The skin is the largest barrier, as it separates and defines the internal body from the outside environment. It physically prevents most pathogens from entering the body.
The body also has a normal set of bacterial flora that can outcompete pathogens for resources and nutrients if they do manage to get into the body. The body's own flora are beneficial and help with digestion, as well as other physiological needs.
Lysozyme is an enzyme which lyses pathogen cells open, and it is present in saliva, tears, and mucus. This helps prevent pathogens from surviving entry through the eyes, mouth and nose.
Mucus attempts to trap pathogens in the respiratory tract, so that when the mucus is expelled, the pathogens are also removed. In this manner, mucus also helps to filter foreign particles that could cause potential respiratory tract issues.
Cilia remove mucus and the stuck pathogens out of the body by forcing expulsion of mucus through the respiratory tract and out of the body.
Should any pathogens advance far enough to make it to the stomach, the harsh acidic environment and digestive enzymes make it unlikely that those pathogens survive. There are some pathogens that are resistant to acidic conditions and can survive in the stomach, but most will die and be expelled through the excretory system.
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