The hydrochloric acid in your stomach is usually heavily diluted in the first place, and only long-term exposure can erode their membrane away. Most, however, reside in your gut lining, which has a nice, thick layer of mucus to protect then from your stomach fluids. Some of the mucus gets washed down when the contents of your stomach move from your stomach to the small intestine, where bile acts as a general transmitter for bacteria to your large intestine. Basically, your gut bacteria spreads throughout your GIT due to pure luck. Pretty good luck for the both of you, too, because you have a mutual symbiotic relationship.
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