Probiotics: Replenishing Your Healthy Bacteria

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Probiotics are microorganisms that live in our mouth and intestines and help us greatly with our health. (Pro means ‘in favor of’, and bio means ‘life’.) Over a thousand strains of beneficial microorganisms live in the colon alone. These microorganisms, mostly bacteria and certain yeasts, produce substances that nourish and protect the tissues around them, as well as throughout the body. Some bacteria can even make substances used by our brains for cleaning up debris in brain cells! Probiotics also prevent or control the overgrowth of harmful microbes in the mouth and throughout the gut.

A healthy human is supposed to have trillions of microorganisms (4-7 pounds!) in the bowel, all living in a harmonious ecosystem. This allows the beneficial bacteria to dominate the environment and control or eliminate all other microorganisms such as parasites, unwanted bacteria, harmful yeasts, molds, mycoplasmas and viruses. The beneficial bacteria cover the lining of the bowel, taking on all invaders. They help keep the bowel too acidic for the pathogenic organisms to thrive, and they denature certain toxins. They even produce substances such as butyric acid that nourish the intestinal lining. When we have abundant levels of probiotics, our digestive systems work better, and our immune systems are stronger. 

What Happens When We Don’t Have Enough Friendly Flora

Deterioration of oral and gut flora leads to a wide variety of common conditions. A partial list includes:

·      Indigestion, heartburn, constipation, diarrhea, abdominal bloating, gut infections

·      Failing vision, ear pain, ear infection, gum disease, sinus congestion, sinus infection

·      Depression, irritability, mental fogginess, poor memory

·      Fatigue, headaches, dizziness, muscle pain, muscle weakness, joint pain

·      Skin rashes, itching, airborne allergies, delayed wound healing

Many health scientists around the world believe the imbalance of gut flora, known as dysbiosis, is also a root cause of more serious diseases and illnesses. These include infections (from colds to tuberculosis), food allergies, autoimmune diseases and even some cancers. A serious condition called Leaky Gut Syndrome is becoming more common. This degenerative condition is marked by a loss of friendly gut flora, inflammation and deterioration of the gut lining, and the subsequent development of multiple food allergies and weakened immunity. 

Restoration of probiotics has recently been linked with weight loss. This makes sense, because low probiotic levels contribute to food allergies, and eating allergenic foods contributes to weight gain and water retention.

Why Are We Losing Our Beneficial Gut Flora?

Most Americans don’t have adequate levels of probiotics in the colon (large intestine/lower bowel). One of the main causes of this is the overuse of antibiotics to treat infections in humans. Antibiotics can’t distinguish between beneficial and harmful bacteria and kill both. The addition of antibiotics to animal feeds also adds to the problem, because antibiotic residues in meat and milk are ingested by humans.

Contributing causes of imbalanced gut flora include: 

·      Chlorine added to municipal water supplies for the purpose of killing microorganisms also kills probiotics in the gut. 

·      Regular intake of sugar promotes the growth of faster-growing, harmful microorganisms, especially yeast, which then crowd out the dwindling population of beneficial bacteria. 

·      High levels of heavy metals in the body.

·      Lack of vegetable and other plant fibers in the diet.

·      Eating allergenic foods.

·      Any condition or habit that causes bowel inflammation.

Always Take Probiotics When Taking Antibiotics

No matter how long ago you had your last course of antibiotics, diet alone is unlikely to have restored your healthy flora. Even yogurt and fermented foods aren’t enough to replenish the beneficial bacteria. But, it’s never too late to restore bowel flora. Probiotic supplements that contain the beneficial bacteria and yeasts which are normal inhabitants of a healthy gut are readily available for purchase. 

Just as with prescription antibiotics, natural antibiotics can kill both bad and good bacteria. Garlic is probably the most protective anti-bacterial, leaving more of the good guys unharmed, but garlic isn’t usually strong enough for an infection. More powerful natural antibiotics, such as olive leaf, cat’s claw and oil of oregano can wipe out good flora as well as bad. Whether your antibiotic is prescription or herbal, you need to restore your flora during and after treatment in the same way.

Every time you take an antibiotic, you need to restore your probiotics again. This takes anywhere from 4–12 weeks. The time depends on factors such as health history, current diet, heredity, and stress levels, so I recommend 8–12 weeks of supplementation.

When you start an antibiotic, start probiotics immediately. You need to take the antibiotic and the probiotic at least 2 hours apart. Otherwise, the antibiotic will kill the good bacteria. Since antibiotics should be taken with food, take the antibiotics with meals and the probiotics two hours away from meals.

Choosing a Probiotic Supplement

Probiotics are available in dry capsules, pearls (spherical gelcaps), loose powder and liquid. Look for one with about 3 to 6 strains of bacteria listed. Most probiotic supplements contain only bacteria, but some contain beneficial yeasts and others are combinations of bacteria and yeast. It can be beneficial to change brands over time to get as many different strains of healthy bacteria established in the bowel as possible.

Regular grocery stores aren’t usually the best place to find a good brand. Choose something from a natural food grocery or supplement store. Check the label to see how many CFUs (colony-forming units, or number of viable cells) are provided per pill or dose. If they don’t list the CFUs per pill or dose, don’t purchase it. 

