I have had extensive experience LIVING on MREs ..... though it was years back (late 80's to mid 90's). They may be different now, but the basic idea is the same: Shelf stable 2000 calorie meals that don't NEED any preparation (though it helps) sufficient to keep a young active soldier killing other young active soldiers. 6,000 calories a day is a pretty rich diet- if your metabolism isn't "eating" what you are..... could be trouble..... if you are sedentary, 1 MRE will keep you going, but you will feel hungry.
A lot of the stuff is (or was- I am speaking of MREs I ate) dehydrated, either completely or partially. The crackers were a belly filling miracle ..... and a money maker for unscrupulous
old salts: find some noob and bet them $50 that they can't eat a pack of MRE crackers in 5 minutes
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Another thing that may be causing your gastro-intestinal distress is that you are not drinking enough water and or getting enough/too much fiber. (If you only eat only the peanut butter and crackers, you will bind your colon up to to medical emergency level......)