by Lawrence Wilson, MD

© March 2013, The Center For Development


 The human intestinal tract is a very complex internal environment.  It is filled with various species of bacteria and yeasts that should assist digestion, kill harmful or pathogenic infections and even help produce many vitamins and other chemical substances needed for our health and long life.  The name given to these organisms that live in our intestines is the intestinal flora.

In order for the intestinal tract to work correctly, it must contain only the ideal species of bacterial and fungal organisms or flora.  Unfortunately, this is rarely the case today.  When a person has the wrong species of bacteria and yeasts in the intestines, the condition is called intestinal dysbiosis.

This article discusses why the intestinal flora is so important, the causes for and symptoms of an incorrect flora, and how to correct the flora easily in most cases without the need for costly tests or products in most instances.




The correct or so-called “friendly” flora in the human intestine includes yeasts such as lactobacillus acidophilus, lactobacillus bifidis, and perhaps a few others.  Most people either don’t have any of these in their intestines, or the numbers are too low.  Products sold that contain these particular organisms are called probiotics.  Other products are available in health food stores that may promote the growth of these particular organisms, and these are called prebiotics.

When the good or friendly flora are missing or in low concentration, it allows others to multiply in the intestine.  This will hamper the digestion of food, but can also cause many other symptoms, since the incorrect flora produce toxins that are absorbed into the body.




The incorrect flora include many possible species of bacteria such as Escherichia coli, usually called E. coli.  However, there are literally hundreds of other bacteria such as streptococcus, staphlycoccus, clostridia and others that can and do infect the human intestinal tract.

The other very common yeast or fungus that grows in the human intestinal tract is candida albicans, along with other species of yeasts.  These yeasts live on sugars that are often present in excess in people’s intestines, thanks mainly to their diets that are too high in either simple sugars or complex carbohydrates such as starches in foods like potatoes, bread, rice, cookies, cakes, pies, pizza dough and the like.  For more about candida albicans infection, read Candida Albicans Infections on this website.

Many people also have some amoebas, giardia lamblia, parasitic worms such as tapeworms, trichina worms from eating pig products, and perhaps other parasitic organisms in their intestinal tract.  These organisms irritate the intestines badly, and in rare cases burrow through the wall of the intestines and can enter the general blood stream and spread throughout the body.


Parasites around the world. In many warm parts of the world, parasitic infections are the major cause of disease and death.  They take literally millions of innocent lives each year. This is sad because these infections are easy to prevent if only the leaders of these nations started simple educational programs to teach the people proper cleanliness procedures such as boiling the water and cooking the food properly.  Human and animal waste must also be disposed of properly and children must not play in contaminated dirt.

That this is not done in these nations is a sign of their lack of development and severe lack of wisdom of their leaders.  The leaders of these Central and South American and African nations, mainly, are content to allow their people to suffer and die miserably when simple educational campaigns could change it all within a few years.

To read much more on this very important subject, read Parasites on this website.




            Ill health.  If the entire body chemistry is not in balance, it is very difficult to maintain the proper intestinal flora.  It does not matter if one takes probiotics such as lactobacillus acidophilus, or eats yogurt every day.  If the pH, mineral balance, vitamin content and other parameters of health are not correct, one’s internal environment will not support the healthful intestinal flora and harmful organisms gain a foothold easily.  This is the case with almost everyone today, and it is the most important fact to recall about balancing one’s intestinal flora.   


            Improper diet.  Often the most important cause for overall poor health today is an incorrect diet.  Features of the modern Western diet that damage the intestine and its flora include:


·           Yin foods that subtly unbalance and seriously weaken the body.  These include all types of sugars, sweets, fruit, fruit juices, and others.  This is discussed separately below.

·           Chemical additives that irritate the intestines.  Even extra vitamins and minerals, such as iron-enriched bread, is quite irritating to the intestines.

·           Unclean food.  This includes all raw food unless you are absolutely sure it is washed with soap and water to kill parasites and other harmful organisms.

