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How to Achieve and Maintain a Healthy Gut Microbiome

Updated January 28, 2022

This article originally appeared in the August 2005 McDougall Newsletter.

By John McDougall, MD

My guess is the welfare of the bacteria living in our colons was not a topic for discussion at your last social gathering – but that may change. Within our intestines live trillions of organisms that are so important to our health and survival that they should be thought of as a vital organ – just like our livers or kidneys. The gut microflora is the name we give to this living factory, whose beneficial functions include: completing the digestion of our foods through fermentation, protecting us against disease-causing microbes, synthesizing water-soluble vitamins, and stimulating development and function of our immune systems.1 

Most people think of bacteria as dangerous and dirty.  In truth, the vast majority of organisms living in this microscopic world are helpful, or at least not harmful, to our lives. Our intestinal tracts contain a complex and diverse society of disease-causing (pathogenic) and “friendly” bacteria.  Rule number one is simple: dominance by the “good guys” will crowd out and leave no room in our intestines for the harmful ones. In addition to digesting remnants of our meals and synthesizing vitamins, the helpful bacteria play an important role in the development of the immune system by maintaining a constant dialog with our internal bodies through the surface of the gut. Our microflora also influences many of our hormones. The health consequences from an imbalance of our sex hormones can lead to precocious puberty, fibrocystic breast disease, PMS, uterine fibroids, prostate enlargement, and breast, uterine, and prostate cancer. When our bowel bacteria really get out of control severe forms of colitis and colon cancer can be the consequences.

The Microbial Factory

Bacteria are not distributed randomly throughout the intestinal tract, but are found in different numbers and kinds in different regions of the gut. The mouth provides a fertile garden for millions of bacteria; but the stomach, because of the acid, and small intestine contain very low numbers. The final five feet of the intestine, known as the large intestine or colon, works as a microbial factory with more than 500 different species of bacteria living in a 3 pound (1.5 Kg) mass of partially digested matter. Within the colon the concentration of bacteria reaches 1,000,000,000,000 (one trillion) organisms per gram (1/30th of an ounce) of feces. Bacteria make up about 60% of the weight of the feces. The microflora are so important to our well-being that after a person’s colon is surgically removed (colectomy), the last part of the small intestine (ilium) takes over this vital role and becomes colonized with a similar biomass of bacteria.2

The health of the flora can become impaired by temperature, illnesses, antibiotics and other drug treatments, and changes in our diets. The effects of antibiotic therapy can be profound and persistent, even causing a life-threatening infection with overgrowth of pathogenic bacteria (called Clostridium difficile).

Benefits of a Healthy Gut Microflora

  • Increase the natural resistance to infections from bacteria, yeast, and viruses
  • Prevent traveler’s diarrhea
  • Speed healing from diarrheal diseases and relapsing colitis
  • Improve digestion
  • Relieve constipation
  • Stimulate the immune system
  • Lessen symptoms of inflammatory arthritis
  • Suppress cancer development and growth
  • Reduce sex hormones
  • Reduce cholesterol and triglycerides

Colonization Begins with the Newborn

Before birth the gastrointestinal tract of a normal fetus is sterile. During the birth process the newborn is inoculated, by passage through the birth canal, with organisms from the mother’s vagina and bowel.3 Benefits to the infant begin immediately with this natural defense barrier of “friendly” bacteria standing against harmful microbes that will enter later on with touching, suckling, kissing, and caressing. The importance of this early invasion should not be underestimated. This initial invasion makes a permanent impression on our immune systems, thereby affecting a person’s well-being throughout his or her life. Newborns delivered by cesarean section do not get a healthy dose of mother’s bacteria. Born through the abdomen, much of their initial bacteria come from the unhygienic environment of a hospital. However, this setback can be remedied by the initiation of proper infant feeding after birth – and helped by the addition of infant probiotics (see below).

Breast feeding encourages the growth of “friendly” bacteria known as Bifidobacterium. These vital organisms protect the baby from gastrointestinal infections that can result in illnesses severe enough to require hospitalization, and sometimes cause death. Mother’s milk contains sugars (galacto-oligosaccharides) which encourage the growth of these friendly bacteria. By the fourth day of life, Bifidobacterium represent 48% of the bacteria in breast-fed infants as opposed to 15% in bottle-fed infants.4 Eventually, over 95% of the bacteria become Bifidobacterium bacteria in an exclusively breast-fed baby. Introduction of small amounts of formula to a breast-fed baby will result in shifts from a breast-fed to a formula-fed pattern of the microflora. After weaning from breast milk – ideally after the age of 2 years – the child’s flora become similar to an adult’s.

