Another reason I believe there is an increase in allergies is the various man-made protein-type products being sold as fillers for food like burger, or as weight gain supplement (whey protein) or as flavor enhancers. A good example of this is Hydrolyzed Vegetable Protein (HVP).

Acid-hydrolyzed vegetable protein, or HVP is derived by using acid to break down the protein in vegetables into their component amino acids. The resulting liquid has various vegetable based amino acids including glutamic acid which is used as a flavor enhancer. This neutralized liquid is salty, hence HVP products such as Braggs Liquid Aminos. Other HVP sources are autolyzed yeast extract and hydrolyzed yeast extract. Similarly there is dairy originated hydrolyzed whey protein. Most prepackaged gravy mixes have HVPs in them. High levels of glutamate in hydrolyzed vegetable protein can negatively affect people with MSG sensitivity.

So the best way to deal with food allergies is to avoid the one that causes allergic reactions in you. Also I think it is important to avoid designer foods that the body will naturally see as foreign.