·           Irritating and hot herbs, spices and condiments. This includes hot sauce and many others that inflame and can slowly damage the intestines.

·           Empty calorie foods. These are white bread, white rice, white sugar, soda pop and most prepared restaurant foods.  These simply lack the needed vitamins and minerals required for their proper digestion.  As a result, they slowly deplete the body of vitamins and minerals, and damage the intestines in the process.

·           Other damaged or poor quality foods such as pasteurized and homogenized milk products, refined grains and others. These often cause subtle allergic reactions in the intestines and damage the intestinal tract in other ways.

·           Drinking water problems. While this may be less critical, most people do not drink enough fresh, pure water each day.  Adults need about 3 quarts of water daily.  Also, much of our city drinking water is contaminated with chlorine, fluoride, and toxic chemicals and even residues of medical drugs.  This can damage to the intestines.  I know this because when people switch to a quality spring water, it occasionally provokes vigorous diarrhea for a few days as it cleans out some of the debris or harmful bacteria in the intestinal tract.


Yin disease.  A primary cause for incorrect flora is often a diet that is yin.  This means that the diet contains either too much sugar, fruit, fruit juice, alkaline water, or raw food such as salad, sweets or other yin foods.  Other yin items include alcohol and even medical or over-the-counter drugs.  In fact, taking too many vitamins, minerals or herbs is also very yin and can upset the digestion enough to unbalance the flora.  To read more about yin conditions and its effects, read Yin Disease on this website.


            Antibiotic use. Taking antibiotics, especially wide-spectrum antibiotics, often destroys the friendly intestinal flora.  This allows other bacteria, viruses, yeasts and parasites to grow in the intestinal tract.  Medical doctors should know this and should always recommend eating live culture yogurt or taking a probiotic product after a course of antibiotics, but they rarely do so.

A far worse problem with antibiotics is that small amounts remain in the liver and elsewhere for years, and can exert harmful effects on a person for many years as a result.  These residues are removed on a nutritional balancing program, but the process takes months to several years on a properly designed program.


            Other drugs.  Many medical and over-the-counter drugs interfere with digestion or stomach acid production, or irritate and damage the digestive tract.  These include acid-blockers, pain killers, anti-inflammatory drugs such as Tylenol and Aleve, and hundreds of others.


Food chemicals.  Many seemingly harmless food additives that are in most prepared foods may upset digestion and kill off or damage the friendly or proper intestinal flora.  This is especially the case when these are eaten regularly.  They often irritate the intestine and alter its pH or other delicate chemical balances in the intestine.

These chemicals include flavorings, preservatives, dough conditioners, artificial and natural sweeteners, MSG, aspartame and literally hundreds of others.  One never knows how sensitive one’s digestive system is to a particular chemical, so reducing them to a minimum is the best policy for a healthy digestive tract.


              The presence of toxic metals and other mineral imbalances.  The presence of too much mercury, in particular, and perhaps copper, has a very damaging effect upon the intestinal flora in some people.  Autistic children often develop this problem, causing food allergies and leaky gut syndrome.  Other minerals exert a protective effect such as zinc, which is commonly deficient in our diets today.


            Mental upset and tension, and incorrect eating habits.  This can seriously affect one’s digestion in some cases. Please always rest a few minutes before and after eating, eat slowly, eat sitting down, and chew thoroughly.  Try to be at peace when you eat and do not overeat or eat in your car or while on the phone at work.  These simple habits can assist digestion and assimilation and actually help keep the bowel flora normal and healthy.


            Illnesses.  For example, some fevers can kill the healthful flora, as can illnesses that make the body too cold.  Parasitic infestation can irritate the intestines very badly in some cases.  Diseases that deplete one’s vitality like cancer and diabetes can also alter the flora in a few cases.  Even severe grief and sadness may damage the intestinal flora.




