[dualogy]

> And how do the bacteria get there?

Pre-seeded during breast feeding, as happens across all mammals. How many billions of years do you want to go back on this question?

> And are the bacteria killed off by the antibiotics they're given?

Evidently not, as in developed country sick animals don't get turned into meat foods on principle and by law --- so they don't show up deficient. If they lived for 9 decades like we do, they might (or not). But they don't.