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It's really unlikely that alien bacteria and viruses (if alien life even uses the same building blocks ours does, such that microscopic life forms could even be called "bacteria" and "viruses") would find our bodies terribly hospitable or be well adapted (at first) to live inside us. It's much more likely that
Even if an alien biosphere produces some mix of oxygen / nitrogen / carbon dioxide, that the atmospheric balance will be WAY off and we won't be able to breath it (Avatar may have gotten a bunch of science stuff wrong, but it got THIS right, unlike every other sci fi movie ever). Changing it so that we COULD breath it would probably be a major extinction level event for most life in the native biosphere.
We won't be able to eat the local life (and it won't be able to eat us). Our crops won't grow in the soil (until we change it and introduce earth microbes and fungi). Once Earth life and alien life have co-existed for millions of years (long after we're gone or evolved into something else) this may CHANGE (life forms from both biospheres may co-evolve and figure out how to parasitize and eventually consume each other).
I'm not saying we won't die (if we ever try) for a whole host of reasons (and fuck up someone else's environment in the process), just it won't be (biological) alien diseases colonizing our bodies.