Neither of those really has anything to do with microbiology whatsoever. Physiology will cover a little bit of microbiology when you talk about symbiotic organisms living in the intestinal tract and the mouth. But that is hardly microbiology it is just a attribute of the organ system, you will not really get any microbiology out of either of those courses.
The topics in biology that do have a little more to do with microbiology are:
Immunology (kind of)
and other classes that have to do with microorganisms.
If you have to pick between those two, pick the one that has the better teacher (if you know) or the one that you think you would enjoy more. Personally I like anatomy more than physiology.