I mean, besides the fact that Superman is fictional and all.
Follow me here: Kal rockets to Earth with a full load of Kryptonian intestinal flora, which would enter the Earth’s biosphere with his excreta. Why haven’t they killed all of us by now? Super-powered bacteria are nothing to mess with!
Well, newborns don’t have any intestinal flora; it takes a few days of exposure to the environment and taking in fluid for those to develop. So, depending on how soon after his birth his parents sent him to us, his GI tract might have been sterile.
Just because they’re super doesn’t mean they’re pathogenic. His bacteria are equally devoted to Truth, Justice, the American Way, and the Lack of Horrible Intestinal Squirty Diseases.
But, depending on how Silver Agey we’re being, Kryptonian powers are inherent in everything Kryptonian – including inanimate objects.
Anyway, this sort of stuff is why Kryptonians come equipped with x-ray vision. Kal just has to give the ol’ stink-eye to his stinky pie, irradiate the whole mess, and the world is safe for humanity once more.
Superman’s intestinal flora cannot flourish on Earth. Their own superpowers prevent them from doing so.
Consider: under a yellow sun, Superman himself does not need to eat. Therefore, there is every reason to assume that his intestinal bacteria do not need to ingest nutrients either. And just as Superman does not suffer from constant hunger pangs, his superpowered *K. coli * likewise do not experience any impetus to metabolize; all their energy needs are already satisfied. Since they never actually absorb any nutrients, they never increase in size and never reproduce.
More than that, Terrifel, intestinal flora are usually looking for specific proteins to eat and it’s rather iffy that they would turn up on Earth. If he had any they probably died out harmlessly and been replaced by Earth bacteria a long time ago.
Though I do wonder what happens when you expose Kryptonian bacteria to red kryptonite.