How to restore intestinal flora, and what happens if you don't?
If you see a thirty something man with gray hair, or a forty year old woman with balding head, or a fifty year old stroke victim in a coffin, or a sixty-five year old grandpa with shaking hands, or a seventy year old grandma with dementia — look no further than inside their compromised guts.
You see, besides making passable stools, gut bacteria also synthesize vitamins B-7 (biotin), B-12, and K. The deficiency of these essential vitamins contributes to diabetes, obesity, hair loss, gray hair, eczema, seborrhea, anemia, internal bleedings, ulcers, strokes, cancers, degenerative disorders such as Parkinson and Alzheimer disease, and common gastrointestinal, respiratory, and autoimmune disorders.
Healthy intestinal flora is also vital for prevention of constipation, for maintaining your primary immunity (phagocytosis), for shielding your large intestine from colon cancer, and for averting yeast infection inside your mouth or vagina.
After bacteria inside the gut are killed by antibiotics, laxatives, heavy metals, surgeries, and colonoscopies, fiber is broadly recommended to replace bacteria and form stools, otherwise they turn into grayish rock-hard pebbles, and turn a routine trip to the bathroom into a torture. This condition is called dysbacteriosis or dysbiosis.
Unlike live bacteria, the dead cells of plants — which is what fiber is — can't perform bacterial functions, essential for humans. The loss of these functions contributes to impaired immunity, diabetes, obesity, hair loss, eczema, seborrhea, anemia, internal bleedings, ulcers, strokes, cancers, and common gastrointestinal, respiratory, and autoimmune disorders.
Despite all of these well known and thoroughly studied facts, the American medical establishment adamantly refuses to recognize the role of intestinal flora in health and longevity, and does everything possible to obliterate bacteria, starting at birth. Then, it profits enormously from treating the resulting diseases.
I found your website 3 years ago because of constant constipation even when eating vegetables, fruit etc., and was scheduled for my second colonoscopy. After reading all your information I have been taking probiotics with every meal and am amazed at the ease of passing bowel movements... and EVERY DAY! Thank You for the website!" E.-J., Canada (via e-mail)
I can't fathom the half genocidal, half suicidal, and 100% negligent attitude because it's an open secret among medical professionals that dysbacteriosis harms patients, particularly children and seniors, who are the most vulnerable. Children — because of their dysbacteriosis-related diarrhea and underdeveloped immunity. Seniors — because of practically all age-related diseases, impaired immunity, and antibiotic resistance. That's the genocidal aspect of this travesty.
And, yes, dysbacteriosis harms doctors, nutritionists, dietitians, pharmacists, and microbiologists just as ruthlessly. In fact, it harms more medical professionals and their family members than the general public, because they are more likely to use fiber and antibiotics for themselves and their families, indiscriminately. That's the suicidal aspect of this unfathomable “fiasco of judgment” and, perversely, poetic justice.
The perils of dysbacteriosis are well known to anyone who has ever seen Activia's ads, or visited a health food store, or perused the Internet's health sites, or attended medical school. Ignoring the role of dysbacteriosis in health and/or death is the negligence aspect of this story — the mainstream American doctors don't look for it, don't diagnose it, and don't treat it.
There isn't, for example, a single reference in The Merck Manual of Diagnosis and Therapy either about “dysbacteriosis” or “dysbiosis.” And there is only a single reference to the term “microbiota” -- an umbrealla medical term for intestinal bacteria. It is used only once in relationship to the “Clostridium difficile Induced Diarrhea” article 
This isn't surprising — the negligent attitude towards this condition encourages the indiscriminate use of antibiotics and fiber from the cradle to the grave.
Fiber, in essence, was embraced and promoted by Big Pharma as a cheap and expedient antidote to expensive and overprescribed antibiotics. Since Merck and its brethren can't sell “bugs” with an enormous profit reserved for patented drugs, why bother ruining an enormously profitable antibiotics franchise?
The disregard of dysbacteriosis has also been fueling an epidemic of colorectal disorders of immense proportion for some time, including colorectal cancers. It is also behind the proliferation of deadly antibiotic-resistant bacteria (superbugs), and dysbacteriosis-related complications, that are propelling the costs of health care into the stratosphere, increasing mortality, and lowering life-expectancy.
All along, those who are empowered to force change — from the Surgeon General of the United States to the National Institutes of Health, from the Centers for Disease Control and Prevention to the American Gastroenterological Association — keep 'mum' even though intestinal flora, just like the blood, is considered a fully-fledged organ in its own right, and that much is taught in medical schools everywhere: 
How can it be — intestinal bacteria are an essential part of human biology, but dysbacteriosis isn't recognized? This is very much like saying that there are no toothless people in the United States because all people without teeth wear dentures.
