Has he ever been around a puppy? Are you willing to separate the dogs and rotate which is out, if things go south?
A warning about dobes, because I have one – they are NOT gentle with littles. You’ll have to work very hard on teaching a dobe puppy to be gentle with smaller animals – our girl is nearly three and still occasionally stomps my cat. They’re also tough puppies and are quite literally a full time job until they’re around 2 years of age…I’ll happy talk more about the breed if you want, but I don’t want to flood this particular answer with my babble. 🙂
I really don’t have an answer it could be an infection (bacterial, fungal or viral), cancer or a traumatic injury (like a burn). My advice is to take him to the vet for an accurate diagnosis. If he stops eating or seems painful it is more important to get him to a vet quicker, however, if he is still eating and not painful he doesn’t need to see the vet as fast.