Change the Diet – Change the Microflora

The partially digested remnants of our meals, after arrival in our large intestines, become the foods for our microflora. Each species of bacteria survives best on specific kinds of nutrients. In short, “friendly” bacteria prefer to dine on plant-food remnants, and pathogens thrive when the diet is low in plant foods and high in meat and other “junk-food.” Therefore, what we choose to eat determines the predominance of the bacteria species that will live in our gut. By changing from a diet based on animal- and highly processed-foods to whole plant-foods, you can suppress the growth of harmful bacteria and stimulate those that are beneficial.  Major alterations in the microflora take place within one to two weeks of changing a person’s diet.5

Bacteria enjoy the parts of the plant foods that we don’t use. Undigestible complex carbohydrates, known as dietary fiber, and other smaller undigestible sugars, called oligosaccharides, provide the bulk of the food for our bowel bacteria. Only plants contain these complex and simple carbohydrates (except for milk as above). The undigestible simple sugars are abundant in artichokes, onions, chicory, garlic, leeks, and to a lesser extent, cereals. Beans, peas, and lentils contain the oligosaccharides, raffinose and stachyose, that feed our bowel bacteria and, quite noticeably, form the infamous flatus. Purified wood cellulose, which has been used to manufacture some “high-fiber breads,” is not broken down by the microflora. Because only plants contain these microflora-nourishing sugars, strict vegetarians (vegans) have been found to harbor much higher counts of “friendly” bacteria than do meat eaters.6,7

Manipulating Our Microflora with Probiotic Supplements

Purposefully adding particular species of bacteria has the potential of rebalancing the intestines and thereby improving a person’s health. Probiotics are used for this purpose and are sold as foods and pills (supplements) that contain millions of friendly bacteria, and sometimes yeast. Probiotics can be purchased in natural food stores – they are usually found in the refrigerated section; some are labeled as “newborn formulas” and others are sold for improving the flora of a child or adult. Probiotics have no toxic effects. Scientific research has discovered specific species of bacteria must be used in order to achieve specific benefits when treating health problems.

Conditions Helped by Specific Probiotics8-14
Used as single agents or in combinations
Dental Caries Lactobacillus rhamnosus (GG)
H. Pylori (stomach ulcer) Lactobacillus johnsonii, Lactobacillus paracasei
Acute and Chronic Diarrhea Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus reuteri, Lactobacillus rhamnosus (GG), Bifidobacteria bifidum
Irritable Bowel Syndrome Lactobacillus acidophilus, Lactobacillus plantarum
Lactose Intolerance Lactobacillus acidophilus, Lactobacillus bulgaricus, Bifidobacteria longum
Constipation Lactobacillus casei, Lactobacillus reuteri, Lactobacillus rhamnosus (GG), Bifidobacteria animals, Saccharomyces cerevisiae (yeast)Propionibacterium freudenreichii
Crohn’s Disease Lactobacillus rhamnosus (GG)Saccharomyces boulardii, Escherichia coli, Nissle strain (1917)
Ulcerative Colitis Escherichia coli, Nissle strain (1917), BIFICO (3 Bifidobacteria species), Saccharomyces boulardii, VLS 3 brand (Lactobacillus and Bifidobacteria)
Diverticular Disease of Colon Escherichia coli, Nissle strain (1917)
Vaginal Candida Lactobacillus acidophilus, Lactobacillus rhamnosus (GG), Lactobacillus fermentum
Elevated Cholesterol Lactobacillus acidophilus, Lactobacillus bulgaricus, Lactobacillus plantarum, Streptococcus thermophilus, Enterococcus faecium
Elevated Blood Sugar (Diabetes) Saccharomyces cerevisiae (yeast)
Rheumatoid Arthritis Lactobacillus rhamnosus (GG)
Eczema (atopic dermatis) Bifidobacteria lactis, Streptococcus thermophilus, Lactobacillus rhamnosus (GG)
Premenstrual Syndrome Saccharomyces cerevisiae (yeast)
General Immunity Lactobacillus plantarum, Lactobacillus johnsonii, Lactobacillus rhamnosus, Bifidobacteria lactis, Bifidobacteria bifidum, Escherichia coli, Nissle strain (1917)
Growth or Weight of Infants Bifidobacteria bifidum, Bifidobacteria breve, Streptococcus thermophilus
Colon Cancer Prevention Bifidobacterium

Vegans Do Not Harbor Bacteria Toxic to The Arteries

Intestinal bacteria have recently been discovered to play a causal role in atherosclerosis. On a meat-based diet bacteria grow in the intestine that convert choline, L-carnitine, and betaine into trimethylamine (TMA) which is then oxidized by the liver to produce Trimethylamine oxide (TMAO).15 This has become a well-accepted mechanism for the Western diet causing heart disease, strokes, and other major vascular problems: macular degeneration, hearing loss, claudication, gangrene, impotence, etc. And one important means by which the McDougall Diet keeps us healthy. People following a vegan diet do not produce bacteria in their intestine to make this toxic metabolic conversion.16

