You eat a harmful microorganism, it infects you, and you get sick. It is pretty amazing that the pathogen managed to avoid getting digested. Anywhere else in the body, the immune system has to strike a balance: make the environment hostile to invaders but not so hostile as to kill your own cells. In the gut, however, creating an environment that can, for example, indiscriminately chop every single protein down to amino acids and chop every carbohydrate down to simple sugars is acceptable and desired.
I suppose the catch is, whatever mechanism the digestive system uses to avoid digesting itself a pathogen can mimic.
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