The best approach to start will be to use a stripping soap on him. This should remove the majority of anything on his skin which may be causing him to smell. Often flea treatments compound unpleasant odors coming off of a dog, so it would be ideal to start with a product that is meant to remove oils from the skin and not just serve as flea treatment. For this, your best choice will be a degreasing kitchen soap like Dawn, Joy, Dial, etc. Wet your dog well, apply a liberal amount, scrub the entire body well with your fingers and wait 10-15 minutes. Rinse clean with cool water to close the cuticle and apply any conditioner you wish to use. Rinse with cool water once more. If you are having problems with fleas, do not use soaps like this to be the treatment. Use a topical product that lasts for a full month to prevent them. Not only does it work more effectively but you will not have to deal with ailments like tapeworms, anemia, etc which can occur following a flea infestation. Additionally, the directions above should be used just before you're ready to apply flea prevention and repeated once every 30 days unless you use an oral flea prevention, which cannot be washed off of the coat.
You should also consider having a professional groomer bathe your dog in the event that the anal glands might be lending to the smell you're detecting. Expression of these glands can help greatly in preventing malodor.
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