I think that we, for the most part, misunderstand microorganisms and classify them as "good" or "bad", when what is "good, or "bad" is the health of the individuals terrain... which directs the expression (function) of the microorganism.
That and we have been incessantly conditioned in germ theory... even in "alternative" health circles; germ theory - which I believe is profoundly wrong.
I believe that a pathogenic microorganism can become beneficial if the terrain is changed and vise versa.
Illustrated by the H. pylori post I made in the Ask Curezone forum.
In any case, it is easy for us to become confused when a formerly beneficial microbe becomes pathogenic for any number of reasons... all having to do with what we eat/ingest, put on our bodies, and how we live.
BTW - a few natural health practitioners have apparently used pastes of live, beneficial microflora on open wounds to great benefit, including the elimination of inflammation, and shorter healing times.
I will most likely try this some day myself if the time comes... just for kicks.