The gut lining is only one cell-layer thick. Each cell is connected by a "tight junction". These tight junctions are critical, as they keep what is in the digestive tract out of the rest of the body, and vice versa. If these tight junctions become compromised, then it means that substances which should be eliminated with our stool such as bacteria, viruses, or components of food which haven't been completely digested, can gain access to our blood stream. Over time, that will stimulate an immune response, and the body will begin fighting itself, as foreign matter is being chronically allowed to exit the gut and wreak havoc on the body.
The solution? Lower the immune response the body has mounted, decrease the inflammation, and heal the gut lining. When that happens, the tight junctions are back to doing their job, and the body's immune system is no longer being triggered.