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Q: Is rubbing a puppy's nose in its urine or feces harmful to its health?
A: The old idea of rubbing a puppy's muzzle and nose in their urine or manure is now rejected as part of potty training. Some people still "show" the pup the "mistake," but certainly don't push their noses into the urine or manure. Many trainers don't use that approach at all, preferring a pro-active, positive training approach.
Remember, feces carry bacteria and viruses that cause disease. You wouldn't want a pup to get feces into their nostrils! Here's a reference on this aspect of dog waste:
Here's a detailed article on step-by-step puppy housetraining which activities such as the use of a bell for signalling "I want to go out" that I agree with: