I don’t think they came with. You’re not born with a gut biome, it has to be introduced. If they basically prevented this or the pod’s life support system purged them all before he got to Earth to contaminate it with super bacteria, that would solve the problem. Feasible enough given the tech level of Krypton. Enough for my suspension of disbelief anyway. But it’s comics, they hand wave that shit away constantly because “alien microbes exterminate earth within a year of ship landing” doesn’t make for a good story in anything but the hardest of sci-fi. Even a lot of decent sci-fi writers do that, or else don’t think about it.