Bottles and Cavities

My second son recently had his first dental appointment and was diagnosed with multiple cavities. This was not surprising to me, since I had noticed discoloration in his teeth early on. The dentist advised against milk consumption from a bottle, but I am concerned that my son is not getting enough protein now that we have restricted that mode of drinking. He will hardly drink any milk now, but would consume lots as long as he could drink it from the bottle. My oldest son has had milk in the bottle up until this point without any adverse consequences. The dentist thinks genes are involved. My question is whether or not there are any studies that either prove or disprove the theory that tooth decay is linked to bottle drinking.