We previously discussed how 70% of the immune system is in the gut.
According to Thomas T. MacDonald, Professor of Immunology and Dean for Research at Barts and the London School of Medicine, “The gut immune system has the challenge of responding to the pathogens while remaining unresponsive to food antigens and the commensal flora. In the developed world this ability appears to be breaking down, with chronic inflammatory diseases of the gut commonplace in the apparent absence of overt infections.”
In other words, the job of the immune system is to determine what is you and what is not you. The reason 70% of the immune system is located in the digestive system is because an enormous amount of food that we ingest contains foreign material that needs to be sorted. If you consider the fact that our modern diet of processed foods is high in chemicals and preservatives, all of which are foreign material, you can see why the immune system can become overactive and confused. When this happens (as in autoimmune disease) the immune system has lost the ability to distinguish foreign invader from self.