I have a question about Natural breeding, which I do a lot of, should you wipe the penis and/or vagina with anything before breeding to eliminate bacteria?

We never do. If you are concerned about dangerous bacteria then my advice would be to culture your breeding dogs prior to breeding season. Bacteria are everywhere and in healthy dogs shouldn’t cause a problem. It’s when the bacteria levels get out of control (for whatever reason, usually a stressed or ill dog ) that it can become a problem.