It could be several things. Most likely it's parasites - either worms, coccidia, giardia, clostridicum, camphylobactor or a combination of a couple of them. You should be able to take a stool sample into the vet for a prescription that will clear up the problem. Usually 14-21 days on flagyl will take care of everything but worms. Please let me know if I can assist further.
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Lori McLaughlin
Your veterinarian should ALWAYS be consulted first and foremost when your pet's welfare is at stake.