            Many times, there are no symptoms.  One may appear to digest one’s food adequately, and the bowel movements may appear to be normal in size, shape, texture and even odor.  One reason for this is if the body has gotten used to having the incorrect flora present.  In other cases, the reason is that a person may have fairly strong digestion so that no symptoms are noticeable.

            However, if one notes carefully, usually there are symptoms of incorrect intestinal flora.  Here are the most common ones:


·           Foul-smelling stools.  The bowel movements should not smell bad. They should smell a little like a barnyard, but not overly stinky, putrid or some other smell.

·           Some bloating and gas. 

·           Constipation or diarrhea.

·           Intestinal pain, at times.

·           Food sensitivities or food cravings of some kind.

·           Subtle signs such as weakness, sleepiness after eating a meal, headaches, or other aches and pains or other symptoms.

·           Because the intestinal tract is so complex and connected intimately with the rest of the body, almost any symptom is possible when the intestinal flora are incorrect.




            An interesting and unusual symptom of intestinal problems is feeling better on a vegetarian diet.  I have encountered this many times in clients.  The client finds that eliminating all animal products results in less bloating, less gas, and often a feeling of well being the person has not experienced in years. 

            Most people then assume that a vegetarian diet is best for them, and that meat, eggs and/or dairy are harmful foods that just cause bloating, gas, mucus and so on.  This is not the truth, but it sure seems to be the truth for them.  Let us explore why this occurs.

            When the intestinal flora contains some E. coli organisms, in particular, and one eats a concentrated protein food such as meat, eggs or cheese, perhaps, it literally feeds the E. coli organisms.  As a result, they multiply.  However, they do not digest the protein, but rather they cause the protein food to putrefy or rot.  That is, they are involved in a different chemical process than digestion.

Digestion is specific chemical process that break the food apart into its components.  It requires very specific enzymes and intestinal flora to accomplish this difficult task.  When the flora is incorrect, digestion does not occur to a great enough extent. Instead, the E. coli convert the protein into very toxic substances such as indoles, skatole, cadaverine and other substances.  This is called rotting or putrefaction.

When a food rots in the intestines, the harmful chemicals that are produced poison the body and often directly or indirectly cause gas, bloating, food sensitivities, weakness, headaches, depression and many other symptoms. 

One answer for putrefaction in the intestines is to stop eating concentrated proteins such as meats and eggs.  The odors and bloating go away and one believes that a vegetarian diet is the answer.  However, we find repeatedly that vegetarian diets are not the real answer.  It is a deficient diet, no matter what anyone claims, and it is too yin.  Eventually, health suffers and restoring health after one has been a vegetarian for years is not easy.  The real answer is not a vegetarian diet, but rather to correct one’s flora.  When this is done, most people have no problem at all digesting meats, eggs and most quality dairy products. 




The goal of restoring the intestinal flora is to make the conditions in the intestine hospitable for the friendly intestinal flora, but not for the pathogenic or harmful ones.  Making the conditions correct includes improving the pH, the digestive juices, and perhaps other chemical qualities of the human intestines.

The method for doing this described below will work in the majority of the cases.  In very severe cases, more invasive methods are needed, and these are discussed later in this article.  The following are the steps needed to correct the flora in almost every case:


1. Eat a diet of mainly cooked vegetables, except for the nightshade vegetables (tomatoes, white and red potatoes, eggplant and all peppers), cucumbers, okra and summer squashes.  Winter squash is okay, although it is a little yin. 

In addition, one can eat small portions of most meats, eggs, and preferably organic or raw dairy products up to 8 ounces of milk daily or one container of plain yogurt or kefir.  Skip all pig products, however, such as pork, ham, bacon, chorizo, and lard, as they often contain some parasite eggs even when well-cooked. 

Other excellent foods are small amounts of some whole grains, particularly organic blue or yellow corn chips or corn tortillas unless you do not tolerate them well.  However, avoid all gluten-containing grains, which are wheat, oats, barley and rye.  After a time, you may be able to reintroduce oats, barley and rye.  However, wheat is irritating and no longer is a healthful food today.

