Chapter 4. Dysbacteriosis
“There are over 400 species of bacteria in the colon; bacteria make up 30–50% of the total dry matter in the feces, or even 75% according to other calculation.”
R.F. Schmidt, G. Thews; Human Physiology, 2nd edition
How do you debunk popular ideas about fiber’s role in digestion and elimination without being accused of committing a sacrilege, when it has already become a gold-standard treatment for “regularity,” a miracle laxative, and a concept so embedded in the minds of doctors and patients alike that it’s no longer even questioned by anyone?
Well, there are “sacred truths,” and then there are long-established, indisputable facts of human physiology:
- Breast milk has zero fiber, yet healthy babies produce abundant (relative to their weight and size) stools several times daily.
- People who fast for weeks at a time have regular stools, even though they consume nothing but water.
- Some people (the lucky ones) who attempted the Atkins Diet, had no problem with constipation, even though their diet contained zero or minor amounts of fiber.
- Indigenous Inuit (Eskimo) people, who inhabit the Arctic coast of North America, some parts of Greenland, and northern Siberia, consume a fiber-free diet, and aren’t affected by constipation.
None of the above makes any sense, conventionally speaking. People can’t have regular stools without consuming any fiber, right?
Wrong! The reason you’re stumped is simple: you’ve been conditioned to believe that normal stools are made mainly from food, and that fiber is required to make them. Inevitably, the next logical inference forms a familiar logic:
If Fiber Makes Good Stools,
Let’s Fix Bad Ones With More Fiber
It seems perfectly logical, right?
Wrong again! Actually, normal stools shouldn’t contain any remnants of undigested food. Dietary proteins, fats, carbohydrates, and even fiber must digest completely. If something you ate exits your body as is, it means it wasn’t digested or couldn’t get digested to begin with, such as denaturated protein (burnt meat). Technically, even indigestible fiber should be fermented by intestinal bacteria.
That’s why a stool exam that shows any visible remnants of undigested fats, proteins, or carbohydrates, or even specks of undigested fiber (any at all), points to impaired digestion, and one disease or another that affects the organ(s) responsible for digestion and the absorption of a specific nutrient. That much is written in any medical reference book, and the observation of stools is widely used as an effective diagnostic tool for disorders of digestion and the digestive organs.
So what, then, are stools made from, if not food and fiber? Primarily water, intestinal bacteria (single cell, free-living microorganisms), dead bacteria and cells shed by the body, mineral salts, coloring pigments, and traces of fat. Intestinal bacteria are by far the largest component of stools. Let’s repeat again the quotation that opens this chapter:
Human Physiology: There are over 400 species of bacteria in the colon; bacteria make up 30%–50% of the total dry matter in the feces, or even 75% according to other calculation.
Besides other important tasks, these abundant bacteria make normal stools, unless they are completely or partially decimated by the vestiges of civilized living, or even—harder to believe—by dietary fiber.
Bacterial functions : Welcomed everywhere but in the West
When babies are born, their digestive organs are sterile. Their large intestines get “cultured” after the first few sips of colostrum, a thin yellowish fluid “infested” with the mother’s bacteria and rich in essential nutrients. Colostrum precedes the flow of fat- and protein-rich breast milk. The process continues with breast milk, and the intestinal flora of newborns matures to “adult” status by the sixth month.
Placing newborns on formula without first letting them taste colostrum and breast milk is a serious mistake. It may hound young parents for years to come as they grapple with their offspring’s food allergies, diarrhea, constipation, and poor general health. But for many breastfed babies, even the breast milk may lack essential bacteria because of their mothers’ prior exposure to environmental pollutants, antibiotics, and mercury in dental amalgams. That’s why nowadays, many newborns develop gastrointestinal and autoimmune disorders as often as their formula-fed brethrens: their mothers suffer from acute dysbacteriosis, a change of composition and/or volume of normal intestinal flora.
