If you are interested in pathogenic microbiology, schools which have combined microbiology/immunology PhDs should be good for you (since pathogens and immune responses go hand in hand). Of course every program is different, and each program should list requirements on their website or be willing to send you that information. For my search, I knew I was more interested in environmental micro than pathogenic micro so combined immunology programs were obviously not appropriate. I did not want to be bogged down in immuno coursework, knowing I am not interested in pathogenesis or mammalian host systems at all. I guess think hard about the type of lab you want to be in, the type of research you ultimately want to do, and ask if having an immunology component to your curriculum is a help or a hindrance to your goal.
Also think about the size of the programs... a school with 12 labs that is ~half Immunology would have left me with only 6 to choose from, but this might not matter to you. A larger program with 24 labs would not have bothered me as much if half the labs were Immuno focused since I would still have 12 potential labs of interest. Just DON'T go to a school that only has one PI or lab you are interested in The more potential labs the greater chance you have for 6 years of happiness and good fit.
Last, I suppose if you want to teach it would open up more job prospects if you could be hired to teach Microbiology and Immunology courses...... It's all about what's right for you. Sorry for rambling.