This may be a simplistic view but I was thinking of the germ theory and our "immune system". Correct me if I'm wrong but the germ theory holds that if our immune system is strong, then we can handle the bacteria and viruses that try to attack us. So doesn't that mean that our body is under constant assault. In our bodies now we have E. Coli, Staph bacteria, listeria, and all the other "bad" ones. And I have come to the conclusion that if this was a war between bacteria and so called "viruses" and our immune system, then we would lose this battle in very short order. Maybe days or weeks. Bechamp's theory that bacteria are only there to clean up the toxemia seems so correct. But yes, people cannot even fathom a different opinion. Critical thinking has been diminished greatly.
Right, the commonly believed and established consensus says that its these bacteria/viruses that cause the illness, but it fails to understand why they do not cause illness in "everyone".
So far i see them as something thats everywhere and is inherently opportunistic. Research (from my limited understanding atleast) seem to indiciate that both bacteria, fungi and other parasites have ambivalent functions within our body, being both capable of ruining and improving a individuals life.
If, in the sense you put it, they come up when certain areas malfunction, the question in research should focus its endevours in optimizing and understanding the bodys mechanisms instead of putting artificial produced immune responses, contaminated injections/supplements and highly problematic medication into the throat of gullable people.
Highly elevated bacteria or fungi counts may be found in ilness because they make up the slack of the body (lets just go with this assumption, idk if its true), then i have the feeling this is only useful temporary, and might create its own host of problems long term.