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Germ theory is very much real. A person's individual immune system, however, may tolerate some bugs more than others. The intestinal flora of someone swimming in the Ganges is likely incredibly different than someone swimming in a lake in Vermont. This is why traveler's diarrhea is so common--traveling to other countries can introduce you to other bacteria that you've never encountered, making you sick. People who live there, though, have lived with it forever and it doesn't make them sick.

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