What causes allergies and autoimmune disease?

Another excellent post at http://gettingstronger.org
In summary*:-
We should be sure to include ample amounts of prebiotic fiber in our diet

Fiber is required by the microbes we co-evolved with and rely upon intensely for our health.  The most important type of fiber is soluble fiber, particularly fructooligosaccharides and other non-starch polysaccharides that we can’t digest without the aid of bifidobacteria, lactobacilli and other beneficial bacteria.  To ensure a robust colonization of our gut by these microbes, we don’t need to “eat” them as probiotics and yogurts or transplant them through the rear end.  The most natural way to colonize your gut is to feed them by eating a high fiber diet, and to minimize the sugars that lead to intestinal “blooms” of deleterious bacteria like E. coli and C. difficult — which you might think of as “intestinal weeds”

So: increase the volume of green, leafy cruciferous vegetables — such as kale, broccoli, brussel sprouts;  colored and bitter fruiting bodies like red and green peppers, herbs and spices like curcumin. Of course, fiber can be introduced from a great variety of vegetable sources beyond the cruciferous ones.  Avocados, artichokes strawberries, mushrooms, sweet potatoes…the list goes on.

*See http://gettingstronger.org/2013/03/what-causes-allergies-and-autoimmune-disease/#more-4190