Pretty much. We are completely blind to the other members of the micro ecosystem that are probably living happily on and around us under non-pathological condit

Pretty much. We are completely blind to the other members of the micro ecosystem that are probably living happily on and around us under non-pathological conditions. There are theories out there that suggest that many infections are caused not by too many bad bacteria but too few or unstable populations of good bacteria (vast over simplification). In addition, we actually have quite a bit of trouble culturing bacteria that might be pathological (our inability to culture them is quite related to our inability to determine their pathological status).