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You might want your vet to check him for intestinal parasites as they can bother a dog when the stomach is mostly empty or the dog is anticipating breakfast and the stomach acids are flowing. You could start by bringing your vet a fresh stool sample to check for parasite eggs.
If that isn't it then you may want to go the next step of a vet visit for an exam and to find out if this is being triggered by a swallowed non food item, a problem with liver or kidneys etc.
If you just started a new bag of food its possible the dog food company changed the food formula. They don't have to change the bag for 6 months after changing the food so you could check for the customer service number on the bag and call and ask them if there have been any changes.
An over the counter med you might try to sooth the digestive tract would be Pepcid or Tagamet or Zantac given before you go to bed. Be sure to tell the vet when you see them if you use any of these. You can read about dose amounts (and cautions) scrolling down on the pages here http://www.petplace.com/drug-library/cimetidine-hcl-tagamet/page1.aspx http://www.petplace.com/drug-library/famotidine-pepcid/page1.aspx http://www.petplace.com/drug-library/ranitidine-hcl-zantac/page1.aspx
Its not a cure and you'd still want to find out why the dog is being ill.
Hope this helps you!