The whole "only the object/person is teleported, not any pathogens" is nice & all, but it doesn't explain the natural gut bacteria being okay in the transfer. If they were killed off/left behind, then MC & anyone being teleported wouldn't be able to eat properly.
The symbiotic bacteria we have in our intestines is so important to our digestive systems that there is such a thing as an excrement transplant. You take a sample of excrement from a person with healthy gut bacteria & surgically insert it into the patient's intestines, thus 'seeding' the intestines with bacteria that will help stabilise the 'local ecosystem'. I can't remember the proper name for the procedure, but that's essentially it.
If the bacteria inside the body isn't counted as being a foreign pathogen, then what length of time does a pathogen have to be in a body before the teleportation doesn't kill it/leave it behind?
Does it have to be a conscious thought to bring a pathogen with you?
Am I overthinking? Yes. Do I care that I'm overthinking? Not really.