Wellllllll actually the triggers for AI dz are pretty well known and viruses are not at the top of our worries list. More commonly it occurs because of "leaky gut" which activates the immune system to recognize (and attack) epitopes which should be considered "food" or "self". Some people have HLA markers on their cells that are very much like food, esp gluten, and they are highly susceptible to a failure of immune tolerance.

The phages in our mucus are there because there is a constant stream of food for them. Phages tend to be very specific: one particular type of bacteriophage will infect one particular type of bacterium. Phage therapy involves finding the right one to attack the bacteria involved...and nature does this for us. The lovely thing is that when the bacterium isn't available, phage populations specific to it naturally reduce.