The presence of bacteria in dairy milk—good ones from the inside of the cow, bad ones from a dirty udder, contaminated hands, or unsanitary utensils—explains why, by law, raw milk must be pasteurized. This is true not so much to prevent human infections (humans drank raw milk for ages), but to prevent spoilage from bacterial fermentation.
Before the statutory pasteurization of dairy milk, lactose intolerance to milk protein wasn’t as big an issue as it’s become today, because milk’s innate bacteria would assist in fermenting lactose and breaking down protein while the milk was still in the stomach or upper intestine—a process similar to yogurt-making. That’s why fermented dairy products, such as yogurt, buttermilk, kefir, and others don’t cause lactose intolerance or allergies as much (or at all) as regular pasteurized milk does.
In special circumstances, such as allergies, malnutrition, impaired immunity, severe burns, and others, doctors may prescribe a donor’s breast milk to babies or even adults. Unfortunately, human donor milk also must be pasteurized, and is useless for its primary functions: proper digestion thanks to the innate flora, and restoration of intestinal flora.
Intestinal flora—the sum of all indigenous bacteria that reside inside the intestinal tract (the host)—is considered an organ in itself, just like the liver or bone marrow, because the bacteria perform a range of essential, health-critical functions that can’t be reliably duplicated by any other means. Researchers determined those functions by comparing sterile lab animals (without any intestinal flora) with control animals that had normal flora. All of these findings have been confirmed in people as well. Here’s a brief listing of the intestinal flora’s most important functions:
- Water retention in stools. Single cell organisms, such as bacteria, contain mostly water, encircled by impenetrable membranes. In large quantities, they provide normal stools with its amorphous qualities. That’s why dry stools reliably point to dysbacteriosis.
- Formation of normal stools. Since bacteria represent the most dominant component of normal stools, their absence may cause persistent chronic diarrhea.
- Manufacturing of essential vitamins. Bacteria synthesize a whole range of substances, including certain B-complex vitamins, vitamin B12, and vitamin K, which is essential for proper blood coagulation.
- Protecting intestinal epithelium (mucosa) from pathogens. Normal intestinal flora controls the population of undesirable bacteria, such as Candida albicans (yeast) or the infective strains of E. coli. The mechanisms of protection are numerous—competition for food supply, adhesion to intestinal mucosa, maintenance of desired pH balance, and production of peroxides and enzymes, which kill foreign bacteria.
- Tissue development and regeneration. The intestinal mucosal membrane (epithelium) and lymphatic tissues (Peyer’s patches) of sterilized lab animals are poorly developed vis-à-vis healthy animals. The shortcomings of weak mucosal membrane for intestinal health and underdeveloped lymphatic tissues for immunity are self-evident.
- Immunity. Normal intestinal bacteria are responsible for enabling phagocytosis—the body-wide destruction of pathogenic bacteria, viruses, allergens, and other foreign objects by phagocytes, which are specialized blood cells responsible for non-specific (before antibodies) immune system defenses.
Besides the obvious conditions (constipation, diarrhea, and disorders related to B- and K-vitamin deficiencies) other common conditions that have been associated with dysbacteriosis are irritable bowel syndrome, ulcerative colitis, Crohn’s disease, fatigue, diabetes, colon and breast cancers, acne, eczema, psoriasis, asthma, allergies, joint diseases (rheumatoid arthritis, gout, osteoarthritis), and others.
Despite all this, dysbacteriosis (a.k.a. dysbiosis)—literally, a sterile gut—isn’t recognized by mainstream Western medicine as a disorder, even though it’s a bona fide medical condition in the rest of the world, particularly in Eastern Europe.
You won’t find a single reference to this condition on the Web sites of either The American Gastroenterological Association or The American Medical Association, while in fact the 1908 Nobel Prize in Medicine was awarded to Paul Ehrlich (Goettingen University, Goettingen, Germany) and Ilya Mechnikov (Institute Pasteur, Paris, France) “in recognition of their work on immunity,” specifically the discovery of phagocytosis.