Prebiotics and Synbiotics

Prebiotics are nondigestible simple sugars (oligosaccharides) sold as pills and liquids that stimulate the growth and/or activity of “friendly” bacteria already present in our intestines. Prebiotics are very effective for relieving constipation, and hold some promise for the prevention of gallstones and for the treatment of inflammatory bowel diseases. Examples of undigestible sugars used as prebiotics are: FOS (fructooligosaccharides), GOS (galactooligosaccharides), inulin (not insulin), lactulose, and lactitol. Two prebiotics prescribed by doctors, lactulose and lactitol, have been effectively used to treat patients with liver failure (hepatic encephalopathy).5 They may also be helpful in the prevention of colon cancer.13,14

These commercial products have no toxic effects. They can act as a mild laxative in small amounts, but may produce flatulence when consumed in large amounts. Combining probiotics (the bacteria) with prebiotics (the bacteria’s food) results in a logical partnership, called synbiotics. You will most often find synbiotic products sold as mixtures of bacteria with FOS. Because the McDougall diet is made of starches, vegetables and fruits which contain a wide variety of undigestible sugars that feed and stimulate the growth of “friendly” bacteria, people consuming such a diet require no additional prebiotics to obtain optimal health benefits from their microflora (natural or enhanced by probiotics).

Dairy as a Probiotic Source

The best known examples of food with probiotics are yogurts containing lactic acid-producing bacteria, called Lactobacillus bulgaricus. These organisms are non-toxic and survive passage through the intestine. However, they cannot live and reproduce in the colon (they do not colonize the colon); therefore, they must be ingested regularly for any health promoting properties to persist. I do not recommend yogurt as a source of friendly bacteria for two reasons. First, these bacteria’s beneficial effects have not been conclusively proven.17 More importantly, yogurt brings with it all the negative qualities of dairy products: high in fat and cholesterol, allergy producing dairy proteins, and infection with harmful viruses and bacteria. (See my May 2003 newsletter article “Marketing Milk and Disease”.) Acidophilus milk is made by culturing milk with Lactobacillus acidophilus bacteria and has similar drawbacks.18 Any benefits provided by any species of Lactobacillus can be obtained much more safely and effectively in supplement forms (pills), avoiding the health risks of dairy products.

Who Should Alter Their Gut Bacteria?

Everyone should encourage the growth of a healthy microflora by eating the right foods, and avoiding antibiotics, whenever possible. This means a “breast milk diet” for infants and a healthy pure vegetarian diet (like the McDougall diet) for children and adults. Newborns, delivered by cesarean section, and bottle-fed babies may benefit from probiotics specifically designed for infant use. Probiotics may be warranted after a course of prescribed antibiotics in order to help reestablish a healthy gut flora. Lastly, if, after doing all you can for yourself with a healthy diet and lifestyle, you still suffer from unresolved problems, such as irregular bowel movements, indigestion, elevated cholesterol, or arthritis, then you may want to try enhancing the activity of your microflora with these kinds of supplements. You have little to lose – there are no undesirable side effects and the costs are minimal. You have everything to gain with the probability of improved health thanks to your always working factory of “friendly” microflora.


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5) Peltonen R, Ling WH, Hanninen O, Eerola E. An uncooked vegan diet shifts the profile of human fecal microflora: computerized analysis of direct stool sample gas-liquid chromatography profiles of bacterial cellular fatty acids.  Appl Environ Microbiol. 1992 Nov;58(11):3660-6.

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12) Peltonen R, Nenonen M, Helve T, Hanninen O, Toivanen P, Eerola E.  Faecal microbial flora and disease activity in rheumatoid arthritis during a vegan diet. Br J Rheumatol. 1997 Jan;36(1):64-8.

13)  Reddy BS. Prevention of colon cancer by pre- and probiotics: evidence from laboratory studies. Br J Nutr. 1998 Oct;80(4):S219-23.

14)  Buddington RK, Williams CH, Chen SC, Witherly SA.  Dietary supplement of neosugar alters the fecal flora and decreases activities of some reductive enzymes in human subjects.  Am J Clin Nutr. 1996 May;63(5):709-16.

15) Verhaar BJH, Prodan A, Nieuwdorp M, Muller M. Gut Microbiota in Hypertension and Atherosclerosis: A Review. Nutrients. 2020 Sep 29;12(10):2982.

16) Argyridou S, Davies MJ, Biddle GJH, Evaluation of an 8-Week Vegan Diet on Plasma Trimethylamine-N-Oxide and Postchallenge Glucose in Adults with Dysglycemia or Obesity. J Nutr. 2021 Jul 1;151(7):1844-1853.

17) Adolfsson O, Meydani SN, Russell RM. Yogurt and gut function.  Am J Clin Nutr. 2004 Aug;80(2):245-56.

18) Wheeler JG, Shema SJ, Bogle ML, Shirrell MA, Burks AW, Pittler A, Helm RM. Immune and clinical impact of Lactobacillus acidophilus on asthma. Ann Allergy Asthma Immunol. 1997 Sep;79(3):229-33.