animal microbiota on diseases; identification of novel pathogens; finding probiotics; research and development for new drugs and biological agents; research and development for new vaccines; new, simple and effective measures.