The gut microbiota is a stable and complex ecosystem that forms a protective barrier by forming a membrane barrier and promoting proliferation and differentiation of intestinal epithelial cells, and plays an active role in maintaining and promoting immune homeostasis during intestinal pathogen infection and threats. The paper focuses on the mechanism of anti-pathogenic infection in host-intestinal microbial interactions and the involvement of intestinal microbes in the synthesis of antibacterial compounds against intestinal pathogens and threats, and to provide a theoretical reference for regulation of intestinal microbes to solve clinical gastrointestinal diseases and related symptoms.