advice needed for a new pitbull owner :)

Hi! I just recently adopted a 5(?) month old pit from the shelter. He is absolutely awesome and has wonderful manners for being a shelter dog. My one main complaint is he is soo smelly! He smells like super strong urine. I have bathed him twice but the smell always comes back!
He is getting neutered next month, will that fix the problem? Could it possibly be the food he's eating? I'm feeding natural balance sweet potatoe and bison.
Any suggestions, advice, remedies would be more then greatly appreciated!