There are a large number of microorganisms in or on the body of animals. Each gram of intestinal content contains more than 10 billion bacteria. These bacteria are in close contact with body cells, exchange energy substances, and transfer information to each other. Furthermore, they participate closely with body growth, development, digestion, absorption, nutrition, immunity, biological antagonism, and other aspects. These microorganisms interact closely with the host mainly through small-molecule metabolites. Microorganisms can synthesize, regulate, and degrade a large number of small molecules, thereby providing functional complements to the host's metabolism. In addition, bacterial genomes contribute to primary metabolites production and regulation of secondary metabolites that affect host physiology in multiple ways, including fatty acids, vitamins, neuroactive metabolites, and amino acids with beneficial effects ranging from epithelial homeostasis, immune cell development, and neuronal regulation to nutrient digestion. Using 16S/metagenomics to study microorganisms, combined with metabolome detection, can systematically study the role and function of microorganisms.