Animals are under constant threat of microbial invasion. These potential invaders gain access to the body through the intestine and respiratory tract and the skin. The large and diverse microbiota of the intestine serves to protect the intestine from infectious invaders by occupying a niche that precludes other organisms from establishment there. Other potential invaders are infectious agents spread from other individuals.
To prevent microbial invasion, the body has as part of the innate immune system a series of defenses that collectively constitute a highly effective defense against invasion. These mechanisms include physical barriers such as the skin, which has its own microbiota and utilizes dessication as a mechanism to discourage colonization with other organisms. Inhaled microorganisms and other material are rapidly removed by the mucociliary apparatus, which consists of ciliated epithelial cells and mucus-secreting cells that move inhaled material from the lower to the upper respiratory tract from which they are removed by the cough reflex.
The second line of defense is a “hard-wired” system of innate immunity that depends on a rapid stereotypical response to stop and kill both bacteria and viruses. This is typified by the process of acute inflammation and by the classic illness responses such as a fever.
The third line of defense is the highly complex, specific, and long-lasting adaptive immunity. Because an animal accumulates memory cells after exposure to pathogens, adaptive immunity provides an opportunity for the host to respond to exposure by creating a highly specific and effective response to each individual infectious agent. In the absence of a functional adaptive immune system survival is unlikely.