Fermented foods have been a part of the diet even before humans knew about the existence of microbes—the very organisms that make fermentation possible. Our Paleolithic ancestors consumed honey, fruits, and fruit juices in fermented form without awareness of the trillions of microscopic beings they were concurrently ingesting. Even as long ago as 10,000 years, humans were deliberately fermenting foods as a form of preservation.1 Fast forward to today and one-third of the human diet globally consists of fermented foods.2

Fermentation of food and drink by microbes increases the nutritional status of foods as well as helps preserve the food. Fermentation of cereals, dairy, vegetables, fish, seafood, meats, and alcohol are all a part of our ancestral practices. Researchers from Harvard Medical School recently wrote a scientific review exploring the connection between fermented food and mental health, recognizing the intestinal microbiota as key to this integral relationship. They stated, “It is our contention that fermentation may amplify the specific nutrient or phytonutrient content of foods, the ultimate value of which is associated with mental health; furthermore, we also argue that the microbes associated with fermented foods may also influence brain health via direct and indirect pathways.”3

The researchers discuss the recent shift away from a traditional diet toward one high in processed, high-fat, high-sugar foods. This modern, Western dietary pattern has been linked to increased rates of depression and other mental health disorders. The researchers highlight the role of the microbiota in conjunction with the modern diet on markers of inflammation and oxidative stress as it relates to mental health. “The intestinal microbiota, via a number of mechanisms, may play a role in mediating the glycemic and mood related effects of the Western dietary pattern,” they state. Furthermore, “The burden of oxidative stress and inflammation is emerging as a vicious cycle that can directly influence mood, and the combination of the two appears to be both a cause and a consequence of depression.”

Ten years ago, the idea that gut microbes could positively affect mental health was still viewed as preposterous, although it was promoted by Logan et al.4,5 Back then, they proposed that our beneficial microbes could influence mood or fatigue in the following ways (many of which have since been investigated):

  • Direct protection of the intestinal barrier
  • Influence on local and systemic antioxidant status, reduction in lipid peroxidation
  • Direct, microbial-produced neurochemical production (i.e. GABA)
  • Indirect influence on neurotransmitter or neuropeptide production
  • Prevention of stress-induced alterations are related to overall intestinal microbiota diversity and numbers
  • Direct activation of neural pathways between gut and brain
  • Limitation of inflammatory cytokine production
  • Modulation of neurotrophic chemicals (i.e. brain-derived neurotrophic factors)
  • Limitation of carbohydrate malabsorption
  • Improvement of nutritional status, for example, better absorption of omega-3 fatty acids, minerals, dietary phytochemicals
  • Limitation of small intestinal bacterial overgrowth
  • Reduction of amine or uremic toxin burden
  • Limitation of gastric or intestinal pathogens
  • Analgesic properties

The Harvard researchers go on to discuss a number of studies that have been done on the mood effects of probiotic bacteria, some of which Brenda and I have discussed here on the blog or in our books. Overall, they call for more research that helps blend the separate pathways that are currently investigating mood disorders on one hand and the intestinal microbiota and fermented foods on the other.

The authors state, “Evidence would suggest that the two major themes of these mostly separate highways of research should converge; in other words, the fermented foods so often included in traditional dietary practices have the potential to influence brain health by virtue of the microbial action that has been applied to the food or beverage, and by the ways in which the fermented food or beverage influences our microbiota . . . The clinical world of mental health involves one where consumption of convenient, high-fat, or high-sugar foods is the norm; these foods, at odds with our evolutionary past, are not only undermining optimal nutritional status, they have untold effects on the microbiome and ultimately the brain.” Well said.

Maybe it’s time to wake up and include fermented yogurt and vegetables as a part of breakfast to start the day. When traveling in Europe, you may notice many hotels have fermented yogurt included on the buffet or as an option to add to breakfast. We would do well to follow this practice here in the United States.



  1. Caplice E and Fitzgerald GF, “Food fermentations: role of microorganisms in food production and preservation.” Int J Food Microbiol. 1999 Sep 15;50(1-2):131-49.
  2. Borresen EC, Henderson AJ, Kumar AJ, et al., “Fermented foods: patented approaches and formulations for nutritional supplementation and health promotion.” Recent Pat Food Nutr Agric. 2012 Aug;4(2):134-40.
  3. Selhub EM, Logan AC, and Bested AC, “Fermented foods, microbiota, and mental health: ancient practice meets nutritional psychiatry.” J Physiol Anthropol. 2014 Jan 15;33(1):2.
  4. Logan AC, Venket Rao A, Irani D, “Chronic fatigue syndrome: lactic acid bacteria may be of therapeutic value.” Med Hypotheses. 2003 Jun;60(6):915-23.
  5. Logan AC and Katzman M, “Major depressive disorder: probiotics may be an adjuvant therapy.” Med Hypotheses. 2005;64(3):533-8.


Leonard Smith, MD

Dr. Leonard Smith is a prominent Board-Certified, general, gastrointestinal and vascular surgeon who had a successful private practice for 25 years. In addition to his active surgery practice, he also incorporated lifestyle, diet, supplementation, exercise, detoxification, and stress management into many of the therapies he would prescribe. Many of his patients with cancer, cardiovascular disease, and other serious illnesses did so well under his treatment regimes that he began to devote most of his career to foundational health care and preventive medicine.