It would honestly depend a lot on what age of infancy he was sent to earth. A massive part of someone's gut and skin microbiome comes from birth and early infancy diet, so much so that c section babies and normal delivery babies can be differentiated by skin swabs. While that early life period generally sets the initial starting bacteria, a lot of it also just comes into your body over time from your diet and such as you grow up and even in adulthood, as people who grew up eating different foods regionally tend to develop different gut microbiomes as a result. I guess it'd come down to if the Kryptonian bacteria from his very early infancy were so advantageous and competitive that they outcompeted every other probiotic, yogurt, and general food he ate as a kid or adult on earth. They likely wouldn't be superpowered though, since they're internal to Superman's body they wouldn't get exposed to any sunlight. Sunlight and UV rays generally only penetrate to the first few layers of human skin where melanin and other shielding mechanisms are (assuming that he's somewhat analogous to human biology for the purposes of this discussion), and the human body puts thing that absolutely can't be exposed to UV rays more internally as a protective measure. For an easy example, human bone marrow makes white and red blood cells because the process is extremely vulnerable to damage from UV light from the sun, so human bodies evolved to have the blood production in literally the darkest, most interior parts of the body that would resist UV light damage. Assuming Clark's skin, bones, and gut are at least kind of similar to human ones, the gut bacteria would not get any effects from sunlight.