Make Your Microbiome Work For You

Article by Dr. Michael Donaldson

The importance of microbial balance in the gut has been the subject of intense investigation since the time of Élie Metchnikoff, the Russian microbiologist who shared the 1908 Nobel Prize in Medicine & Physiology with Paul Ehrlich for the discovery of phagocytosis. In his later years at the Pasteur Institute in Paris Élie Metchnikoff focused on longevity, looking for factors that promoted longevity. He examined cultures with higher numbers of centenarians, looking for their keys to health and longevity. Soured, cultured milk was highly regarded among the Georgians of the Caucasus Mountain region of Europe. He promoted the use of these bacteria-laden drinks, and thus became the grandfather of the modern probiotic movement. Our modern understanding of the importance of microbial balance in the gut got its start back under the microscope of Élie Metchnikoff.

To this day we are finding out more and more about the importance of the balance of microbes in the gut. We are able to classify the bacteria much more carefully now, with modern genetic sequencing. With about ten times more bacteria in our gut than we have cells in our body, you literally could say there is more of them than there is of us.

Some things remain very confusing about microbiome research, but a few things have become very clear. First, the balance of microbes that grow in your gut depend on what you feed them [1]. If you feed them a diet heavy in animal fat and high in animal protein you will have bugs that survive bile and are particularly good at breaking down excess amino acids. This metabolism yields smelly and toxic by-products containing ammonia and sulfur that are detrimental to the human frame. If you feed your gut microbes a lot of fiber and complex carbohydrate (not the white bread kind), you will get more bacteria that breakdown these foods and yield branched chain amino acids and short chain fatty acids, which fuel the cells of the colon wall and much more.

A second concept has also become clear. Long-term balance of your gut microbiome is fairly stable. Short term studies supplementing fiber or probiotics don’t change the balance very much [2]. If you stop the fiber or stop the probiotic, your microbiome goes back to the state it was in before you began the supplement. You can change your long-term balance of your gut microbiome by changing your diet and lifestyle permanently. Permanent changes get permanent results.

A third clear point is that the microbiome is not to be neglected in understanding health and disease [3]. Several lines of investigation have given us clues into understanding how important the microbiome really is. Fecal transplant experiments, as gross as they seem, actually have had some positive benefits. Benefits for autism [4], infections of Clostridioides difficile, obesity, ulcerative colitis [5] and metabolic syndrome have all been seen with fecal transplant experiments [6]. However, the results were somewhat transient, so this experimental method is not a permanent solution either. However, it does show that changing the microbiome is a big key to getting results.

Another line of investigation that has shown the power of the microbiome is with metformin, the oral diabetic drug. Its exact mechanism of action hasn’t been elucidated, and now it appears metformin works by changing the microbiome. These changes are what actually affect blood sugar control, not some direct effect of metformin itself. When fecal transplants from people taking metformin were given to germ-free mice, a benefit in lowered blood sugar was demonstrated in the mice, even though they didn’t take any metformin themselves [7].

The microbiome has also been shown to help predict blood glucose response to foods. Blood sugar response to foods varies a lot between different people, and formulas and indexes don’t predict individual responses well at all. The glycemic index is based on averages from experiments on several people. An Israeli study of 800 people predicted blood sugar control much better when they included gut microbiota as one of the factors in their formula. Then the formula was tried on 100 new people. Using the formula to create a personalized diet for each person the researchers were able to successfully lower the blood sugar response to meals in the new group [8]. It even worked on American in the Midwest once the abundances of Prevotella (fiber-loving bacteria) and Bacteroides (fat and protein loving bacteria) were taken into account [9].

What can we take away from these data? Pay attention to your microbiome. It is important. How to do that? While taking a probiotic is helpful, especially after taking antibiotics, it can’t be your only strategy. You need fiber, and lots of it. The beneficial bacteria that protect your gut from disease-causing bacteria and produce vitamins and short chain fatty acids for you, live on fiber. You need to include a variety of rich sources of fiber in your diet. A whole-foods plant-based diet, or the Hallelujah Diet, or some variation of these diets provide about 60 grams of fiber for 2,000 calories. Much of this fiber comes from fresh, raw produce, which already is seeded with beneficial bacteria. This dietary pattern will grow a healthy microbiome in most people most of the time.

It turns out that Élie Metchnikoff was on the right path, along with many others who have since advocated cultured foods and fiber to improve health and longevity. While we don’t advocate cultured dairy products, we do think quite highly of sauerkraut and other fermented vegetables. Check out Melody Hord’s “Power Up Your Produce” webinar on this topic for ideas of how to incorporate more of these beneficial foods into your diet today.

References

1. Dahl WJ, Rivero Mendoza D, Lambert JM (2020) Diet, nutrients and the microbiome. Prog Mol Biol Transl Sci 171:237–263. https://doi.org/10.1016/bs.pmbts.2020.04.006
2. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, et al (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–108. https://science.sciencemag.org/content/334/6052/105
3. Hills R, Pontefract B, Mishcon H, Black C, Sutton S, et al (2019) Gut Microbiome: Profound Implications for Diet and Disease. Nutrients 11:1613. https://www.mdpi.com/2072-6643/11/7/1613
4. Kang D-W, Adams JB, Gregory AC, Borody T, Chittick L, et al (2017) Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome 5:10. https://doi.org/10.1186/s40168-016-0225-7
5. Costello SP, Hughes PA, Waters O, Bryant RV, Vincent AD, et al (2019) Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis: A Randomized Clinical Trial. JAMA 321:156–164. https://jamanetwork.com/journals/jama/fullarticle/2720727
6. Choi HH, Cho Y-S (2016) Fecal Microbiota Transplantation: Current Applications, Effectiveness, and Future Perspectives. Clin Endosc 49:257–265. https://doi.org/10.5946/ce.2015.117
7. Wu H, Esteve E, Tremaroli V, Khan MT, Caesar R, et al (2017) Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug. Nat Med 23:850–858. https://www.nature.com/articles/nm.4345
8. Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, et al (2015) Personalized Nutrition by Prediction of Glycemic Responses. Cell 163:1079–1094. https://www.cell.com/cell/abstract/S0092-8674(15)01481-6
9. Mendes-Soares H, Raveh-Sadka T, Azulay S, Ben-Shlomo Y, Cohen Y, et al (2019) Model of personalized postprandial glycemic response to food developed for an Israeli cohort predicts responses in Midwestern American individuals. Am J Clin Nutr 110:63–75. https://academic.oup.com/ajcn/article/110/1/63/5490305

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