There is an adverse immune reaction to naturally occurring bacteria. Bacteria moves between (epithelial) cells in the intestinal wall tissue. The bacteria is engulfed by Dendritic cells.
The bacteria is aggressivly attacked by t-cells causing extensive damage to intestinal tissue. Additional factors are released from dying epithelial cells that amplify the overactive immune system.
The damage can be treated by specially modified bacterium.
The modified bacteria releases a signaling molecule which inhibits t-cell activation and causes the t-cell itself to release additional signalling molecules.
The overactive immune condition of the intestinal wall is stopped, and the bowel starts to heal.