Beverages should be mainly pure spring water, or for a few months only, steam distilled water.  Adults need to drink about three quarts of water daily.  Mild herbal teas are also fine, as is one cup of regular coffee, not cappuccino or latte, and one or two cups of black, green or white tea.  Ten to twelve ounces of carrot or green juice daily is helpful for most people to provide a very bioavailable form of calcium.  This basic eating plan eliminates most yin foods and beverages, and will slowly move the body into a more yang condition.


2. Stop eating all yin foods and beverages.  This means reducing and eventually eliminating all sugars and sweets from the diet.  These include white sugar products, but also honey, maple syrup, agave nectar, Rice Dream, and most fruit, fruit juices, and smoothies or other drinks with fruit or sweet items in them. It also means reducing and eventually eliminating alcohol, soda pop, ice cream, or other sweetened food items.

              More difficult for some people is to stop eating almost all raw food.  Raw food is very yin.  This includes salads and even most fermented foods as these are yin as well.

Also, avoid the nightshade vegetables, which are extremely yin.  They are really fruits in a botanical sense, as they contain seeds, and include tomatoes, all peppers, eggplant and white or red potatoes.  Also stop eating most squashes, cucumbers and okra, as these are also really fruits.  Some winter squash is okay.


2. Avoid irritants.  These include coffee, some irritating herbal teas, other sources of caffeine or theobromine like chocolate, and all hot spices.  Also avoid table salt, table pepper and all irritating condiments.  A little plain mustard and even a little ketchup are fine, however.  Mild herbs and spices are also excellent.

Also avoid all pig products such as ham, pork, lard, bacon, chorizo and others.  These are quite irritating and may contain parasite eggs even if they are well cooked.

Wheat, spelt and buckwheat are also somewhat irritating foods today and best avoided.  For a time, eliminate all gluten-containing foods until the intestines heal.


3. Limit some other foods.  Whole grains such as brown rice, blue and yellow organic corn products, oats, rye, barley, quinoa, millet and others are okay in limited amounts, but only if you can digest them well.  Otherwise limit these until your digestion improves, which it usually will very quickly.

            Other hybridized and genetically modified foods today that are best limited are most soy products and white corn. 


            Following this diet is the main thing to do.  It relaxes, strengthens, and heals the intestine like nothing else I have seen.  Do not be tempted to add back items such as lime or lemon juice, or reintroduce salads, fruit or other items.  This will wreck the quite delicate process of rebuilding and reconditioning the intestinal tract.

Many people who have failed to improve their intestinal candida abicans problem, their food allergies, their gas and bloating, diarrhea, constipation and other intestinal symptoms find that they go away quickly on this diet, with the help of the supplement discussed below.




The other essential item is to take a product called GB-3 or another product that contains pancreatin, ox bile, and bile acids. The reason is that this product – and only this type of digestive aid – by enhancing bile in the intestinal tract, seems to be able to restore the flora faster and far easier.  For more details on this product, read GB-3 on this website.

Other digestive aids such as betaine hydrochloride and pepsin, bromelain, papain, or fungally-derived digestive enzymes that are often labeled as protease, lipase, etc. do not work as well as the animal product discussed in the paragraph above.  The animal product is more yang, for one thing, and apparently much more physiological as well.  This means it better approximates the normal digestive enzymes in the body.

A major reason why GB-3 or an equivalent product works well and is essential to take is that most people who are not feeling their best do not produce enough high quality bile.  This is one of the major causes for their intestinal dysbiosis.  Until the bile is restored, changing the flora is difficult, if not impossible.  So be sure to include this product with each meal, and even with each snack for a while until the liver begins to produce more bile.


Replacing stomach acid with betaine hydrocloride and pepsin.  Some doctors also recommend taking extra betaine hydrochloride and pepsin to replace stomach acid that is low in most people.  This supplement is fine as an extra supplement, but it is more yin and somewhat irritating.  We find that GB-3 is much better and usually sufficient.




