From 70-85% of the immune system and immune-like cells are found in the lining of the gut. This complex network of cells helps the body discriminate between helpful, commensal bacteria, and pathogenic bacteria that cause illness.

There is significant cross-talk between the immune cells and the organisms living in the intestines.
The immune system in the intestines is constantly balancing the kinds and numbers of bacteria and other organisms that live in the gut. And the bacteria are changing the population of immune cells. Both work to try to achieve balance, immune homeostasis.

Chronic inflammation of the digestive tract may be a reaction against specific bacteria found among the trillions of microorganisms living in the intestines. Inflammatory bowel diseases, IBDs, are characterized by unhealthy levels of inflammation occurring in different sections of the intestine. The bacterial strains found in the GI tracts of IBD patients differs from those seen in healthy controls and IBD patients have the most amount of inflammation in the areas of the GI tract with the highest concentration of bacteria.

Many of the cells in the gut directly recognize and attack infectious organisms. Upon exposure to pathogens, intestinal immune cells are stimulated to generate immune molecules such cytokines and natural antibiotics called defensins. Defensins kill microorganisms by punching holes in their membranes, or linking up small proteins into a “net” that stops pathogens from crossing the gastrointestinal barrier. These molecules also help the immune system control the types and numbers of beneficial microbes populating our intestines, and help in the recruitment of additional immune cells.

Individuals with IBD have imbalances of immune cells and intestinal microbes and without a sufficient immune response intestinal microbes invade the mucosa and an inflammatory response is triggered.

The intestines strive to achieve and maintain a delicate homeostatic balance. Complex interactions between the microorganism and immune components keep the beneficial bacteria “content” while simultaneously using inflammatory processes to keep infectious agents in check.

The key in recovery is to help the body limit unhealthy inflammation. Probiotic bacteria have been the first therapeutic agents for IBD shown to induce the production of defensins. Other agents such as worms, worm eggs, vitamin D, specific bacteria, and omega-3 appear to modulate inflammatory cytokines in test systems, yet these approaches have failed to correlate strongly with reducing IBD or its symptoms.

http://iai.asm.org/content/76/8/3360
http://www.sciencemag.org/content/337/6093/477.abstract
http://www.ncbi.nlm.nih.gov/pubmed/21423246
http://www.ncbi.nlm.nih.gov/pubmed/23398152
http://www.ncbi.nlm.nih.gov/pubmed/23176791
http://www.ncbi.nlm.nih.gov/pubmed/19800289
http://www.ncbi.nlm.nih.gov/pubmed/?term=morningstar+hyperimmune+egg