Feeding Your Probiotic Microbes

Trillions of organisms live in your digestive tract. These microorganisms are sometimes called intestinal flora, gut flora, or gut microflora, but the vast majority of them aren’t really flora in the sense of being plants, so I refer to them as microbes. In any case, these little critters are so important to your health and survival that some researchers consider them a vital organ.  You might think of microbes as dangerous, but 85% of them are helpful, or at least not harmful, to your body. You want the helpful microbes, which are known as probiotics, to be so plentiful and dominant in your body that there is no room or food for the harmful, disease-causing microbes, known as pathogens.  The benefits of a healthy colony of probiotic microbes include:

Where do these probiotic microbes come from? The gastrointestinal tract of a normal fetus is sterile. Babies born vaginally became inoculated with microbes from their mothers, including Lactobacillus, Bifidobacterium, E.coli and Enteroccoccus. This mixture gives them an immediate natural defense barrier of probiotic microbes that protect against pathogens, and affect their health throughout life.

Your mouth is a fertile home for millions of bacteria. Your brain tells your mouth to prepare for the arrival of food by secreting saliva, which is why your mouth waters when you see, smell, or even think about food. Saliva contains the enzyme amylase, which begins the digestion of starchy foods, such as potatoes and rice, and it moistens and lubricates food to help swallowing. Saliva also contains antimicrobial substances that inhibit the growth of pathogenic bacteria. But Streptococcus mutans thrives in your mouth and can easily bypass these defenses. It also loves sugar, and uses it to form a film, or plaque, on the surfaces of teeth. Bacteria thriving within these plaques turn sugar into acid, which then creates cavities in your teeth. However, large numbers of S.mutans suppresses the growth of another bacterium found in the mouth, Streptococcus pneumoniae, which can cause pneumonia and meningitis. By restricting the numbers of S.pneumoniae, S.mutans decreases the risk of these serious diseases developing, so it’s more important to keep sugar and refined carbohydrates out of your mouth than it is to try to eliminate all the bacteria.

The next part of your digestive tract, your esophagus, is a difficult place for bacteria to thrive, as your esophageal contents are continuously flushed into the stomach when you swallow. Your stomach processes food for around three hours, giving microbes plenty of time to attach themselves to your stomach wall. The gastric juices secreted to liquefy food into chime and start the breakdown of protein, are five times more acidic than lemon juice. Yet some microbes, including Helicobacter pylori, thrive in your stomach. H.pylori causes gastric ulcers and may promote gastric and duodenal cancers. Helicobacter is found in the stomachs of half the population, yet only about one fifth of them become sick, so lifestyle factors must also play a role in the development of disease. Your stomach also contains lactic acid-producing bacteria, including strains of Streptococcus and Lactobacillus, that convert sugar into acid. Lactobacilli may also inhibit the growth of H.pylori and decrease the enzyme activity needed for its survival in the acid environment. Lactic acid-producing bacteria of the stomach are anaerobic: they do not require oxygen to survive. However, unlike most anaerobic bacteria, certain strains can tolerate oxygenated environments. The stomach is a well-oxygenated area because air swallowed with food arrives here within moments of ingestion. So some lactic acid-producing bacteria grow well here alongside bacteria that need to use the available oxygen. Most microbes die and dissolve in the harsh acidic conditions of your stomach. The ones that survive into the intestines are either resistant to acid or have a protective alkaline coating.

Your small intestine comes after your stomach. Food moves through here in about four hours. Enzymes released from your liver and pancreas help to break down food into molecules, which are absorbed across an enormous surface provided by micro-villi, finger-like projections covering the surface of the small intestine. The first part of your small intestine, called the duodenum, is only slightly less acidic than your stomach. However, bacteria living higher up in the digestive tract have already consumed most of the oxygen, so it is much less available in the duodenum. Therefore, this environment is ideal for microbes able to resist acid in the stomach and which are able to grow with or without oxygen. The main microbes at the relatively acidic top end of the small intestine are Lactobacillus and Enterococcus faecalis. Microbes encounter decreasing acid and oxygen as they descend through the jejunum and then the ileum of the small intestine. Towards the bottom of this section, where the living conditions are more appealing to more microbes, Lactobacillus and E.faecalis coexist with other bacteria such as E. coli and Bacteroides.

