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Many problems can cause bad breath in a dog. The most common cause is dental problems and you can usually spot these as you can see tartar on the teeth and possibly red gums and darkened teeth. However some tooth issues may not be readily seen especially ones in the back teeth. You also need to look at the folds around the mouth looking for redness, whitish discharge or discoloration that might indicate yeast dermatitis in the folds around the mouth that can cause pretty bad mouth odor. Kidney problems or diabetes can also cause bad breath as can a stomach upset or your dog licking his anal glands which are seeping due to being overfull, though you usually can smell this cause at both ends of your dog.
An anal gland odor is frequently reminiscent of a fecal odor though the odor can vary greatly since each dog's odor is unique to them. If the dog also has a similar odor near the rear as well, then I would suspect anal gland problems.
Since he is also doing a bit of gagging, this might indicate an infection further down the trachea or even in the nasal passages. There really isn't a way for you to examine those areas. You might see some swelling under the eye or on the muzzle that might also indicate an infected tooth. Your vet will need to check the throat and nasal passages. . I would look into a probiotic since I'm sure he's been on antibiotics before. Check with your vet for a suitable probiotic that won't interfere with any other medications or trigger his allergies.
I'd also get a senior checkup done to check organ function and check for diabetes as well.
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