This tragic farce reminds me of the not-so-distant practice of bloodletting (phlebotomy) to alleviate a high fever. Countless millions of people, George Washington among them, had died from this barbaric 'treatment' because there was a universal belief among doctors that the body can easily replace lost blood. Come the 21st century, they still believe that fiber from dead plants can replace 400 species of once live bacteria.
Well, anything that kills bad bacteria also kills good bacteria, which are identical single-cell living organisms, albeit better behaving. Here‘s just a brief list of the most egregious villains. You will not find any particular recommendations here, because they‘re self-evident: don‘t use fiber, avoid antibiotics, remove amalgam fillings, use natural soaps, etc. Here we go:
Protein deficiency. The intestinal flora derives its energy and plastic nutrients not from food, but from mucin, which is secreted by healthy mucous membranes. Mucin is a glycoprotein—a molecule that bonds glucose with amino acids. Gastric and intestinal mucus is formed by combining mucin and water. Mucus protects the lining of the stomach and intestines from mechanical damage, enzymes, gastric acid, astringent bile, and food-born pathogens. The deficiency of the essential amino acid threonine, for example, curbs the body‘s ability to produce mucin, and, correspondingly, the bacteria‘s ability to function and procreate.
Excess dietary fiber. (Yes, you‘re reading it right.) The by-products of fiber‘s bacterial fermentation (short chain fatty acids, ethanol, and lactic acid) destroy bacteria for the same reason acids and alcohols are routinely used to sterilize surgical instruments—they burst bacterial membranes on contact. And that‘s how fiber addiction develops: as the fermentation destroys bacteria, you need more and more fiber to form stools. If you suddenly drop all fiber, and no longer have many bacteria left, constipation sets in as soon as the large intestine clears itself of the remaining bulk.
For some reason this point is causing intense consternation and controversy among the “experts” on all things fiber. If you are one too, and believe that I am stretching the facts to fit my point of view, please note the following:
(1) The operative phenomenon here isn't that “fiber causes dysbacteriosis,” — but 'excess fiber' — as in “the fermentation of excess dietary fiber.”
(2) Let me remind you that wine in the vat left for too long turns into vinegar, all the bacteria die off, and the fermentation stops. Bacterial fermentation in the wine vat, dear opponents, and in the pile of feces happens to be exactly the same process.
(3) Finally, consider this corroborating quote: “Colonic bacteria ferment unabsorbed carbohydrates into CO2, methane, H2, and short-chain fatty acids (butyrate, propionate, acetate, and lactate). These fatty acids cause diarrhea. The gases cause abdominal distention and bloating.” (Malabsorption Syndromes; The Merck Manual of Diagnosis and Therapy.) Let the diarrhea run its course a day too long, and dysbacteriosis will soon follow. (God, I love those rare moments when Merck and I are singing the same tune.)
Intestinal acidity. Besides fermentation, excess acidity may occur when the pancreas fails to neutralize the stomach‘s content because of pancreatic disorders or an obstruction. In this instance, acidic digestive juices spill into the large intestine and destroy bacteria. Interestingly enough, the most likely cause of obstruction in an otherwise healthy person is the blockage of the pancreatic ducts by—you guessed it—too much indigestible fiber in the duodenum. Normal acidity (i.e. safe for bacteria) for stools is within the 6 to 7.2 pH range.
Diarrhea. Acute intestinal infection, food poisoning, laxatives, medical intervention, and other conditions may cause prolonged diarrhea, which will literally wash out all of the bacteria from your gut. An appendectomy (the removal of the appendix) also increases the risk of dysbacteriosis, because the appendix preserves the “starter” culture when diarrhea occurs.
Antibiotics and antibacterial medication (such as sulfanilamide, sulpha derivatives, Dynapen, Urex, Nydrazid, Macrodantin, Rifadin, and many others). Antibiotics and antibacterial drugs play an important, life-saving role in many circumstances. However, these drugs are widely and indiscriminately overprescribed to children and adults alike. One such prescription is often sufficient to wipe out the entire bacterial population of your gut.
Antibiotic residue in fowl, fish, livestock, and milk. Industrial farming necessitates the use of continuous, large doses of antibiotics to keep crowded, confined animals alive. Inevitably, some of these antibiotics transfer to the food supply, and affect humans.
Heavy metals. Mercury, lead, arsenic, cadmium, nickel, silver, and other metals are extremely toxic, even in trace amounts. The sources of contamination vary from industrial pollutants to household chemicals, batteries to electronic components, measuring devices, and other sources. Children are the most vulnerable.