Many doctors recommend the use of supplements called probiotics.  These are capsules, tablets or liquids containing high concentrations of the friendly or healthy yeasts that our bodies require such as lactobacillus acidophilus and others.  Many are available in health food stores.

Which is best?  I recommend one called Bio-K original formula.  It is widely available in health food stores, and works well. One takes about ½ to 1 teaspoon about 20 minutes before each meal.  A container lasts about a week or less and is very inexpensive.  One usually need not continue it, although it is fine to take more if needed.

An interesting probiotic is called Lactobacillus Plantarum.  This unusual organism is the only one I know of that digests both sugars and proteins in the intestines.  As such, it is extremely powerful.  I do not believe it is a normal flora of the human intestine, but it can help clean out hundreds of parasitic and harmful organisms, according to its manufacturer.

Many other probiotic products in the store may work, although some are simply not powerful enough.  Probiotics must be refrigerated in most cases or they lose their potency very quickly, so always look for them in the refrigerated case of the health food store.

Eating live-culture yogurt can often provide plenty of probiotics.  This is the simplest way to get them.  Be sure the label states that it is live culture yogurt, as some companies pasteurize or kill the probiotic organisms after they have fermented the milk to make yogurt.  Unfortunately, some products are much better than others, and it is not easy to tell which are best.

Prebiotics are substances that nourish the healthy organisms found in probiotic supplements and in our bodies.  The most well-known is called inulin.  It is a slightly sweet soluble fiber.  However, there are problems with inulin as some people are sensitive to it.  I do not think prebiotics are needed if one eats correctly.

When to take a probiotic?  I find that probiotic products are usually not needed if one follows the diet above and takes GB-3 with each meal.  I have a lot of experience in this area, and this is our experience.  Probiotics can add a lot of cost to a nutrition program, and will not work well if the diet is not correct, as there is just too much debris and toxins for the incorrect flora to feed upon.

Taking a probiotic or live-culture yogurt may be needed, however, in the following situations:


·           If one is not eating correctly.  If the diet is incorrect, the food may contain items such as sugars or too much starch that feeds the incorrect organisms and prevents healthful organisms from remaining in the intestines.

·           If one’s health is very poor for some reason such as an illness.

·           After taking antibiotics, or even some other drugs such as antiparasitic drugs that damage the intestinal flora. Natural products such as colloidal silver seem to do much less damage to the body’s intestinal flora, but they can alter it as well. In these cases, a probiotic is also helpful.

·           Perhaps after a severe emotional upset.


  Other important suggestions to heal the intestines and rebuild the natural flora.  These include reducing or eliminating all medical and over-the-counter drug use as much as possible.  Also, eat some live-culture plain yogurt at least once a week.  Also, improve your eating habits and living habits.


What about doing coffee enemas when one is improving the digestion and intestinal flora?  I have a lot of experience with coffee enemas, as we recommend them to everyone – at least 40,000 people so far.  Coffee enemas should not interfere with the intestinal flora, and they can significantly speed up the healing of the intestinal tract by helping to remove parasites in the colon and stimulating bile flow from the liver. 

They also help remove toxic metals and toxic chemicals from the body and normalize liver and pancreas secretions that are very beneficial for digestion.  Colon hydrotherapy and coffee enemas, of course, can also assist with constipation and removing debris from the colon to assist the colon and the entire body to heal.




In some rare cases, the intestinal tract is so damaged and the flora so deranged that more work is needed, such as food allergy testing, stool or bowel contents examinations, colonoscopies and other tests.  However, I believe doctors, including most holistic doctors, take the wrong approach.  They often begin with food allergy tests and parasite tests instead of starting by correcting the diet and adding GB-3 or an equivalent product.  Their approach costs the patient hundreds of dollars and will not solve the flora imbalance if the diet and one’s general health is not addressed first.  However, in fairness, food allergy testing can sometimes reveal which foods are doing the most damage and removing them reduces stress on the intestines.  Later, when the intestine heals, most of them can be reintroduced.


