There are many factors which cause the gut lining to become "leaky", including stress, antibiotics, infection, food toxins, diet, and many medications. Once damage has occurred and the gut lining becomes permeable to undigested food particles, these leak through into the blood stream and activate the immune system.
Multiple types of immune cells get involved, pumping out mediators meant to "heal" or rid the body of harm. The problem is, when these mediators are released too often (like every time you have a meal!) they cause chronic inflammation, hormone changes, tissue damage, and other physiological disturbances.
These changes eventually become noticeable in your body as bloating, fatigue, chronic congestion, pain in your muscles and joints, depression, skin rashes, eczema, hormone imbalance, digestive issues, weight gain and eventually disease.