'Do you harm' means 'harm you'. In this case, it means it can make you sick.
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amgcA way of rephrasing the whole sentence would be:OP question: Certain bacteria in the wrong areas of your body would do you harm.
You would be made ill by certain bacteria being in the wrong areas of your body.
dimsumexpressThe original was clear and needed no rephrasing or rewriting.The original may not have needed rephrasing / rewriting to be clear to you however the person who asked the question was unclear on the meaning of the sentence. As such, rephrasing the sentence was likely to be of help to them.