Could be IBS, but I'm not sure I'd treat for that until other things are tried, to settle the tummy. Have you tried feeding her a little something right before you go to sleep? It could be that her tummy is so empty upon waking that she actually feels nauseous. You could also try giving some Nutrical right upon waking or give a bit of cracker (if she'll take it) to settle the tummy. Does she have free-feed kibble available at night? Are her stools firm and normal? What are you feeding?
