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Live Microbes Intake Linked with Better Health

    Microbes, yogurt, berries, milk, dairy food

    Written by: Alice Callahan, PhD | Issue # 114 | 2023

    • Previous research has focused on probiotic supplements or fermented foods, with little work on total dietary microorganisms and human health.
    • Researchers classified foods as being low, medium, or high in live microorganisms and estimated the overall amounts of microbes in people’s diets.
    • In a U.S. sample, people who consumed more live microbes had better markers of cardiometabolic health; more research is needed to determine if the relationship is causal.

    If you’ve given much thought to the healthfulness of your diet, you may have considered how many grams of protein or fiber you consume, or how many servings of fruits and vegetables you eat each day. But have you ever stopped to wonder how many living microbes are on your plate?

    It’s a question worth pondering, given that we live in a world teeming with microbes, trillions of which live on our bodies and within our gastrointestinal tracts—making up our microbiomes. Over the last several decades, more and more research has revealed the complex interactions between the microbiome and human health. And while there have been many studies on the effects of probiotic supplements and a smaller number on fermented foods, there has so far been little attention paid to the amounts of living microbes in our overall diets.

    Recently, an international group of scientists set out to change this, testing an overarching hypothesis that a dietary pattern that includes more live microbes is associated with better health [1]. Led by researchers at the University of California, Davis, University College Cork in Ireland, and the International Scientific Association for Probiotics and Prebiotics, the group worked to first develop a system of classifying foods as containing low, medium, and high numbers of live microorganisms, including bacteria, yeasts, and molds [2]. From there, they were able to estimate people’s total microbial intake from dietary records and look for associations with health outcomes, said Dan Tancredi, a statistician at UC Davis who was part of the team [3].

    “Despite the obvious public health benefits that more hygienic foods and environments provide, there may also be unforeseen negative health consequences as a result of these reductions in microbial exposures,” the researchers wrote in an opinion paper published in The Journal of Nutrition in 2020 [1], suggesting that our more sterile diets may have contributed to a shift in our gut microbiota that has coincided with the rise in chronic immune, metabolic, and other “lifestyle” diseases prevalent in the industrialized world [4].

    In 2022, the group published their system for classifying foods based on live microbe levels, along with an analysis of dietary records from 74,466 children and adults in the United States who participated in the National Health and Nutrition Examination Survey (NHANES) between 2001 and 2018 [2]. NHANES is a nationally representative survey of Americans that includes an in-person interview to capture participants’ dietary intakes, as well as a range of health assessments collected at mobile clinics [5].

    In the food classification scheme, the high-microbe food category included fermented foods, mostly dairy products such as yogurt, buttermilk, kefir, sour cream, and most cheeses. Medium-microbe foods included fresh vegetables, fruits, and fruit juices, which can acquire microorganisms during cultivation, harvest, and other steps in the supply chain. Most food items were classified as being low in live microbes, including foods that are generally cooked or heat-treated before consumption, such as milk, meat, poultry, seafood, sauces, gravies, and pasta.

    The researchers found that vegetables, fruits, and dairy products contributed most of the living microorganisms found in the diets of NHANES participants. On average, only about 5% of adult participants’ caloric consumption came from foods with medium to high levels of live microbes.

    In the group’s most recent study [3], published online in the Journal of Nutrition in February, they looked at associations between live microbe intake and several health parameters, again using data from NHANES collected between 2001 and 2018. Overall, they found that people who consumed more foods containing live microbes had lower systolic blood pressure, waist circumference, body mass index, and blood levels of glucose, insulin, triglycerides, and C-reactive protein, a marker of inflammation. They also had greater high-density lipoprotein, which is associated with lower risk of heart disease and stroke. The researchers reported similar positive associations for fermented food intake. Their analyses included adjustment for age, sex, ethnicity, poverty incomes ratios, physical activity, smoking status, alcohol intake, and body mass index.

