No, ubers are not artificially bred. They are simply humans (or mutants, there is no difference really) who over hundreds of years adapted to metabolizing hellerium.
Remember, ubers normally live in the Zones, which are whole ecosystems operating on hellerium (due to its local abundance). We have uber wheat, uber potatoes, uber apples, uber people.... And also many more uber life forms which are not directly shown in the game (like gigantic monsters, gigantic trees, mosquitoes the size of pigeons, etc.). These changes occurred simultaneously in many separate places, so we can assume that this is what happens naturally when you have a biosphere existing over depleted hellerium deposits. Humans are no exception.
If you really want to look for possible proto-ubers, then the Luchadores from The X-Com Files are a potential candidate (we've briefly discussed it with Dioxine once). They are a subculture/sect of people who eat zombie flesh and can somewhat metabolize its high energy content, though it's not a pretty process and tends to make them cuckoo (though they certainly weren't very sane in the first place, they eat zombies).
As for the mutons, it seems that indeed it is a medical procedure rather than a species. However, the original mutons from 1999 must have been something before, probably. Sometimes I wonder semi-seriously if they aren't the same species as the Floaters...
