OK, I work in human, not veterinary healthcare. But in the human version, there is very bad cramping/diarrhea due to overgrowth of the clostridium difficile bacteria.
I would think that probiotics (good bacteria) would help to put things back into balance. You could start with some yogurt (with active cultures) and perhaps experiment with sprinkling a bit of probiotics from the health-food store on the food.
This, of course, if your dog's condition is the same as the human version.