The Merck Manual of Diagnosis and Therapy indirectly acknowledges the “possibility” of dysbacteriosis (but not the condition) while discussing antibiotic-associated colitis, a condition that occurs when “various antibiotics may alter the balance of normal colonic flora and allow overgrowth of C. difficile, an anaerobic gram-positive bacillus.” Much to the Merck’s credit, it states “...lactobacillus or rectally instilled bacteroides may be required in patients who have multiple relapses”; doctor-speak for the restoration of intestinal flora with oral supplements or enemas, a subject discussed in Chapter 11, Avoiding the Perils of Transition.
When I was growing up in the late nineteen-fifties, pediatric clinics in Ukraine routinely dispensed specially prepared “Acidophilus milk” for children affected by diarrhea, constipation, or any other digestive disorder. It was a fermented dairy drink made daily from cow’s raw milk, specifically inoculated with live bacterial cultures essential for intestinal health. Today, you can find somewhat similar (sans raw milk) “live” preparations in food health stores, but not in pharmacies, which dispense antibiotics.
Besides the GI tract functions, non-pathogenic bacteria maintain a healthy bioecology of the epithelium, the upper layer of skin and mucosa.Indigenous bacteria prevent colonization by pathogens of the entire skin surface, the epithelium of eyes (conjunctiva), nose, oral cavity, pharynx, urethra, penis, and vagina.
Antibacterial drugs, soaps, shampoos, creams, gargles, and vaginal douches destroy normal flora, and cause a rapid proliferation of pathogens, expressed in conditions such as conjunctivitis, cellulitis (a bacterial skin infection, not to be confused with cellulite), seborrhea, acne, sinusitis, mouth sores, gingivitis, periodontal disease, vaginal yeast infection, chronic inflammation of urethra and bladder, and many others.
Restoring normal flora becomes exceedingly difficult, if not impossible, if a person becomes dependent on antibacterial means of infectious control. That’s why anything with the words “antibacterial” on it should be avoided like the plague, unless specifically prescribed by a physician for a confirmed life-threatening infectious disease.
Common causes of dysbacteriosis
What causes dysbacteriosis? 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. 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, 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.
- Intestinal acidity. Besides fermentation, excess acidity may occur when the pancreas fails to neutralize the stomach’s content because of pancreatic disorders or 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.
Then there are things most city dwellers don’t do that may cause harm. In the past several years, popular media and medical journals widely reported that children who attend day care, live on farms, or grow up cuddling pets or livestock don’t suffer from asthma or other respiratory disease as often as children who don’t.
What’s going on in the kindergartens and on the farms that makes these kids cold- and asthma-resistant? Well, they sneeze at each other, don’t wash their hands as often, play with domesticated animals, and eat unwashed produce from manured land, so their little guts “stay current” and their immune systems are continuously challenged. It’s a self-vaccination, of a kind.
This phenomenon is called the “hygiene theory,” though it should probably be called the “dirt theory.” Enlightened English pediatricians are now advising the parents of sickly city kids to take them to play in the sand boxes. If you don’t yet know this, sand boxes happen to be the favorite outhouse for neighboring cats. For similar reasons, toddlers, puppies, and even adult dogs, unburdened by a leash and social mores, eat feces (coprophagia), an instinctive survival trait in action.
This book doesn’t condone eating feces at any age—it’s gross, dangerous because of stool-born pathogens, worms, and toxoplasmosis, and ineffective because bacteria can’t survive the strong acidity of the human stomach. The proper way of inoculating the large intestine with fecal flora is called fecal bacteriotherapy. It’s been employed for ages by natural practitioners of Eastern medicine to ward off diarrhea and constipation. Even some allopathic (mainstream) doctors, although not in the United States, aren’t too squeamish about it, because it effectively cures otherwise incurable ulcerative colitis.
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 who’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 specs. 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 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 damaged 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.
As you can see, when the bacteria are suffering, everything else suffers too: your immune system doesn’t protect you as well as it used to, your blood doesn’t coagulate, your stool lacks moisture, and your colon gets irritable and inflamed from a multitude of factors. Once the bacteria are gone, something must take their place and restore some of their functions. That’s how and why dietary fiber entered the picture:
- First, to stimulate the growth of intestinal flora by feeding remaining bacteria with abundant fiber. It kind of works initially, but it’s a bad idea, really, because the excess acidity from fermenting too much fiber kills off an already dwindling population of hard-working microbes.
