The primary gastrointestinal function is to get those positive things in required for nutrition and keep out those things that are negative or toxic and invasive. In this process the lining of the intestinal tract is the first barrier. The liver is the second line of processing and defense, called upon to process the initial introduction of nutrients and to remove and or neutralize those "xenobiotics" (chemicals that should not be there) and bacteria that accompany the food and make it through the intestinal barrier. Dr. Pavlov, famous for his demonstration of the conditioned reflex in dogs, salivation at the sound of a bell, also demonstrated the importance of these defenses by tying off the portal vein, the route that nutrients, and toxins, take from the GI tract to the liver. Fever, kidney disease and generalized toxicity in the animal resulted. The toxins that were normally neutralized by passing through the liver were not, with disastrous results. His experiments were performed over a century ago.

If one or both of these functions, getting the good things in and keeping the bad things out, are compromised, not all the building blocks, co factors and fuel required to keep the bodies systems functioning are available, even if ingested. Leaky gut can result in large food molecules passing the barrier, sensitizing the body to the food and triggering an immunologic response.  This response is to large molecules getting into the blood stream and "upregulating" the immune system. Cytokines released from the "Kuppfer cells", fixed lymphocytes in the liver which are a first line of defense, stimulate the immune system in general. This constant up regulation drains finite energy from the system, similar to that drained from your body when fighting infection.  This results in fatigue and a reduction in energy available for fighting other infection and for repair. It also uses up reserves that are used for detoxication of other toxins, making you more susceptible to toxicity from alcohol, drugs and other environmental chemicals. Identification to those foodstuffs that you are sensitive to and eliminating them from your diet, frees up energy for enhanced immunity.

Another example of  insight into the importance of gastrointestinal function in maintaining health occurred early in the twentieth century. Elie Metchnikoff MD is better known for his description of phagocytosis, the process whereby bacteria are engulfed by white cells. He won the Nobel Prize for this work and also succeeded Louis Pasteur as the director of the Pasteur Institute. He theorized that unfriendly bacteria in the gut could produce illness through toxins they produced. This produced a wave of enthusiasm in cleaning the gastrointestinal tract through purging and even led to colectomies that were done for constipation. Performing these procedures during the pre-antibiotic age led to inevitable deaths and the whole theory was thrown out as a result. While in medical school during the early seventies, I was taught that there were no reasons for laxative use other than to prepare the bowel for testing or surgery.

The views held by Dr Metchnikoff are gaining acceptance again, although in a much more measured and scientific way. Three types of bacteria are categorized in the gut. Those whose presence and activity benefit us, the symbiotic bacteria. They help maintain the immune system, help digestion and even, in some cases, produce vitamins and substances that defend us against unfriendly bacteria. Large amounts of these bacteria could even be considered another organ of the body and health requires their presence.

Commensal bacteria such as normal escherica coli and streptococci are well represented and do not produce good or bad effects. They can, when exposed to antibiotics, develop resistance that can be passed on to the third group of bacteria called pathogens.

Those very unfriendly bacteria that cause acute disease are well known and consist of those that your local hospital tests for. Staphylococcus, shigella, salmonella, and clostridium are representative of this group. Other, less well known intermediate pathogens can produce proteolytic (putrefactive) enzymes and toxins that produce chronic symptoms through overgrowth. Toxins liberated producing damage to the lining of the intestinal wall can result in the leaky gut.  (Many of us have experienced exposure and comment in the public restroom that "something must have crawled up and died there"). This further compromises the earlier referenced hepatic reserve.  Examples of this include candida, the yeast responsible for vaginitis in women, thrush and diaper rash in infants. It remains less known when in the gut because there is no easy test for it and the signs and symptoms are not clear cut as with vaginal overgrowth. Although we all have small amounts in our GI tracts normally, overgrowth of candida in the gut is the result of high carbohydrate intake and rampant overuse of antibiotics which kill off the symbiotic organisms. The resulting imbalance can result in chronic illness through the production of intestinal inflammation, liberation of toxins and production of a leaky gut. Other organisms such as Klebsiella and Pseudomonas which produce acute illness when in the lungs or when immunity is compromised, cause chronic inflammation not recognized as acute illness but which can, through these mechanisms , produce a state of chronic unwellness.  Parasites such as amoeba, worms, blastocystis and others are felt to be the province of tropical medicine. They are present in our temperate regions as well and produce a broad spectrum of symptoms and chronic illness that often goes undetected. Unlike giardia that makes itself known through acute illness, these can contribute to chronic syndromes. Fermentation of carbohydrates in the presence of yeast can even lead to an "autobrewry" syndrome, resulting in detectable levels of ethyl alcohol in the non drinker and adding to depressive symptoms already triggered by simple carbohydrates. The toxins from candida may also contribute to "brain fog", complicating the picture. The chronic up regulation of the immune system and abnormal inflammation that results may even predispose to autoimmune disease.

Careful examination of bowel flora is not done in most labs that physicians call upon for examination of the stool. There are only a few labs that do a thorough examination of bowel function by this means. Given that there are over four hundred species of organisms present in numbers that approach 60-80 trillion, this  garden is very important. Reestablishment of balance, controlling or eliminating the intermediate pathogens and reestablishing the symbiotic bacteria is important. Reducing toxic load, healing the intestinal wall and resuming healthy defense and absorption of nutrients is a prerequisite to health in the chronically unwell.  Reducing the load on our hepatic system, our immune system and our neurologic system, compromised by toxins and antigens leaking through the intestinal wall, is a necessity. As part of a multi-variable intervention geared toward controlling poorly defined syndromes, presently treated only symptomatically, it is invaluable.