G.J.
Yes, honey, it does sound like he could have a bacterial or yeast related problem. Has he had any digestive upset? Organic yogurt could really help out by raising his probiotic level. I'm sure that brushing is fine, but when you do start using toothpaste, please use fluoride-free, as the fluoride is toxic. Hmmm....has he had any health issues lately, or been on any medications or antibiotics lately? Sometimes a little bit of dandelion root or grapeseed extract in the yogurt or in some applesauce can make a big difference. Something else that our family is using (though I caution--I haven't tried it on an infant. Our six year old all the way up through mid seventies grandpa have used it with great results, though) is food grade hydrogen peroxide. You might check out earthclinic.com.
Hmmm...did you mention that you give him nuts? He's probably much too young to chew nuts...do you grind them? he could have a little bit of a nut stuck somewhere in his mouth decaying and causing the odor. I'd check for an abcess or wound. Also, an allergy to something, like possibly nuts, can cause a really bad odor from the digestion. Babies are really programmed to operate on dairy--admittedly dairy from mama,--but organic goats milk is a helpful substitute and more easily digested than veggie or nut based "milks"
Hope some or any of this helps, feel free to contact me if you like,
Best wishes and blessings