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When you have a stomach virus and it causes extreme bowel movements to the point of almost pure stomach acid, does this kill off the bacteria in our intestinal tracks?

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No, since the pH and the conditions are different in the different compartments (stomach, small intestine, colon) of the bowel. See this figure (taken from this website) for the differences:

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There are not that much bacteria in the stomach, so even even nothing else than acidic stuff comes out, the bacteria are not affected. And even when you have a severe diarrhea, there are still enough bacteria left to keep it colonized.

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