I believe we need to eat plenty of microbes to be healthy, an idea I call the umami hypothesis. I have blogged about it many times. Here is an overview of those posts.
1. Psychological. We like foods with sour, umami, and complex tastes/flavors. My evolutionary explanation: these preferences increased microbe intake, which increased health. Fermentation, which increases microbes, easily produces all three of these characteristics. They are not easily produced otherwise (in the absence of lemon trees). As a result, until recently these three characteristics were correlated with the microbe content of food. For example, until recently, the more sour a food, the more microbes. Seeking out sourness caused us to eat foods with more microbes. It’s easy to see this correlation today. As milk becomes yogurt, it becomes more sour and more microbe-rich at the same time. As juice becomes vinegar, same thing. The Chinese character for sour connects it with fermentation. As meat ages, it gets a stronger umami flavor and becomes more microbe-rich. For example, umami in dry-cured hams increases with time. Umami flavor is produced by glutamate molecules. They increase in concentration when proteins break down into components. Nowadays meat is aged because it tastes better aged than fresh. The flavor improvement with age presumably caused our ancestors to age their meat. Microbes add complexity to flavor because they produce many byproducts. Many experiments support the idea that our food preferences are a guide to what we should eat. When children chose their own food, they turned out very healthy.
2. Food traditions. Fermented foods are found in huge variety in a wide range of culinary traditions. Sour fish soup. Aged cookie dough. This suggests they taste good for genetic reasons. Animals appear to like fermented foods — more evidence that this preference has an ancient genetic basis rather than a recent cultural one. Fermented oat husks. Eskimos eat “rotten” fish.
3. Benefits of probiotics (experimental evidence). Many experiments have found that children or adults given probiotics fare better than a control group. Irritable bowel syndrome (IBS). Competitive cyclists — men benefited but women didn’t. Probiotics help Italian children with IBS. Probiotics reduce ventilator-associated pneumonia. Probiotics help preterm infants ward off necrotizing enterocolitis — reducing the death rate by more than half. Cheese with added bacteria stimulated the immune system of elderly subjects. A probiotic reduces sick days among employees of a large company. Probiotics reduce diarrhea and C. difficile infection among hospital patients. Probiotics prevented colds in children. Probiotics reduce/prevent diarrhea caused by antibiotics.
4. Benefits of fermented food (experimental evidence). An experiment found a big protective effect of Vitamin K2, which is found in much larger amounts in fermented foods than other foods. An experiment found that fermented bean paste is more protective against cancer when it is fermented longer. A review article about the anti-allergic effects of fermented foods. A book about the benefits of fermented foods cites hundreds of experimental studies. Fermented noni juice fights cancer in rats, apparently because it stimulated the immune system. Benefits of natto.
5. Hormesis. Small amounts of many “poisons” — chemicals or radiation in large amounts will kill you — produce big health improvements, especially less cancer. The usual explanation is that the small amounts of poison activate repair systems. The benefits of probiotics are easy to understand if the microbes in fermented foods activate the immune system. Introduction to radiation hormesis. Small amounts of radiation activate DNA repair. Moderate radon exposure associated with less lung cancer. Mortality of atomic bomb survivors in Hiroshima and Nagasaki. The Baltimore shipyard study. The implausibility of hormesis and more examples. Reviews of the vast evidence.
6. Bad effects of antibiotics. Fermented foods add microbes inside the body, antibiotics reduce them. Antibiotic use associated with higher risk of later infection. Mosquitos made microbe-free via antibiotics are more susceptible to infection than untreated mosquitos.
7. The Hygiene Hypothesis. The hygiene hypothesis is that exposure to dirt in childhood reduces childhood asthma and allergies. The author’s original idea was that the dirt caused infections. That didn’t seem to be true but many studies have found that living on a farm and similar experiences reduce childhood asthma and allergies. This supports the general idea that exposure to microbes improves immune function. Asthma and farm life. Maternal exposure to farms helps babies. Less allergic disorders among children in a polluted German city than in a clean one. Benefits from biodiversity around the house where you grow up. Review of the hygiene hypothesis. What was wrong with the original proposal.
8. Epidemiology. Many studies have found that people who eat specific fermented foods are healthier. Benefits of moderate drinking. Yogurt consumption associated with less allergies in Japanese schoolchildren. The later in life your family gets a refrigerator, the lower your chances of getting Crohn’s disease. Refrigeration reduces microbial growth.
9. N=1. Cases in which fermented foods improved one person’s health. Kombucha. Do fermented foods shorten colds? High-dose probiotic, but not several fermented foods, eliminated exercise-induced asthma. Kombucha eliminated heartburn. Probiotics cure extreme coughing fits in a young girl. Kefir improves digestion disrupted by antibiotics. Yogurt apparently reduces how long colds last. Yogurt reduces seasonal allergies. A four-year-old gets sick less often after she starts eating more yogurt. After eating lots of yogurt and acidophilus pearls, sinus congestion greatly reduced. Soon after a big increase in fermented food and probiotic consumption, sinus congestion went down 90%. Kombucha improves bee health. Acid reflux cured by kombucha. Stonyfield yogurt employee gets sick less often, maybe because she is eating much more yogurt. Professor of immunology starts taking probiotic and yogurt, stops needing asthma inhaler.
10. Unusual remedies. Several unusual remedies produce effects inside the body similar or identical to the effects of fermented foods. Bee stings. Hookworm infection (also here). After parasites greatly reduced on a remote island, allergies greatly increase.
11. The importance of gut bacteria. They must come from outside — our bodies do not make them. They protect us against disease. Japanese but not Americans have gut bacteria that digest seaweed. Babies with diaper rash had less diverse fecal bacteria than babies without diaper rash. William Parker, a professor of medicine, has proposed that the evolutionary reason for our appendix is that to allows quick repopulation of gut bacteria when they are lost due to diarrhea.
12. Miscellaneous. High fermented-food consumption in Japan, the healthiest country in the world. Japanese men who smoke have considerably less lung cancer than American men who smoke the same amount. Filthy socks smell like kimchi, in spite of vastly different bacteria, suggesting the existence of a detection system that lumps different bacteria together. Benefits of bacteria found in soil. The value of readiness in another domain (military). The health benefits of smoking. Bacteria-free mice have malfunctioning immune systems. Irradiated food (irradiated enough to kill microbes) makes cats sick. Wild mice with more parasites have better functioning immune systems. Analogy with pagophagia (ice chewing).
Disagreement with my view includes the following. To prevent asthma you should avoid all triggers, says one group. Health claims for probiotics were dismissed by scientists at the European Food Safety Agency. A UCLA professor of medicine who specializes in infectious disease says we “will have to” produce more antibiotics to reduce infectious disease. According to one writer, all “modern sane eating guidelines” say “fresh is better”.