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I like to think that the bacteria are only on the outermost layer of the body, i.e. skin. It just happens so that the respiratory and the digestive systems are the exterior part of the body which are inside our body. In other words epithelial cells mark the boundary of inside and outside and bacteria are usually tolerated on the outside and not inside.
https://firebase.google.com/docs/gemini-in-firebase#:~:text=...