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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:

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.[1]

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:

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,[2] while in fact the 1908 Nobel Prize in Medicine[3] 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 whenvarious antibiotics may alter the balance of normal colonic flora and allow overgrowth of C. difficile, an anaerobic gram-positive bacillus.”[4] 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:

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,[7] 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.[8]

Symptoms of dysbacteriosis

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:

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:

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.

Chapter summary


1R.F. Schmidt, G. Thews. Colonic Motility. Human Physiology, 2nd edition. 29.7:733.

2Search on keywords “dysbacteriosis” and “dysbiosis”: [link],[link], on 6/19/2004.

3The Nobel Prize in Physiology or Medicine 1908. Nobel e-Museum. [link]

4Antibiotic-Associated Colitis; 3:29; The Merck Manual Of Diagnosis and Therapy; [link]

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]

6Mercury Compounds. U.S. Environmental Protection Agency. [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.