Fermented Foods — Benefits Deep Dive

Fermented foods — sauerkraut, kimchi, kefir, kombucha, yogurt, miso, natto, tempeh, kvass — are “foods made through desired microbial growth and enzymatic conversions of food components”, in the definition of a 2021 expert panel of the International Scientific Association for Probiotics and Prebiotics (ISAPP). The panel notes that they have been eaten for thousands of years, that fermentation would have been regarded as one of the most effective ways to preserve food, and that fermented foods were adopted by nearly every culture worldwide. Many fermented foods contain living microorganisms, some genetically similar to strains used as probiotics, along with compounds formed during fermentation, such as organic acids, bacteriocins, vitamins and, for particular microbes, gamma-aminobutyric acid (GABA). The 2021 Wastyk et al. Stanford trial published in Cell assigned 39 healthy adults to a high-fiber or a high-fermented-food diet over a 17-week protocol. Fermented-food intake, built up to about six servings a day, steadily increased microbiome diversity (the high-fiber diet did not) and decreased 19 of 93 measured inflammatory proteins, including IL-6; the trial’s primary outcome, a cytokine response score, did not change. The four deep-dive pages below cover the diversity findings, the immune and inflammatory markers, the microbes found in each ferment, and the cultural history of food fermentation.

Deep-Dive Articles

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Gut Microbiome Diversity

The 2021 Wastyk Stanford trial published in Cell — 39 healthy adults, a 17-week protocol, fermented-food intake built up to about six servings a day — in which the fermented-food diet steadily increased alpha-diversity and the high-fiber diet did not. The mechanisms proposed by the ISAPP consensus panel, how fermented foods differ from probiotic capsules, and what the research shows about colonization.

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Immune Function

The 19 of 93 measured inflammatory proteins that fell in the fermented-food arm of the Wastyk trial, including IL-6, IL-10 and IL-12b, and the gut-immune axis. Folk uses of fermented foods in traditional cultures, and the short-chain fatty acid, regulatory T cell and IgA pathways the page describes.

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Probiotic Strains

Lactobacillus plantarum, L. brevis, L. fermentum, Bifidobacterium, Streptococcus thermophilus, Lactococcus lactis, Leuconostoc, Saccharomyces boulardii, and Bacillus subtilis — which species lives in which food, survival through stomach acid, what the research shows about transient versus lasting colonization, and the difference between live-culture ferments and heat-treated or pasteurized versions.

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History and Cultures

Sauerkraut, kimchi (including the Korean kimjang tradition of making and sharing kimchi, inscribed on UNESCO’s intangible cultural heritage list in 2013), kefir, kombucha, miso, natto, tempeh, kvass, and lacto-fermented vegetables worldwide. Where each tradition comes from, why fermentation spread to nearly every culture, its role in making food keep longer, and how fermented-food eating changed in industrialized diets.

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Table of Contents

  1. Deep-Dive Articles
  2. Why Fermented Foods Produce Effects
  3. Research Papers: Microbiome Diversity
  4. Research Papers: Immune & Inflammatory Effects
  5. Research Papers: Probiotic Strains
  6. Research Papers: Postbiotics (SCFAs, K2, GABA)
  7. Research Papers: Traditional Foods & Cultures
  8. External Authoritative Resources
  9. Connections
  10. Featured Videos

Why Fermented Foods Produce Effects

The 2021 ISAPP consensus statement on fermented foods proposes several ways these foods could benefit health: nutritive alteration of the raw ingredients and the making of bioactive compounds, modification of the gut microbiota, and effects on the immune system. The same panel states that hypothesis-driven research on how fermented foods affect human physiology is limited. The routes it describes:

  1. Live microorganisms — multiple studies in humans have shown that microorganisms in fermented foods can survive gastric transit and reach the colon, and many fermented foods with live and active cultures, such as yogurt or kefir, contain up to 1011 lactic acid bacteria in a single serving. Depending on diet, these bacteria can transiently make up between 0.1% and 1% of the bacteria in the large intestine. The panel describes them as unlikely to maintain long-term residence, but some are metabolically active in the gut, and short-term colonization could be enough to make bioactive compounds, inhibit intestinal pathogens and act on the gut lining (for example, through Toll-like receptors). The species depend on the ferment (see the Probiotic Strains deep-dive).
  2. Compounds formed during fermentation — the panel lists organic acids such as lactic and acetic acid, vitamins, amino acid derivatives and cofactors, and, for microbes with specific enzymes, gamma-aminobutyric acid (GABA) and conjugated linoleic acid. Many lactic acid bacteria make bacteriocins that inhibit undesirable bacteria, including Listeria, Staphylococcus and Clostridium. Histamine, tyramine and other biogenic amines can also form during the fermentation of cheese, meats, vegetables, soybeans and wine. Microbial cell components such as peptidoglycan and exopolysaccharides are immune reactive in animal and in vitro studies, and a separate ISAPP panel defines a postbiotic as a “preparation of inanimate microorganisms and/or their components that confers a health benefit on the host”.
  3. Prebiotic substrates — prebiotics have been reported in several fermented foods, including fermented grains and vegetables, and exopolysaccharides with prebiotic activity can form during dairy and cereal fermentations.
  4. Transformed nutrients — fermentation can lower certain sugars (for example, lactose in dairy foods, and raffinose, stachyose and verbascose in soybeans and legumes) and can break down proteins, fats and polysaccharides. During sourdough fermentation some lactic acid bacteria degrade phytate, which the panel links to better calcium, magnesium, iron and zinc bioavailability from those breads. Natto, made from whole soybeans, is fermented by Bacillus subtilis; a 1987 study described a strong fibrinolytic (fibrin-digesting) activity in natto and named the enzyme nattokinase.