CFUs vary widely from as little as 1 million to as high as 100 billion per pill or dose. A good general recommendation for dosing is 15-20 billion CFUs twice a day for adults and 5-10 billion CFUs 1-2 times a day for children. Some adults can work up to as much as 100 billion organisms a day with no ill side effects. So, choose a supplement that can provide the CFU count per pill that fits your dosing requirements. 

Probiotic Yeasts

In addition to bacteria, certain yeasts are important probiotics too. The best-known are types of Saccharomyces. Florastor, a brand of Saccharomyces boulardii, is the most widely-sold probiotic in the world, because it’s so effective for calming dysentery and crowding out the fast-growing, harmful yeasts so that good bacteria can take over again. Many people carry Florastor when traveling because it works quickly to calm traveler’s diarrhea. 

Storing Probiotics

Some probiotic supplements need to be refrigerated and others don’t. Check the label. If yours needs refrigeration, it’s okay to take the day’s pills out of the bottle in the morning and leave them at room temperature for the day. Loss of potency from warmth is a gradual process and leaving pills out for 1 or even a few days is fine, unless the temperature inside is above 80°. 

Supplements kept in the refrigerator are easily forgotten, so find a way to remind yourself. I use an empty supplement bottle with tape over the label and “fridge” written on it. I keep this with my other supplements to remind me to take the refrigerated ones.

Taking Probiotics

Study results vary on whether it’s best to take probiotics with or away from food. Since the usual recommendation is one capsule or dose twice a day, I usually recommend taking one dose at the beginning of breakfast and the second dose at bedtime, at least 2 hours away from food. Whenever you take them, make it convenient so you’ll take them regularly. If taken with food, take them just before eating or early in the meal.

Taking too high a dose can cause gas and loose stools, so I recommend starting with half of the recommended amounts and work up gradually over a week or more. 

If you’re taking antibiotics, keep the probiotic at least 2 hours away from your medication. If taken too close together, the antibiotic will kill the good bacteria from the supplement. Take the antibiotics with meals and the probiotics two or more hours away from meals.

Other Probiotics

The beneficial flora in the small intestine are different than those in the large intestine. Dysbiosis in the small intestine is more and more common and can lead to such degenerative conditions as SIBO (Small Intestinal Bacterial Overgrowth) and Leaky Gut Syndrome. If you’ve been diagnosed with dysbiosis in the small intestine, you will need a probiotic specifically for the small bowel. Find more information at:

Probiotics for oral health are also available. Oral probiotics can make a positive difference in controlling gingivitis, gum inflammation, and other oral imbalances and diseases. Jarrow, Hyperbiotics and Life Extension all make good oral probiotics. Be aware that antimicrobial mouthwashes kill beneficial oral bacteria as well as harmful ones, so use them sparingly. If you need a mouthwash daily for clean breath, you probably have a digestive issue that is causing halitosis, and this needs to be addressed at its roots rather than treating the symptom with mouthwash. 

Probiotics Grown on Dairy or Soy May Actually Be Dairy- and Soy-Free

Growing probiotics requires a substrate (food) for the bacteria. Dairy and soy are often used as substrates. If you’re allergic to dairy or soy, you need to know that probiotic supplements grown on a substrate of dairy or soy may still be dairy-free or soy-free and labeled as such. To create a dairy- or soy-free product, any dairy or soy residues are removed after the bacteria are grown, so the end product actually is free of dairy or soy. Due to an old regulation, substrates may still be listed in the ingredient list, which can create confusion. If your sensitivity is unusually extreme, you may want to avoid these products due to the possibility of minute trace residues or contact the company to find out for sure if the product is 100% free of the substrate.


Prebiotics are substances that support the growth of probiotics. These are mostly indigestible plant fibers. When these substances reach the colon, they ferment and enhance the growth of helpful bacteria. This is one more reason why plant fibers are so important in our diet. The most recommended prebiotic foods include asparagus, onions, garlic, chicory root, jicama, leeks, dandelion greens, dandelion root tea, Konjac root, cabbage, apples, bananas (slightly underripe), oats, and barley. Prebiotics can be purchased in pill form for people who are unable to get adequate prebiotic fiber or who want to speed up the colonization of probiotics. 

Fermented Foods Can Help

Even though food alone can’t restore your friendly bacteria, fermented foods can help. These include sauerkraut, yogurt, kefir, kombucha and miso. Keep in mind that many American store-bought versions of fermented foods are not fermented long enough to have generous bacteria levels and may even be pasteurized after fermentation, leaving the flavor but killing the good bacteria. Homemade versions of these foods are the most reliable source of beneficial bacteria.

Help for Repairing the Bowel

After restoring your healthy flora, you may need to nourish and strengthen the lining of the bowel. This is essential if you have any degree of Leaky Gut Syndrome. I recommend L-glutamine to help heal the small intestine lining and butyric acid (butyrate) to help heal the large intestine lining. These are available in supplement form and can be taken per label dosing for 2-3 months along with or after restoring your friendly bacteria.

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