There's a difference between food allergies and food intolerances. Food allergies can be life threatening while food intolerances can cause discomfort because your body is unable to break it down properly. If you have food intolerances, this will almost never show up right on the allergy tests which makes them unreliable. There are a fecal tests available for this kind of intolerances which is more concrete. Food intolerances doesn't produce a reaction from antibodies but they can cause symptoms like you stated; bloating, gas, diarreah, nausea etc. Food allergies have the symptoms of hives, shortness of breath, swelling, inflammation for example as you would see in people allergic to peanuts. If you have life threatening allergies, it may or may not show up on tests and I think the allergists use these tests as a baseline. They use the baseline to recommend you avoid certain foods at that time. I agree that if you think a certain food is bothering you, keep a food diary. Record everything you have eaten, even a stick of gum and record your body's reaction if any. You should do this for a month and see if there is any similiarities in the foods you eat and the reactions to them.
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