I get really bad aching pain in my stomach whenever I eat eggs, broccoli and almonds. MSG bothers me too but nothing like the pain I get with these foods. No one seems to know why. I was hoping someone out there might have some insight concerning this.
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Try to do more trials or get an allergy test, if you haven't already.
There are some nuts that totally screws up my intenstines, many people have chicken egg allergy (try other kinds), but brocolli allergy I haven't heard of (try cauliflower, it is the same kind, or the other way, try kale to check for K-vitamins).
If it is not allergies, I have had trouble with fungus in the stomach, that was fighting back at paleo (it lives of sugar). I just kept going, and eventually it stopped.
I just got a food allergy blood test. They can test for sensitivities and allergies. I've heard that it's not terribly accurate..but it may be a place to start for you. I'm allergic to just a few things but "sensitive" to many. Almonds is on that list :(