In Blog, Diet, Research

Increasingly people are aware that the health of their microbiome determines how well their cells run the chemistry of life. The gut-brain-immune connection is now recognized by more primary care physicians and specialists as well as patients as an important factor in restoring health for those with neurological1,2, psychiatric3, and/or autoimmune conditions4,5. People often ask me if they need to eat fiber and fermented food to reset their microbiome, or if they can just take supplements instead and keep eating what they want.

Over millions of generations, random mutations in DNA have led to evolutionary changes and created the diversity of species that populate the globe today. Those random mutations occurred in our ancestral mothers, which made some genes no longer effective at coding for the protein that governed a particular step in the chemistry we needed for optimal health. But if the bacteria living in her bowels could do that step and the metabolites of that chemical reaction pass into the bloodstream, health is maintained and reproductive success continues. In that lifetime, the gene for that step moved from her DNA to her gut microbe’s DNA. Because many of the gut bacteria also live in the vagina, she passed those microbes to her children as they passed through her vagina. Slowly, through these evolutionary changes, the chemical steps that can be done by bacteria were exported to the bacteria in our gut.  Those that cannot be done by the microbiome stayed in the human DNA.

Humans have about 25,000 genes. But our gut microbes have 5 to 9 million genes that digest the food we eat and therefore feed them. For millions of years humans ate mostly leaves, gradually increasing amounts of animal protein. Approximately 250,000 years ago, humans became a distinct species, and approximately 100,000 years ago our ancestors began cooking and fermenting food. For 5,000 generations, our ancestors ate diets that were much higher in fiber–over 100 grams per day as compared to today’s average, which is less than 25 grams per day. We have radically changed our diet, which is the most powerful driver of what species live in the gut. As the mix of bacteria and fungi living in the gut changes and some populations disappear entirely, we are at risk of losing the genes needed for all the chemical steps associated with health and vitality.

Modern scientists are investigating the health benefits of probiotic bacteria and fermented foods. They reduce the leakiness of the gut, suppress pathogens, and provide important metabolites that are associated with better blood sugar and other markers of health6. Fermented foods have been shown to be beneficial in reducing symptoms in animal models of anxiety and depression7. Increasing fermented food intake is also associated with increased gut microbial diversity and improved biomarkers of health8,9. Taking additional dietary fiber increases gut microbial diversity, which is associated with improved biomarkers of better health. However, if the fiber intake is stopped, the gut diversity returns to baseline. Similarly, probiotic bacteria disappear from the gut after the person stops taking the probiotic supplement.

A recent study9 compared a high fiber diet to a high fermented foods diet. The fermented foods group had a target of 6 servings of fermented vegetables (1/4 cup = one serving) or dairy. The high fiber group increased dietary fiber to over 36 grams per day. The high fiber group increased the diversity of microbes in the gut but did not change the balance of T regulatory cells (an important marker of autoimmune risk). The high fermented group increased the diversity of microbes in the gut. Notably, the new microbes were different from the microbes in the fermented foods that people consumed and these new microbes continued in the gut even after the fermented foods were discontinued. This suggests that fermented foods may be able to create a sustained shift in the microbiome that high fiber diets cannot. In addition, the high fermented group created a change in the T regulatory cells associated with reduced risk of autoimmunity. Furthermore, that change was sustained even after the fermented foods were stopped. This is a small study and the results will need to be replicated. However, it is very exciting to see that we have the possibility of creating a sustained change in the gut microbiome using fermented foods.

In summary, our microbiome does speak to our immune cells and our brains. In a small pilot study, eating more fermented foods was associated with more microbiome diversity and immune biomarkers that were associated with lower risk of autoimmunity. Increasing fiber in our diet also improves microbiome diversity, but benefits disappear when the fiber consumption drops.

I tell my patients to eat fermented foods daily, preferably several servings, as well as enough fiber to have soft, easily passed bowel movements. If you need help learning how to incorporate fermented foods into your diet, the Premium Menus, Level two will help you achieve that goal. The Premium Menusprovide recipes, shopping lists, and menus to help you implement a fiber-rich diet that will give your gut microbiome what it needs to thrive. These are important tools to support your return to health!

1. Wang Y, Kasper LH. The role of microbiome in central nervous system disorders. Brain Behav Immun. 2014;38:1-12.
2. Hirschberg S, Gisevius B, Duscha A, Haghikia A. Implications of Diet and The Gut Microbiome in Neuroinflammatory and Neurodegenerative Diseases. Int J Mol Sci. 2019;20(12).
3. Dash S, Clarke G, Berk M, Jacka FN. The gut microbiome and diet in psychiatry: focus on depression. Curr Opin Psychiatry. 2015;28(1):1-6.
4. Proal AD, Albert PJ, Marshall TG. The human microbiome and autoimmunity. Curr Opin Rheumatol. 2013;25(2):234-240.
5. McKenzie C, Tan J, Macia L, Mackay CR. The nutrition-gut microbiome-physiology axis and allergic diseases. Immunol Rev. 2017;278(1):277-295.
6. Lin L, Zhang J. Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol. 2017;18(1):2.
7. Aslam H, Green J, Jacka FN, et al. Fermented foods, the gut and mental health: a mechanistic overview with implications for depression and anxiety. Nutr Neurosci. 2020;23(9):659-671.
8. Stiemsma LT, Nakamura RE, Nguyen JG, Michels KB. Does Consumption of Fermented Foods Modify the Human Gut Microbiota? J Nutr. 2020;150(7):1680-1692.
9. Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021.
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