The final five feet of your gastrointestinal tract, your large intestine or colon, has almost no oxygen. By the time food reaches your colon, your body’s work of digestion is almost over. The remaining task for your large intestine is to remove the excess water from what’s left of your food, or feces, over the next 12 to 24 hours. If the feces stay in the colon any longer, they will become dehydrated and impacted as more water is removed. On the other hand, feces that travel too quickly through the colon as the result of intestine-damaging infections for example, result in loose stools, or diarrhea. The slow pace in your colon makes it an ideal place for microbes to colonize. Your colon contains more than 500 different species of bacteria living in a 3-pound mass of partially digested food, with one trillion organisms per gram of feces. The microbes in this part of your digestive system include EnterococciClostridia, and Lactobacilli, but by far the most abundant species are Bacteroides and the oxygen-intolerant, lactic acid-producing Bifidobacterium. Probiotic microbes outnumber potential pathogens like E.coli by as much as ten thousand to one. Bacteria make up about 60% of the weight of your feces, and you excrete your own weight in fecal bacteria every year.

When your partially digested meal arrives in your large intestine, it becomes the food for your microbes. Mother’s milk contains sugars (galacto-oligosaccharides), which feed probiotic bacteria known as Bifidobacterium, which protect babies from gastrointestinal infections. In addition, probiotic bacteria thrive on the parts of plants that you can’t digest directly, including oligofructose and inulin. These indigestible materials are known as prebiotics. Oligofructose is a fructooligosaccharide, which refers to a short chain of fructose molecules. Inulins are a group of polysaccharides, which means a long chain of sugar molecules. Since these prebiotics are composed of sugars, they are carbohydrates, and since they are indigestible and able to be dissolved in water,  they are soluble fibers. Although you can’t digest prebiotics, the probiotic bacteria in your colon can metabolize them through fermentation, releasing significant quantities of carbon dioxide, hydrogen, and methane. This process can sometimes cause intestinal gas; however, if you eat these prebiotic soluble fibers regularly, your body grows accustomed to them, and you experience fewer problems with gas.

Inulin and oligofructose are naturally present in many plant foods, and may help prevent constipation, promote enzyme activity and improve the pH levels in your colon. In addition, inulin promotes Lactobacillus acidophilus to produce butyrate, a beneficial short-chain fatty acid that helps inhibit inflammation in the intestinal tract. The following list shows foods in decreasing order of their average prebiotic content (values per 100 g):

  • Chicory root, raw: 41.6 g inulin, 22.9 g oligofructose
  • Jerusalem artichoke, raw: 18.0 g inulin, 13.5 g oligofructose
  • Dandelion greens, raw: 13.5 g inulin, 10.8 g oligofructose
  • Garlic, raw: 12.5 g inulin, 5.0 g oligofructose
  • Leek, raw: 6.5 g inulin, 5.2 g oligofructose
  • Asparagus, raw: 2.5 g inulin, 2.5 g oligofructose
  • Wheat bran, raw: 2.5 g inulin, 2.5 g oligofructose
  • Wheat flour, baked: 2.4 g inulin, 2.4 g oligofructose
  • Banana, raw: 0.5 g inulin, 0.5 oligofructose

Beans, peas, and lentils contain the oligosaccharides, raffinose and stachyose, that feed bifidobacteria, which suppress the activity of putrefactive bacteria, such as Clostridium in the colon. Good sources include:

  • Adzuki beans, raw: 0.2 g raffinose; 3.9 g stachyose
  • Soybeans, raw: 0.7 g raffinose; 3.2 g stachyose
  • Chickpeas, raw: 0.7 g raffinose; 2.4 g stachyose
  • Lima beans, raw: 0.4 g raffinose; 2.5 g stachyose
  • Black-eyed peas, raw: 0.5 g raffinose; 2.4 g stachyose
  • Peas, split, raw: 0.7 g raffinose; 2.1 g stachyose
  • Mung beans, raw: 0.8 g raffinose; 1.4 g stachyose
  • Lentils, raw: 0.3 g raffinose; 1.9 g stachyose

Beta glucans are sugars that are found in the cell walls of baker’s yeast, shiitake mushrooms, and cereal grains, like barley, oats, rye, and wheat. They increase the number of probiotic bacteria in the intestines, especially in people over the age of fifty. Beta glucans stimulate the activity of macrophages, which are immune cells that ingest and demolish invading pathogens and stimulate other immune cells to attack. Macrophages also release cytokines, chemicals that enable the immune cells to communicate with one another. In addition, beta glucans stimulate lymphocytes (white blood cells) that bind to tumors or viruses, and release chemicals to destroy it. Beta glucans also help to lower total and low-density lipoprotein (LDL or “bad”) cholesterol. Lentinan, a type of beta glucan found in shiitake mushrooms, is believed to reduce tumor activity and lessen the side effects of cancer treatment. Beta glucans also help your body do battle with bacteria resistant to antibiotic treatment and viruses that cause upper respiratory infections. They fight a form of Escherichia coli (ETEC), which cause traveler’s diarrhea. They also fight upper respiratory infections from colds and flu.