In the Wastyk 2021 Stanford trial, the fermented-food diet steadily raised microbiome diversity while the high-fiber diet did not, and 19 of 93 measured inflammatory proteins fell in the fermented-food arm. Only a small share of the new microbial variants that appeared in participants matched those in the foods (the overlap peaked early, at 5.4%), and the authors concluded that the diversity increase “was not primarily due to consumed microbes, but rather a result of shifts in or new acquisitions to the resident community”, an indirect effect of fermented-food intake. The trial was small (18 people per arm in the abstract) and enrolled healthy adults only.

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Research Papers: Microbiome Diversity

  1. Wastyk HC et al. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell 184(16):4137-4153.e14. — PubMed PMID: 34256014
  2. Sonnenburg ED, Sonnenburg JL (2014). Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metabolism 20(5):779-786. — PubMed PMID: 25156449
  3. Alpha-diversity and disease risk: meta-analysis of gut microbiome diversity across conditions — PubMed: Alpha-diversity meta-analysis
  4. Marco ML et al. (2017). Health benefits of fermented foods: microbiota and beyond. Current Opinion in Biotechnology 44:94-102. — PubMed PMID: 27998788
  5. Marco ML et al. (2021). The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol 18(3):196-208. — PubMed PMID: 33398112
  6. Fiber vs fermented foods: comparing dietary strategies for microbiome modulation — PubMed: Fiber vs ferments
  7. David LA et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature 505(7484):559-563. — PubMed PMID: 24336217
  8. Yatsunenko T et al. (2012). Human gut microbiome viewed across age and geography. Nature 486(7402):222-227. — PubMed PMID: 22699611
  9. Schnorr SL et al. (2014). Gut microbiome of the Hadza hunter-gatherers. Nature Communications 5:3654. — PubMed PMID: 24736369

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Research Papers: Immune & Inflammatory Effects

  1. Wastyk HC et al. (2021). Gut-microbiota-targeted diets modulate human immune status (inflammatory-protein results). Cell 184(16):4137-4153.e14. — PubMed PMID: 34256014
  2. IL-6 and chronic low-grade inflammation in metabolic syndrome — PubMed: IL-6 inflammaging
  3. Short-chain fatty acids and regulatory T cell induction — PubMed: SCFA Treg induction
  4. Bacteriocins from lactic acid bacteria: antimicrobial and immunomodulatory effects — PubMed: Bacteriocins
  5. Kimchi consumption and inflammatory markers in Korean adults — PubMed: Kimchi and inflammation
  6. Yogurt consumption and inflammatory biomarkers: systematic review — PubMed: Yogurt inflammation

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Research Papers: Probiotic Strains

  1. Lactobacillus plantarum and human health: comprehensive review — PubMed: L. plantarum review
  2. Bifidobacterium species and colonic health — PubMed: Bifidobacterium review
  3. Survival of probiotic bacteria through the gastric environment — PubMed: Gastric survival
  4. Zmora N et al. (2018). Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174(6):1388-1405.e21. — PubMed PMID: 30193112
  5. Saccharomyces boulardii in antibiotic-associated diarrhea — PubMed: S. boulardii AAD
  6. Kefir microbiology: the polymicrobial grain consortium — PubMed: Kefir grain microbiology

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Research Papers: Postbiotics (SCFAs, K2, GABA)

  1. Salminen S et al. (2021). The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nat Rev Gastroenterol Hepatol 18(9):649-667. — PubMed PMID: 33948025
  2. Geleijnse JM et al. (2004). Dietary intake of menaquinone is associated with a reduced risk of coronary heart disease: the Rotterdam Study. J Nutr 134(11):3100-3105. — PubMed PMID: 15514282
  3. Sumi H et al. (1987). A novel fibrinolytic enzyme (nattokinase) in the vegetable cheese Natto; a typical and popular soybean food in the Japanese diet. Experientia 43(10):1110-1111. — PubMed PMID: 3478223
  4. GABA production by Lactobacillus brevis in fermented vegetables — PubMed: GABA in ferments
  5. Butyrate and colonocyte energy: short-chain fatty acid mechanism — PubMed: Butyrate colonocyte
  6. Exopolysaccharides from lactic acid bacteria and immunomodulation — PubMed: EPS immunomodulation

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Research Papers: Traditional Foods & Cultures

  1. Kimchi: Korean traditional fermented vegetable health benefits and microbiology — PubMed: Kimchi health
  2. Sauerkraut: phytochemistry and probiotic content of traditional cabbage ferments — PubMed: Sauerkraut
  3. Kefir: traditional Caucasus fermented dairy beverage and health effects — PubMed: Kefir history
  4. Tempeh: Indonesian traditional soybean fermentation by Rhizopus — PubMed: Tempeh microbiology
  5. Loss of fermented foods in Western industrial diet: epidemiologic perspective — PubMed: Industrial diet loss
  6. Anthropological evidence for fermentation as a universal human cultural practice — PubMed: Fermentation anthropology

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External Authoritative Resources

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Connections

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