This^

The best way to think of yourself is as a perpetually changing petri dish with multiple organisms competing in a constantly changing environment of nutrients and exposures. Some organisms work together, some outcompete, some change/mutate. Some environments are more acidic, some less oxygen, some sunlight, some dry, some wet, etc some medications are designed to kill certain organisms and then now other competition fills in its place (think yeast infections after an antibiotic kills some bacteria previously occupying an area). Oh, and what's normal for you isn't normal for everyone.

Regarding the spores, if the environment is right and bacteria take hold it's only because the conditions were so that it outcompeted the others in that location in a high enough concentration to produce toxin that at low concentrations cause issues. Botulinum is quite potent.

(my background is microbiology and a family doc for those that care).