Because only plants contain these probiotic-nourishing carbohydrates, vegans have much higher counts of probiotic bacteria than do meat eaters. Vegans who eat starches, vegetables, and fruits, which contain a wide variety of indigestible sugars that feed and stimulate the growth of probiotic bacteria, require no additional prebiotic supplements to obtain optimal health benefits form their probiotic microbes (natural or enhanced by probiotic supplements).

Your intestinal microbes can become unhealthy and die because of fever, illnesses, antibiotics and other drugs, and changes in your diet.  Your diet actually determines the predominance of the microbe species that live in your intestines. Probiotic microbes thrive on plant remnants, and pathogens thrive on animal remnants and processed junk food.  A diet based on unrefined plants suppresses the growth of pathogenic microbes and stimulates beneficial microbes within one to two weeks of changing your diet. In addition, probiotic bacteria that break down a fat found in meat, dairy and some fish set off a chain reaction that leads to the buildup of an artery-clogging substance in your blood, causing cardiovascular disease.

Probiotic foods, including fermented vegetables (sauerkraut, pickles, kimchi) fermented drinks (kefir, kombucha), and fermented soy products (miso, tempeh, natto, soy yogurt) contain probiotic microbes as a result of fermentation or through the addition of a live culture. Eating these foods has the potential of helping you balance your intestinal microbes and thereby improve your health. Probiotic supplements are also sold as pills that contain millions of friendly bacteria, and sometimes yeast. You can buy them in natural food stores, usually in the refrigerated section. Probiotics are non-toxic.

You might have heard that dairy yogurt contains probiotics in the form of 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 your colon (they do not colonize your colon); therefore, you must eat yogurt regularly for any benefits to persist.  While the benefits of Lactobacillus bulgaricus have not been conclusively proven, yogurt brings with it all the negative qualities of dairy products: fat, cholesterol, allergy-producing dairy proteins, and pathogens. Acidophilus milk is made by culturing milk with Lactobacillus acidophilus bacteria and has similar drawbacks. You can obtain any benefits from any species of Lactobacillus much more safely and effectively in supplement forms (pills), avoiding the health risks of dairy products.

Antibiotics don’t kill just pathogens – they also kill probiotic microbes, sometimes eventually allowing the numbers of pathogenic bacteria, previously held in check by the predominating probiotic bacteria, to begin to multiply. Sufficient numbers of these pathogens can cause a variety of symptoms, including diarrhea.  A common antibiotic-associated pathogen is called Clostridium difficile. It produces a toxin that damages the bowel wall, triggering diarrhea.  However, treatment with a yeast known as Sacchromyces bombardii can relieve the symptoms, possibly because the yeast can destroy the toxin, thereby allowing the damaged bowel wall to heal.

Encourage the growth of healthy probiotic microbes by eating healthy foods and avoiding antibiotics, whenever possible.  This means mother’s milk for infants and unrefined plant foods for children and adults.  Babies delivered by cesarean section or fed formula may benefit from probiotics specifically designed for infants.  You may also want to take probiotic supplements after a course of prescribed antibiotics in order to help reestablish healthy intestinal microbes. Finally, if you still suffer from irregular bowel movements, indigestion, elevated cholesterol, or arthritis, then you may want to try enhancing your probiotic microbes with supplements.  You have little to lose, as there are no negative side effects and the costs are low. You have everything to gain with improved health from your colony of probiotic microbes.


This blog uses the latest nutritional data available from the USDA (United States Department of Agriculture), and the FDA (United States Food and Drug Administration), as well as nutritional data provided by food growers and manufacturers about their products. We believe the information on this blog to be accurate. However, we are not responsible for typographical or other errors. Nutrition information for recipes is calculated by Living Cookbook based on the ingredients in each recipe based on statistical averages. Nutrition may vary based on methods of preparation, origin and freshness of ingredients, and other factors.

This blog is not a substitute for the services of a trained health professional. Although we provide nutritional information, the information on this blog is for informational purposes only. No information offered by or through this blog shall be construed as or understood to be medical advice or care. None of the information on this blog should be used to diagnose or treat any health problem or disease. Consult with a health care provider before taking any product or using any information on this blog. Please discuss any concerns with your health care provider.

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5 thoughts on “Feeding Your Probiotic Microbes

  1. Pingback: Understanding Human Nutrition (With a Side of Politics) « Humane Living

  2. Wow this is a really informative article on probiotics. I would like to repost some of this to my site as soon as I get a chance. Thanks so much for the pingback. 🙂

  3. Pingback: Feeling the Benefits of Fiber « Humane Living

  4. Pingback: Eliminating Toxins | Humane Living

  5. Pingback: Connecting With Chlorella | Humane Living

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