I keep two different species in the same room: russians and leopards.
I've sometimes had 2-3 species in seperate enclosures in the yard: russians, leopards, and 3-toed boxies. There was at least 10 ft of space between enclosures to avoid contamination by water runoff.
I don't let one species ever use the same enclosure that another species has used without a thorough cleaning. I don't allow myself to touch a wild-caught animal and then a captive-bred animal without first washing my hands. I sometimes handle my CB russians and CB leopards without washing, but probably shouldn't.
I just try to avoid cross-contamination. I don't consider sharing the same air a problem. It's the food, water, feces, etc. that I worry about.