The mucosal immune system is one of the most complicated systems in the body. The system must not only limit and remove virulent microorganisms but also maintain the delicate balance of the microbiome found in the various mucosal compartments. When in proper balance, the local immune system not only improves health but also positively impacts many body functions, improving production parameters. The first line of interaction in the mucosal immune system is the innate system, which comprises mechanical and chemical barriers, as well as cells of the innate system.