Digestive Enzymes to decrease autoimmune probability?

I attended a seminar last night.  The talk was focused on the gut/brain axis and decreasing inflammatory processes in the body.  When people react to foods (which many of us do), we are reacting to the proteins in the foods.  Proteins are made up of amino acid sequences.  Many of the sequences of inflammatory foods have similar snippets of amino acid sequences as other foods (leading to cross contamination) AND our own brain tissue (like our cerebella!!!).  Well, our bodies do not react to individual amino acids.  Therefore, if all the proteins are broken down before they get to the small intestine, we won't react to the food at all.  It was suggested that people take digestive enzymes (to digest proteins) when we eat to decrease the probability of reacting to foods, and thus decreasing inflammatory processes in the body.