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Microbes have no good or bad side effects any more than trees or deer or horses. It is in the interactions with their environment or with others in that environment that is seen a side effect. You have billions of microbes on your skin, in your mouth, upper respiratory tracts and in your intestines. They are supposed to be there and don't cause problems for you unless they get into the "wrong" place. If you cut yourself, these skin microbes can cause an infection because they like all the "food". The same is true for a burst appendix.

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