Drinking out of the bottle definitely effects the smell (as you pretty much don't smell the beer at all when the bottle is in your mouth) and therefore the taste.
Much of our taste is dependent on smell. Try eating something fragrant like a curry holding your nose.
You should always drink your beers out of a glass for this reason (within reason obviously, I'll drink lagers out of the bottle at Friday night knock off drinks!) It's also partly the reason why there are beer style specific glasses. They're not just gimmicks.