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Through research I have been doing, I read about a study done in 2009 that explains the cause of leaky gut- and how it occurs.

A recently discovery by a Dr Fasano called Zonulin has been found in excess in almost every autoimmune condition(rheumatoid arthritis, multiple sclerosis, Hashimotos, Celiac, Diabetes 1 to name a few). Our intestine has cells that line it and are bound together by structures known as tight junctions. These junctions are made of many different proteins that extend from the inside of the cell to the outside. They weave together to form a tight connection. If these tight junctions are disturbed, they open and allow foreign particles such as bacteria, parasites, environmental toxins and food to pass into the bloodstream. The substances are recognized as a foreign invader and the immune system launches an attack on them. Unfortunately, sometimes our immune system mistakenly attacks an organ (thyroid, pancreas, kidney, etc) and can set off an autoimmune condition. A protein called Zonulin is supposed to regulate the opening and closing of these tight junctions. If there is too much Zonulin, the junctions are over-stimulated and stay open. This is also what is known as “leaky gut”. The most common causes of Zonulin hyper secretion are gluten(gliadin ) exposure and small intestine bacterial overgrowth.This protein modulates the permeability between the tight junctions of the intestine. A condition called “Leaky Gut” results from the increased permeability of the gut lining. Food particles and other offensive substances are able to travel from the intestines to the blood stream through the loosened junctions. Once this happens, the immune system reacts to the substances as foreign bodies and creates antibodies against them. This results in a confused immune system attack on the thyroid gland- it mistakenly recognizes the thyroid gland as a foreign invader. Two of the most common causes of Zonulin hypersecretion are  gluten(gliadin) exposure and pathogenic (dangerous to health) bacteria.