The world of microbes that ferment foods such as sauerkraut, kimchi, and kefir are truly a strange and wonderful thing. Unlike our favorite microbe of all, Lactobacillus reuteri, that ferments at human body temperature, here I am focusing primarily on microbes that ferment at room temperature. Human body temperature-fermenting species such as L. reuteri, L. gasseri, and B. longum were meant to be obtained by passage through the vaginal canal at birth, suckling at your mother’s breast during breastfeeding, contact with your mother and other humans with whom you are intimate, microbes largely lost due to our over-exposure to antibiotics as well as other factors such as glyphosate, stomach acid-blocking drugs, preservatives and emulsifying agents in food, and others. On the other hand, microbial species that ferment at room temperature are meant to be obtained via consuming wild plants, meats and other foods that undergo the natural process of fermentation.

Species such as Leuconostoc mesenteroides, Pediococcus pentosaceus, Pediococcus acidilactici, Lactobacillus plantarum, various Weisella species and others are normally resident on the surface of plants such as eggplant and tomatoes. They are therefore ubiquitous, colonizing plant surfaces everywhere. Touch a red pepper and you have touched some Leuconostoc or Weisella. You consume them when, for instance, you eat a salad containing lettuce, tomatoes, and cucumbers. You also kill them when you heat, for example, tomatoes to make tomato sauce or steam some leaves of spinach. Deprive them of oxygen and they proliferate to high numbers over time, consuming the carbohydrates and sugars contained in the plant.

We are therefore in constant contact with such microbes, though at relatively low numbers. We can increase our exposure through fermentation, i.e., allowing these species to proliferate in an anaerobic (without air or oxygen) environment. Curiously, most of these bacterial (and some fungal) species are only transient residents of the human gastrointestinal (GI) tract, passing through from mouth to anus without taking up residence. So how can they play a role in human health, gastrointestinal and otherwise?

Fermentation has been a part of the human diet for thousands of generations, surely discovered by accident that proved to be a fortuitous way to preserve foods long before refrigeration became available. How else would a family preserve produce or meats through a long winter, for instance, unless microbes came to the rescue, proliferated in the food and keeping pathogens such as Staphylococcus aureus, E. coli, Listeria and various molds and fungi from taking up residence to cause rot?

Thanks to recent research, especially the groundbreaking work of husband/wife team, Justin and Erica Sonnenburg of Stanford, fermenting microbial species, while not taking up residence in the human GI tract, cultivate the proliferation of other bacterial species that play important roles in the human GI microbiome. Consume some kimchi or kefir, for instance, and species such as Faecalibacterium prausnitizii, Akkermansia muciniphila, and Clostridium butyricum proliferate, species crucial for GI and overall health. Cause these species to proliferate and they:

• Compete and thereby suppress proliferation of pathogens, including those that ascend up from the colon (fecal species) and that are swallowed from the mouth. (Recall that the mouth is second only to the colon in the density of microbes dwelling in that ecosystem.)
• Produce beneficial metabolites–Especially butyric acid that both nourish intestinal cells as well as enter the bloodstream to be exported to other parts of the body, mediating effects such as reduced blood pressure, reduced insulin resistance and blood sugar, reduced fatty liver, deeper sleep, better skin health, better mental health.
• Inhibit bacterial and fungal translocation–This is an emerging and exciting issue, the idea that microbes in the GI tract can migrate to other parts of the body to exert both beneficial and harmful effects. The species Fusobacterium nucleatum, for example, if allowed to colonize the colon from the mouth, is now believed to be a major cause of colon cancer. (Yes: risk for colon cancer begins in the mouth.) Lactobacillus crispatus that originates in a woman’s vaginal microbiome can be transmitted to a male sexual partner where it translocates to the prostate where it can reduce the potential for prostate disease. Fungal species, such as various Candida species and Malasezzia, overproliferate in the GI tract and translocate to the brain where they can be found at high numbers in people with dementia.

Frequent ingestion of fermenting microbes through foods such as yogurts (that you make yourself, not the anemic products sold in supermarkets), kefir, kimchi, sauerkraut and other fermented veggies are among the most important practices that you can follow to cultivate a return to a healthy GI microbiome that has been disrupted by modern life. My current favorite: Bacillus subtilis, a ubiquitous microbe found in soil, the surfaces of plants, and in the human GI tract that is a spectacular producer of bacteriocins, natural antibiotics effective in killing a broad spectrum of both Gram-negative (e.g., E. coli, Salmonella, Campylobacter) and Gram-positive (e.g., Staphylococcus, Streptococcus, Enterococcus) species, species that overproliferate in colonic dysbiosis and in small intestinal bacterial overgrowth, SIBO. B. subtilis is a vigorous producer of carbon dioxide, so I’ve been making fermented fruit juices that are wildly effervescent and delicious, reducing the high sugar content of juices to negligible levels when fermented for around 60 hours at 90°F.

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