Silverware. Silver is traditionally used for kitchen utensils, goblets, plates, and pitchers for its strong antibacterial properties. Silver flatware isn‘t such a good idea after all, especially for babies.
Mercury from dental amalgam. This pollutant is omnipresent in the United States. Amalgam fillings are placed indiscriminately into cavities, because amalgam is cheap and easy to work with. The American Dental Association insists that dental amalgam is safe, while the Occupational Safety Health Administration (OSHA) and Environmental Protection Agency (EPA) classify amalgam as a toxic and hazardous substance: “Another source of exposure to low levels of elemental mercury in the general population is elemental mercury released in the mouth from dental amalgam fillings” (Transportation, storage, and disposal of mercury is regulated by the Code of Federal Regulations, 29 CFR 1910.1000, and its willful violation is a criminal offense, except when mercury is “stored” in your mouth by a licensed dentist.) It isn‘t surprising that dentists in the United States have the highest rate of depression, suicide, and drug and alcohol addiction, and the lowest life expectancy among all medical professionals. This could likely be the result of long-term exposure to mercury, which, as already mentioned, is a potent poison, neurotoxin, and carcinogen; one that gradually destroys nervous systems, causes cancers, kills off friendly bacteria, and brings about... an addiction to fiber.
Artificial food coloring. Years ago, a color pigment called crystal violet (also known as crystal gentian) was widely used as a topical antiseptic. There are good reasons to believe that long-term exposure to artificial food coloring may affect intestinal bacteria in the same way crystal violet affected (killed) topical bacteria.
Medical treatments and environmental pollutants. Chemo- and radiotherapy kill bacteria for the same reason they kill cancerous cells. There are other factors that negatively affect the intestinal flora, such as industrial pollutants, household chemicals, antibacterial soaps, and toxic substances found in toothpaste, shampoo, and detergents.
Quackery. If stools aren‘t “clean,” then the colon must be “dirty.” This apparently logical inference is the base for “miracle cures” of constipation, migraine, halitosis, yeast infection, indigestion, and an endless array of other ills. While most of these conditions are indeed connected to the dysfunction of the large intestine, “cleaning” the colon isn‘t a solution, but a sure formula for creating even more problems by causing even more severe forms of dysbacteriosis.
As you can see, a lot of things, particularly the ones that make a bundle of money for someone without any scruples, have a greater than great potential for killing the bugs inside your gut, ruining your good looks, and dispatching you to the grave.
Advised by their veterinarians, farmers pay big bucks for bacterial supplements imported from Europe to keep their farm animals well and productive, because nobody will buy a bloated, underweight, sickly calf that‘s suffering from chronic diarrhea and digestive distress.
Well, dysbacteriosis in humans isn‘t any more difficult to spot than it is in livestock. Here are the telltale signs of this condition:
Absence of intestinal gases. When dietary fiber (soluble as well as insoluble) is present in the diet, intestinal gases are produced by bacterial metabolism. A complete absence of gases (in the presence of dietary fiber) suggests an absence of fermentation. Small amounts of soluble (digestible) fiber, such as fruit pectin, speed up the proliferation of intestinal flora, while avoiding excessive fermentation.
Undigested fiber in stool can be seen as white or dark specks. This is best determined by a stool exam performed by a medical lab (CDSA, or Comprehensive Digestive Stool Analysis). The same exam may superficially determine the symbiotic and pathogenic bacterial content and ratio, but only for a minor subset of hundreds of innate strains.
Constipation. Constipation is one of the most prominent signs, especially when the stools are dry or hard. This means there is too little bacteria to loosen up the formed feces and keep them moist, because, unlike other stool components, bacterial cells retain moisture.
Intermittent or chronic diarrhea, irritable bowel syndrome, ulcerative colitis, and Crohn‘s disease. As you‘ve read above, the introduction of desirable bacteria into the affected large intestine heals these conditions. So it‘s a no-brainer to assume that, along with fiber, dysbacteriosis plays a significant role in their pathogenesis.
Frequent respiratory infections, asthma, bronchitis, chronic rhinitis, post-nasal drip, nasal voice, sinus congestions, and allergies. These primarily chronic conditions indicate a weakened immune system because of dysbacteriosis. They usually appear after a routine respiratory infection that was treated with antibiotics, which in turn damage intestinal flora.
Blood-clotting problems. Hard-to-stop ordinary bleeding and easy bruising (ecchymoses)—dark, blotchy areas of hemorrhages under the skin—may indicate a deficiency of vitamin K, which is a by-product of bacterial metabolism. Before making this determination, rule out vitamin C deficiency (scurvy) and anticlotting medications such as aspirin, ibuprofen, naproxen (NSAIDs), warfarin, and others.