- Secondly, fiber was introduced to bulk up stools after the bacteria were completely demolished, and when constipation or diarrhea set in. The result of this action, unfortunately, is even worse than the remedy—irritable bowel syndrome, diarrhea, inflammation, and reduced immunity (all outcomes of dysbacteriosis-related diarrhea or constipation).
- Finally, as colorectal disorders, caused by coarse, bulky stools, grow worse, a person requires more and more fiber to “plunge” out ever-larger stools.
Naturally, the enlightened way to prevent and treat dysbacteriosis isn’t with fiber, more fiber, and even more fiber, but with... intestinal bacteria. This concept is discussed in Chapter 11, Avoiding the Perils of Transition (see page 211). Why such a simple, elegant, practical, inexpensive, and foolproof idea escaped Western medicine still escapes me.
- Normal intestinal flora is comprised from hundreds of varieties of bacteria, which are specific to the human body. Humans obtain indigenous bacteria from mother’s milk.
- Children who do not receive breast milk are likely to develop digestive and immune disorders related to the absence of beneficial flora.
- Intestinal flora is essential for the normal functioning of the human body. Despite its role, function, and importance, its utility isn’t fully recognized by Western medicine.
- The deficiency or absence of intestinal flora is called dysbacteriosis. This bona fide medical condition isn’t recognized by Western allopathic medicine either, even though its ill effects (antibiotic-associated colitis) are well known.
- Indiscriminate use of antibiotics in medicine and agriculture is one of the major causes of dysbacteriosis. The restoration of intestinal flora should always follow a treatment with antibiotics.
- Digestive disorders of the upper GI tract can damage intestinal flora by allowing reactive substances such as hydrochloric acid, bile, digestive enzymes, alcohols, and fatty acids into the large intestine.
- The fermentation of dietary fiber may damage intestinal flora by producing excessive acidity and alcohol.
- Intestinal flora is vulnerable to environmental, household, and medicinal agents, which have a pronounced antibacterial effect.
- Intestinal flora comprises the largest organic part of stools. The absence or deficiency of intestinal flora causes a reduction in stools and constipation.
- Instead of restoring intestinal flora, Western medicine relies on its replacement with fiber to alleviate constipation, because undigested fiber increases the volume of stools.
- Treatment of constipation related to dysbacteriosis was the primary rationale for the relatively recent (first part of the nineteenth century) and purposeful introduction of fiber (“bulk,” “roughage”) into the human diet.
- The decimation of intestinal flora exposes the internal organs to colonization with undesirable bacteria, weakens the immune system, and causes a shortage of essential vitamins.
- People who live in natural habitats do not experience dysbacteriosis because they aren’t exposed to factors that can damage intestinal flora. Certain intrinsic factors of natural living (“hygiene theory,” untreated water and raw dairy products) help enhance the natural flora’s viability.
- Diarrhea, constipation, infectious diseases, severe colorectal disorders, and vitamin deficiencies are the primary symptoms of dysbacteriosis.
- Dysbacteriosis and resulting diseases can be effectively treated with the restoration of intestinal flora and with dietary supplements. (See Chapter 11, Avoiding the Perils of Transition.)
1R.F. Schmidt, G. Thews. Colonic Motility. Human Physiology, 2nd edition. 29.7:733.
5American 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]
7Thomas M. Ball, M.D., M.P.H, et al. Siblings, Day-Care Attendance, and the Risk of Asthma and Wheezing during Childhood, New England Journal of Medicine, 2000 Aug;343:538–543.
8 Borody TJ, Warren EF, Leis S, Surace R, Ashman O.; Treatment of ulcerative colitis using fecal bacteriotherapy; Journal of Clinical Gastroenterology. 2003 Jul;37(1):42–7. PMID: 12811208.