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My doctor diagnosed me with IBS and Celiac. Could it be something else?

I was diagnosed with Celiac Disease in May 2016 and have been following a strict diet since then. Some of the symptoms have been relieved with following the diet. For instance, I have gained 8 lbs back (out of the 25 lbs that I lost) and my stomach symptoms have become less severe.

However, I still have nausea on a daily basis and I still have episodes of an irritable bowel 2 or so days out of the week. I have gone to the doctor and got an EGD as well as multiple breath tests for a possible food intolerance. They haven't found any other problems in my stomach and are trying to label my persistent stomach issues as IBS. In addition to this, I have terrible migraines once or twice a week that the doctor has left unexplained.

I am concerned about this because I can sometimes pinpoint certain (gluten-free) foods that trigger the severe nausea I experience every day. For example, I get very nauseated after I eat my (former) daily breakfast of greek yogurt with honey. I also noticed an extreme feeling of sickness when I ate some baked kale chips I bought from the grocery store. It is obvious that these foods are causing me to be ill, but I cannot find a connection between them and Celiac. Does this sound familiar or common to anyone's experiences? I don't feel confident in my doctor's diagnoses of IBS and don't know why I am still so sick.
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