Neurological problems and anemia. Vitamin B12 is essential for the normal functioning of the nervous system and production of red blood cells. Since red meat and eggs were almost eliminated from the “healthy” Western diet until the Atkins-style diet came into vogue, the intestinal flora was the only remaining “natural” source of vitamin B12. Numbness and tingling of the hands and feet, paleness, shortness of breath, chronic fatigue, a sore mouth and tongue, and mental confusion are the most common symptoms of a vitamin B12 deficiency. At this stage, supplements are the only viable option to quickly treat and reverse these symptoms.
Keep in mind that any one of these signs may indicate other conditions. It‘s always best to consult a caring, competent physician and ask him or her to arrange for a comprehensive digestive stool analysis (CDSA) at a medical lab.
Eliminating dysbacteriosis literally means “infecting,” or, as a microbiologist might say, reinoculating your large intestine with synergistic bacterial strains. In practical terms, it means that you need to take a quality pre- and probiotics, such as Enterophilus, which I specifically developed for this purpose.
Supplemental probiotics are the most accessible, inexpensive, and easiest form of oral bacterial therapy. You can take these supplements continuously, periodically, or on an as-needed basis, relying on your observations of stools and other symptoms of dysbacteriosis as described here and in my books.
The Enterophilus is recommended for all dysbacteriosis-related conditions. These include chronic constipation, bloating, diarrhea, irritable bowel disease, diverticulosis, depressed immunity, chronic fatigue, anemia, infertility, amenorrhea, acne, hair loss, graying hair, premature aging, prediabetes, diabetes, neurological damage intestinal disorders, oral sores, asthma, acne, seborrhea, respiratory and urogenital infections, recurring vaginal and oral yeast infections, complications from infectious diseases, cancers, radio- and chemo- therapy, antibiotics and antiviral treatments, and after heavy metal poisoning—such as lead or mercury from amalgam fillings.
The Enterophilus is helpful while breastfeeding and during restrictive weight loss diets, such as the Atkins diet, because it prevents constipation, and eliminates the risk of undernutrition or malnutrition from damaging your eyes, hearing, skin, bones, teeth, hair, and nails.
The Enterophilus is particularly effective when you have a severe case of long-term dysbacteriosis because it contains a high quality prebiotic formula (GI Recovery) that I specifically developed to enhance the survival and effectiveness of probiotics once inside the gut.
Unlike practically all fiber-based prebiotics, GI Recovery contains L-Glutamine — an amino acid that stimulates the regeneration of intestinal mucosa that is actually “home” and source of nourishment for intestinal bacteria. Also, this approach doesn't cause gas or flatulence the way fiber-based probiotics do.
If you are suffering from chronic constipation, hemorrhoidal disease, incomplete emptying, then restoring anorectal sensitivity should be your next goal. Please continue reading the How to restore anorectal sensitivity page to learn how.
Frequently Asked Questions
American dentists are well aware of the amalgam fillings controversy. You aren't likely to find any such fillings in their own teeth, or in the teeth of their children and spouses. Many no longer use amalgams to avoid exposure.
If you have any “black” fillings, get them replaced with composite fillings. Do it for the same reasons you don‘t want mercury in your fish, or lead in your kitchen pipes, or arsenic in your drinking water.
If your dentist tries to talk you out of it — and he or she may for legal reasons — then ask another dentist to do it for cosmetic reasons. Dentists may lose their licenses for replacing a viable filling “without cause” because it's construed as profiteering and malpractice.
When you ask dentists to do the same procedure for cosmetic reasons, or to get rid of a metallic taste in your mouth, that's okay. Hence the charade. Health concerns aren't a good enough “cause” because state licensing boards play along with the ADA's position — amalgams represent zero risk.
If you work in the same office with a person who has amalgam fillings, your exposure to mercury vapors from a breathing person may be similar or higher than from a poorly collected spill from a broken mercury thermometer.
If you would like to learn more about this subject, Amalgam Illness, Diagnosis and Treatment by Dr. Andrew Hall Cutler provides comprehensive information on all issues related to dental amalgams. It's expensive, but worth it.
Let others know about this page! This link may save a life!
2 R.F. Schmidt, G. Thews. Colonic Motility. Human Physiology, 2nd edition. 29.7:733.
3 American Dental Association. “ADA continues to believe that amalgam is a valuable, viable and safe choice for dental patients and concurs with the findings of the U.S. Public Health Service that amalgam has ‘continuing value in maintaining oral health.’» ADA Statement on Dental Amalgam, Revised January 8, 2002; [link]