Fig. 1. The effects of gut microbiota on the host are reflected in different aspects, such as metabolism and gene. Therefore, single-level data is difficult to explain the full impact of gut microbiota on the host. Metagenomics performs unbiased DNA sequencing of whole intestinal microflora, and classifies and summarizes their gene functions using a database. Proteomics, which sequences the protein structure of the host or intestinal bacterial cells to obtain cell metabolism and changes in the cell network, measures the activity of the cell enzymes directly. Metabolomics is used for the quantitative analysis of small molecules produced by cell metabolism. Metabolomics combined with metagenomics can be used to discover relevant pathways in microbial metabolism, expounding its physiological role. Transcriptomics studies the complete RNA molecules in intestinal microflora, measures the dynamic expression of RNA molecules under different genomic conditions and reveals the genotype of gut microbiota under disease conditions. The application of multi-omics takes a new phase in the study of gut microbiota, providing predictions for therapeutic targets for complex diseases.