One thing I'd consider adding to your little pig's diet is vitamin C supplements. One of the signs of a deficiency of vitamin C is eye and nose discharge. Even if a respiratory infection is the prime cause of his sniffles, the vitamin C should help him fight it.
It's best to get vitamin C in the liquid form, and get just vitamin C, not a multivitamin. The instructions will say to put it in his food or water, but it is better to give it to him by mouth. You can give him a whole dropper full every day. It's water soluable so it can't become toxic, and he'll probably like the taste.
Peter Gurney recommends at his website using a tiny dab of Vick's Vaporub on the end of your guinea pig's nose to help with decongestion. He also recommends sudafed 0.2 mg per day and a half a 2 mg capsule of garlic oil. He also recommends a small amount of a product called Bisolvon 3 times per day. The active ingredient in Bisolvon is bromhexine, a synthetic derivative that stimulates secretion of fluid by the mucous glands of the respiratory tract, thus improving its clearance function.
Peter Gurney is well-known and well-respected in his knowledge of guinea pigs, and also his use of home remedies as treatments, however, I think you should check with your vet before using the sudafed and bisolvon, just to make sure she agrees these are appropriate treatments.
Does your guinea pig have a little house to go in when he wants some privacy? These are nice for when he's feeling stressed, wants privacy, and a nice warm place while he's not feeling good. One of those little round cozy beds are nice and soft, too.
These are the links on vitamin C and to Peter Gurney's website:
http://guinealynx.info/scurvy.html
http://www.oginet.com/pgurney/respiration.htm
http://www.bisolvon.com/com/Main/faqs/product/index.jsp
Let me know if there's any other way I can help you with your guinea pig.
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