How to Restore and Improve Your Gut Bacteria

Filed Under: Digestive Health, Gut Bacteria & Probiotics
Last Reviewed 11/16/2015

How to Restore and Improve Your Gut Bacteria

Learn 3 easy ways to help grow healthy digestive flora

When we think about microflora and restoring gut bacteria, probiotic supplements are generally the first thing that comes to mind—but that’s just one thing that needs to be considered. You could take a boatload of probiotics, but it wouldn’t do much good if your lifestyle continues to include habits that damage gut bacteria, such as taking antibiotics and drinking highly chlorinated water. 

The beneficial microflora in and on your body need a stable environment in which to grow and flourish. We know that the ideal pH in the colon should be between 6.7 and 6.9. A pH of 7 is neutral—anything lower than 7 is acidic and anything above 7 is alkaline. The colon needs to be slightly acidic, which inhibits the growth of undesirable bacteria like Salmonella, Shigella, and E. coli.

The best way to restore beneficial bacteria in the gut is to create acidity, which promotes the growth of various Lactobacillus bacteria—the ones with well-known beneficial effects. Here are a few simple yet effective ways to accomplish this:

Traditional Fermented Foods

One of the best things you can do to enhance and improve gut flora is to regularly eat foods that contain a lot of friendly probiotic bacteria—specifically traditional fermented foods. You may also hear these dishes be referred to as "probiotic foods."

See a list of all articles about Gut Bacteria in the Gut Bacteria and Probiotics Index

Traditional fermented foods are rich in beneficial lactic acid-producing bacteria. These bacteria are what naturally make milk products go sour and cause vegetables to ferment. In the digestive tract, these bacteria help ferment carbohydrates that we, as human beings, cannot digest. The byproducts from this process help keep the gut acidic, which prevents harmful organisms from being able to grow while good gut bacteria more firmly establish themselves. Pickled vegetables, fermented milk products, kefir, and fermented soy products are some examples of traditional fermented foods.

Consuming naturally fermented foods not only supplies the gut with more of these desirable microorganisms, but the extra acidity they create helps to support the bacteria that are already there. I find the best way to regularly include fermented foods in your diet is to make your own yogurt and ferment vegetables. Also remember, when adding traditional fermented foods to your meals, the key is to eat a small portion of them every day. Once or twice a day with meals is best.

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Probiotic Supplements

Although eating fermented foods is the most natural way to get the benefits of probiotic bacteria and improve gut flora—not to mention that it's the method I most prefer—many people find it difficult consume fermented foods on a consistent basis, or they simply don't care for the taste of them. An effective alternative is to take a probiotic supplement.

Probiotic supplements are a convenient way to deliver additional beneficial bacteria to the gut because they don't require any cooking or meal planning, plus they're easy to take with you if you're going out for dinner or on a trip. The only catch is making sure you choose the right product. In the 20-plus years that I've been writing about gut health and probiotics, the market for supplements has expanded exponentially. Preferred delivery systems have come, gone, and returned, and the strains of bacteria available have multiplied almost as fast as the number of products that are for sale.

For some guidance on making sure the product you purchase is the most appropriate one for you, I encourage you to read my advice on which strains of beneficial bacteria offer the most digestive health benefits.

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Lactic Acid Yeast Wafers

For most people, taking a probiotic supplement and/or eating more traditional fermented foods will be enough to increase the number of beneficial microorganisms in the gut. These bacteria will then start to ferment more soluble fiber into products like butyric acid, acetic acid, lactic acid, and propionic acid, which in turn provide energy and improve our ability to absorb minerals, vitamins, and fat. 

For some individuals, however, restoring the the intestinal microflora to adequate levels requires an additional step. For decades, I’ve used a product called Lactic Acid Yeast by Standard Process Laboratories. Lactic acid yeast wafers work the same way fermented foods do, in that they help restore the bacterial flora of the lower bowel. Lactic acid yeast is a modified form of brewer’s yeast that works in your intestines to produce significant amounts of lactic acid. The additional acid stops the growth of harmful bacteria while allowing good gut bacteria to flourish. It works rather quickly, and when followed up with a probiotic supplement, the results can be amazing. I suggest chewing one lactic acid yeast wafer with each meal. In most cases, the product will only be needed for five to seven days. During this time, I would also continue taking a the supplement.

Standard Process Laboratories typically sells their products only to physicians, so you’ll have to look for someone who handles the product in your area (chiropractors are a good source). If you are willing to spend some time searching, you also can still find them online. Pure Formulas sells a 100-count bottle of lactic acid yeast wafers for about $20. Visit

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Getting the Balance Correct

At this point in time, we don’t know what the perfect ratio of specific species of bacteria and other organisms should be within the body. We probably never will know and, to be honest, the percentages will likely vary depending on one’s age, pH, diet, digestive enzymes, climate setting, the season, body composition, etc.

Some researchers suggest that for someone to be healthy, their lower intestine should contain 85 percent friendly bacteria to prevent the over-colonization of microorganisms like E. coli or Salmonella. And as long as the bad bacteria percentage remains at or below 15 percent, then the body can remain healthy.

It's hard for me to accept this idea. We are just starting to understand the beneficial and protective role some forms of the bad bacteria play in keeping us disease-free. But rather than get caught up in determining the perfect mix of bacteria and microflora, to restore gut bacteria, we first need to focus on creating the perfect environment for healthy microflora to survive.

Read More About Gut Bacteria and Digestive Health

Gut Bacteria and Probiotics Article Index
See a full list of articles by Dr. Williams about gut flora, probiotics, and the microbiome. Read more
Traditional Fermented Foods That Boost Digestive Health
Learn which traditional fermented foods have the most gut health benefits. Read more
Tips and Tools for Making Your Own Fermented Foods
Learn why store-bought fermented foods don’t deliver as many benefits as they often promise, as well as Dr. Williams’ recommended tools for making your own fermented milk-products and vegetables. Read more
How to Choose the Best Probiotic Supplement
Learn the four criteria that Dr. Williams uses to decide whether a probiotic supplement is worth purchasing. Read more
Lifestyle Habits That Damage Gut Bacteria
Learn how our normal, everyday routines can damage the microflora in our gut. Read more
How to Perform a Fecal Transplant
Dr. Williams explains the benefits of fecal transplants and how to perform this procedure at home. Read more


DISCLAIMER: The content of is offered on an informational basis only, and is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always seek the guidance of a qualified health provider before making any adjustment to a medication or treatment you are currently using, and/or starting any new medication or treatment. All recommendations are "generally informational" and not specifically applicable to any individual's medical problems, concerns and/or needs.

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