A word about food allergy testing.  At times, one or another food is really causing difficulty.  The least expensive way to proceed in this case is called an elimination diet.  One begins by eating a simple diet of perhaps turkey and cooked vegetables that do not seem to cause a problem.  Then one gently introduces other foods, a small amount of one at a time, and notes if there seems to be a problem with them.  This method is often very accurate if one is sensitive enough to feel the effects of the food on a damaged intestine.  However, it is a slow method of testing and sometimes unclear in the results.  It is easy, however, and can be done at home with no cost.

    Another simple home food allergy testing method is called the Coca Pulse Test.  Arthur F. Coca, MD, a renowned allergist, noted that upon eating a food to which one is sensitive, the pulse generally increases several beats per minute.  The exact mechanism is not clear, but the reaction is most likely a sympathetic nervous system response to the allergic food.  The test is easy to do at home with no special apparatus needed.  It is not 100% foolproof.  However, in my experience, no food allergy testing system is foolproof.  This test may not be valid if you are taking a drug that controls your heart rate, such as a calcium-channel blocker or a beta-blocker.  Also, do not do this test immediately after exercising or if you are very stressed for any reason.  Here is the procedure:


·           Sit down calmly and take a few deep breaths to help you relax.

·           When you feel relaxed, establish your baseline pulse by counting your heart beat for at least a full minute or two.  Preferably record your resting pulse rate on a piece of paper.

·           Put a sample of one food item or one food supplement in your mouth, on your tongue.  You may chew it if desired, but refrain from swallowing it.  You need to taste it for approximately one-half minute.  Test only one food ingredient at a time.  For example, testing just chicken is much better than testing a chicken enchilada.

·           Retake your pulse while the food or the supplement remains in your mouth.  An increase of 4 or more beats per minute is considered the result of a stressful reaction to the food.  For 0 Blood Type people, an increase of 3 beats or more is considered a positive reaction.  The greater the stress response of your body, the higher the heart rate will tend to be.

·           After taking your pulse, discard the tested food.  Do not swallow it.

·           If you wish to test another food, rinse out your mouth with purified water and be sure you are relaxed.  Also, before repeating the procedure with another food or supplement, be sure your resting pulse has returned to the baseline level.  You may have to wait 2-5 minutes for your pulse to return to its resting level.


Other methods of testing for food allergies.  These include blood tests, skin tests, and the use of machines such as the Vega and Dermatron.  All have some merit, but all of them, in my experience, are not 100% accurate.  In particular, if you eat a food regularly, the test may indicate sensitivity to that food.


            Stool tests, and bowel contents exams.  These are medical tests that are rarely needed, in my view, if one improves the diet drastically and takes GB-3 and perhaps live culture yogurt on a regular basis.  They may be needed if one is suffering from an acute diarrhea, for example, that is not responding to more conservative measures.  However, in these cases a trial with colloidal silver, garlic juice and a proper diet usually takes care of the problem.

Problems with stool tests. These tests are notoriously inaccurate as it is easy to miss seeing parasite eggs or ova in a random stool sample.  Quality laboratories require several samples and analyze them carefully, but this is rarely done and quite costly.  Electrical machines such as the Dermatron, Computron and many others may be more accurate to assess parasites, but the results are often highly dependent upon the skill of the operator, so one must beware of this problem with electronic machines.


If one identifies a particular bacteria of parasite.  Some books can recommend particular remedies for specific parasites and bacterial or viral infections of the intestines.  I would always begin with natural methods discussed above, rather than use drugs to correct intestinal problems.  I have not encountered instances where anti-parasitic or anti-bacterial drugs were needed, although they might be best in a few cases.  They are often quite toxic, and that is my objection to them.

Most medical doctors do not worry about this, preferring to just kill the pathogens first.  However, there is no reason to do collateral damage if it is not necessary.  Drug residues often remain in the body for years, we find, and damage the liver and kidneys in subtle ways that impair one’s overall health.