Most things that kill bad bacteria in your gut seem to also kill good. The difference is that Antibiotics are almost too specific, leaving too many bad things untouched.
Herbs like oregano and garlic, Colloidal Silver , all this stuff... it still kills the goodies too, as far as I'm aware, but usually it's worth it to kill the bad guys and I believe the body recovers microflora balance quite fast once any particularly bad infections have been removed :)