YOUR WATER BOTTLE IS DISGUSTING
1. Go for a straw-top bottle
Less convenient when you run? Big, bulky, and sort of dorky? Yes. But far less germy.
2. Choose stainless steel over plastic
Won't that make long runs fun? (Hard no.) But stainless steel is naturally antibacterial. And easier to clean (more on that below!).
3. Keep your stash o' bottles clean.
Hand wash plastic -- a lot. A brush will get all those nooks and crannies which are fine on English muffins but nasty hideouts for bacteria everywhere else.