The microorganisms in the gastrointestinal tract 

by William Shaw Ph.D.

Bacteria in the intestinal tract

In order to understand how the widespread use of antibiotics may have such devastating effects, it is necessary to understand the role of microorganisms in the intestinal tract.

There are two main kinds of bacteria in the intestinal tract: aerobic and anaerobic.  The aerobic bacteria need oxygen while the anaerobic bacteria don't need oxygen to live and even may be killed if oxygen is present.  Some bacteria grow faster with oxygen but can adapt to a low oxygen environment.  Another major group of organisms in the intestine are the yeast and fungi.  In the intestinal tracts of some individuals there may be single-celled animals called protozoa as well.  These organisms in a normal intestinal tract are found in a natural balance that is healthy.  It is estimated that there are 500 species, there are perhaps 30 or 40 species that constitute the majority of the bacteria present.  It's estimated that there are about 10-100 trillion cells of bacteria in the intestinal tract at nay one time (1).  To give you an idea of the size of that number, there are about a 100 trillion human cells in the entire human body.  Thus, 10 - 50% of your total cells are due to bacteria in a normal individual who is not on antibiotics.

There are very few bacteria in the stomach because the stomach acid kills them.  But, in the colon there are tremendous numbers: about a million times more in the colon compared to the stomach.  The stomach acid kills most bacteria but the stomach acid is neutralized with bicarbonate from the pancreas in the normal individual as food passes into the small intestine.  Bacteria constitute about 50% of the content of feces. These residents of the intestinal tract are always in a state of flux:  new bacteria are continuously being produced and old bacteria are continuously being flushed out in the moving intestinal contents and later as feces.

In a study that was reported in the Journal of Infection and Immunology (2), it was found oral penicillin administered to experimental animals reduced the total population of anaerobic bacteria by a factor of 1,000 including beneficial bacteria which are called Lactobacilli.  Thee bacteria are present in yogurt. As the good bacteria are killed off, the potentially harmful bacteria increase rapidly.  This study reported translocation of the harmful bacteria out of the intestinal tract and into the lymph nodes surrounding the intestinal tract.  From these lymph nodes, these bacteria were then strategically placed to cause new infections throughout the body.

 Yeast overgrowth of the intestinal tract

Another harmful effect of antibiotics is that killing off all the normal bacteria results in the proliferation of yeast.  There are hundreds of articles in the scientific and medical literature indicating yeast over-growth is associated with antibiotic use.  Some of the most important are included in the references at the end of this chapter (3-13).  There are two reasons for it.  First, when the normal bacteria in the intestine are killed off, the yeast have no competition so they are able to get the lion's hare of all the food that passes through the intestinal tract after a meal.  Secondly, the yeast may actually be stimulated by many of the antibiotics (12,13)

Scientific work on animals is relevant to yeast infection in humans.  Infant mice were much more susceptible to Candida infection than older mice, and once exposed to Candida at an early age, developed persistent Candidiasis (3).  If these mice were given antibiotics at an early age, the Candida in the intestinal tract increased an average 130-fold.  Exposure of infant mice to the hormone cortisone increased Candida in the intestine 8-fold. Similar results are found in humans (5-11).  Largely because of the overuse of antibiotics, the incidence of disseminated Candidiasis has changed from a rare occurrence prior to 1960 to the fifth most common organism encountered in infections acquired at a hospital in Southern California (14).  The reason these bacteria and yeast are important is because they produce chemical byproducts that are normally only present in very low concentrations. When yeast and bacteria, normally present in small quantities, reach extremely high numbers, they produce these byproducts in much higher concentrations.  These byproducts of yeast and bacteria are then absorbed from the intestinal tract into the blood. From there, they circulate throughout the body to all the tissues are are eventually filtered out of the body into the urine.

In addition to the production of these byproducts, the yeast cells may convert to their more invasive colony form.  The yeast in this hypha form imbed themselves into the lining of the intestinal tract like ivy climbing a brick wall.  This attachment is facilitated by the secretion of yeast digestive enzymes at the point of attachment.  The intestinal lining is thus digested by the variety of yeast enzymes including phospholipase A2, catalase, acid and alkaline phosphases, coagulatse, keratinase, and secretor aspartate protease (15-17).  the Secretory aspartate protease is of especial importance; it may destroy the lining of the intestinal tract and may also digest the IgA and IgM antibodies produced by the body to attack the yeast (15).  The destruction of this gastrointestinal lining may be the reason for the abnormal secretin response discussed in the chapter on the digestive system.

Some of the intestinal cells probably die as a result of this attack.  As a result of multiple yeast attaching to the intestinal lining, the linking may appear like Swiss-cheese on a microscopic level.  Ordinarily, undigested food molecules would not be able to pass through this intestinal lining.  However, because of the holes in the intestinal lining, undigested food molecules pas through.  This phenomenon is called the leaky gut syndrome.  A major consequence of the leaky gut syndrome is much greater susceptibility to food allergies.  The undigested food is recognized as an invader by the immune system and as a consequence, antibodies of both the IgE and IgG types may start to be produced.  After a while both behavioral and allergic reactions may occur after eating these foods.  Many times patients with multiple allergies will be retested after anti-yeast therapy and find that their allergies have disappeared. When the yeast overgrowth has been eliminated, the intestinal lining heals, the intestine is no longer leaky, and the immune system diminishes its attacks against the offending foods.  If you child as multiple food allergies in addition to milk and wheat sensitivity, you may find it near impossible to implement a suitable diet.  Therefore, I usually recommend that an underlying yeast problem always be treated at least 60 days before allergy testing is done.

Evidence for abnormal bacteria byproducts in autism

One of the chemical compounds in urine that I initially suspected due to the yeast overgrowth of the intestine is called dihydroxyphenylpropionic acid-like compound (DHPPA).  Several years ago, I began a collaborative study with Dr. Walter Gattaz, a research psychiatrist at the Central Mental health Institute of Germany in Mannheim to evaluate urine samples of patients with schizophrenia.  These samples were very valuable since they were obtained from patients who were drug-free. Thus, any biochemical abnormalities would be due to their disease and not a drug effect.  Five of the twelve samples contained a very high concentration of a compound identified by GC/MS as a derivative of the amino acid tyrosine which is very similar to but is not identical to 3. 4 - dihydroxyphenylpropionic acid.  I have termed this compound dihydroxyphenylpropionic acid-like compound (DHPPA-like compound).  This compound is an isomer of dihydroxyphenylpropionic acid but I have not yet identified the exact isomer.

Reproduced with the permission for Dr. Shaw at the Great Plains Laboratory.

Pages were selected from a chapter in Dr. Shaw's book "Biological Treatments for Autism and PDD."