    In other words, people who regularly ate more fermented foods or other foods containing live microorganisms appeared to be healthier. The study did not assess intake of probiotic supplements, because relatively few NHANES participants consumed them, and the researchers wanted to focus on the dietary contribution of live microorganisms, Tancredi said.

    The researchers estimated that people who ate 400 grams more of live microbe-containing foods (such as one serving each of yogurt, fruit, and vegetables) and 400 grams less of highly processed or heat-treated foods would be expected to have 1 to 4 mm Hg lower systolic blood pressure and waistlines that were two-thirds to two inches smaller.

    But this type of observational research has some inherent limitations, Tancredi emphasized. “We can’t unambiguously attribute the [live microbe] intakes with better outcomes in terms of cause and effect,” he said. People who eat more of foods like yogurt, fruit, and vegetables, might lead healthier lives in ways that weren’t accounted for in the study, such as getting more sleep or having less stress, or have other advantages, such as greater access to fresh foods. Plus, the same foods that contain live microbes may improve health through other mechanisms, such as nutrients, fiber, or phytochemicals.

    Much more research is needed, ideally randomized controlled trials that would include interventions to increase intake of live microbes and measure subsequent health effects, Tancredi said. “There’s a lot we don’t know and need to find out,” he added.

    That said, there’s plenty of evidence to support health benefits of eating fresh fruits and vegetables. And several recent randomized controlled trials have demonstrated that including yogurt or other fermented foods in your daily diet can reduce inflammation [6], improve gut microbiota diversity [7], and even reduce stress [8]. So, while we watch as more microbiome science emerges, it may be worthwhile to think of our meals as more than foods, nutrients, or fuel—but also microbial parties on our plates.


    1. Marco ML, Hill C, Hutkins R, Slavin J, Tancredi DJ, Merenstein D, Sanders ME. Should there be a recommended daily intake of microbes? Journal of Nutrition. 2020 Dec 150 (12):3061–7.
    2. Marco ML, Hutkins R, Hill C, Fulgoni VL, Cifelli CJ, Gahche J, Slavin JL, Merenstein D, Tancredi DJ, Sanders ME. A classification system for defining and estimating dietary intake of live microbes in US adults and children. Journal of Nutrition. 2022 Jul 152(7):1729–36.
    3. Hill C, Tancredi DJ, Cifelli CJ, Slavin JL, Gahche J, Marco ML, Hutkins R, Fulgoni VL, Merenstein D, Sanders ME. Positive health outcomes associated with live microbe intake from foods, including fermented foods, assessed using the NHANES database. Journal of Nutrition. 2023 Feb 22:S0022-3166(23)12622-8.
    4. Sonnenburg ED, Sonnenburg JL. The ancestral and industrialized gut microbiota and implications for human health. Nature Reviews Microbiology. 2019 May 17:383–90.
    5. Centers for Disease Control and Prevention (CDC). National Center for Health Statistics (NCHS). NHANES – About the National Health and Nutrition Examination Survey. Hyattsville, MD: U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, 2002,
    6. Pei R, DiMarco DM, Putt KK, Martin DA, Gu Q, Chitchumroonchokchai C, White HM, Scarlett CO, Bruno RS, Bolling BW. Low-fat yogurt consumption reduces biomarkers of chronic inflammation and inhibits markers of endotoxin exposure in healthy premenopausal women: a randomised controlled trial. British Journal of Nutrition. 2017 Dec 118(12):1043–51.
    7. Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Feiqiao BY, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021 Aug 184(16):4137-4153.e14.
    8. Berding K, Bastiaanssen TFS, Moloney GM, Boscaini S, Strain CR, Anesi A, Long-Smith C, Mattivi F, Stanton C, Clarke G, Dinan T, Cryan JF. Feed your microbes to deal with stress: a psychobiotic diet impacts microbial stability and perceived stress in a healthy adult population. Molecular Psychiatry. 2022 Oct 28:601–10.

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