Gut microbiome is the largest known microorganism in human body, which is closely related to the metabolic health of the host. The maturity and popularization of gene function annotation and metabolomics have enriched the exploration dimension between host and microbiome. Antibiotics affect the composition of gut microbiome and the load of antibiotic resistance gene (ARG). After the use of antibiotics, gut microbiome forms a new homeostasis, which interferes with the process of disease and treatment. There is no clear evidence that fecal microbiome transplantation (FMT) and probiotic supplement can be used to restore gut microbiome after antibiotic disturbance. This paper reviews the research progress of human gut microbiome and the application of antibiotics.