our downstairs is basically one room, so we have always had the rabbits and guinea pigs in the same room. they don't share the same spaces though and have separate cleaning equipment, but other than that, no special precautions.
asked the vet this question when i planned to adopt piggies and he said rabbits seem to get a bad press for bordatella when other animals can pass it aswell. also, there will always be some potential issues with any different species sharing a space, although it is uncommon. :wave: