fbpx Skip to content


How Does Diet Affect the Human Microbiome?

| Earn 1 CEC - Take Quiz

Question: I keep hearing about the “human microbiome” and its importance for health. Could you explain how diet affects bacteria in the intestines?

Answer: You have probably heard that you have more microbes (bacteria, fungi, etc.) in and on your body than you have actual human cells. It is shocking to most people, but when you consider the sheer number of microbes, collectively called the microbiota, you realize they must have an impact on your health.

The standard American diet and other Western industrialized diets, high in animal protein and refined carbohydrates, are associated with significantly different and less diverse populations of gut microbes than diets higher in unrefined foods and plants (Graf et al. 2015; Yatsunenko et al. 2012). Western diets are also associated with higher rates of inflammatory diseases, metabolic syndrome, inflammatory bowel disease and some cancers. A different and less diverse microbiota explains some of the difference in disease rates.

To increase and maintain diversity in our microbiota, we need to feed them. What do they eat? Researchers call it “microbiota-accessible carbohydrate” or MAC (Sonnenburg & Sonnenburg 2014). Mostly, that means fiber from plants. We nourish our microbiota with fiber or prebiotics from a variety of vegetables, fruit, legumes, whole grains, nuts and seeds, which also provide phytochemicals and essential vitamins and minerals. It has been known for decades that low-fiber diets are associated with diabetes, heart disease and colorectal cancer. Another way to diversify your gut is to eat fermented foods containing live microorganisms. These foods include kimchi, sauerkraut, kefir, yogurt, cheese, kombucha and miso (Marco et al. 2017).

Keep in mind that we still have a lot to learn about the microbiota, and we may never know if there is an optimal distribution of gut microbes for everyone, much less the foods that create it. Genetics, birth, childhood diet, medications and environment also help to determine what lives in your gut.


Graf, D., et al. 2015. Contribution of diet to the composition of the human gut microbiota. Microbial Ecology in Health & Disease, 26, 26164. doi: 10.3402/mehd.v26.26164.

Marco, M.L., et al., 2017. Health benefits of fermented foods: microbiota and beyond. Current Opinion in Biotechnology, 44, 94–102.

Sonnenburg, E.D., & Sonnenburg, J.L. 2014. Starving our microbial self: The deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metabolism, 20 (5), 779–86. doi: 10.1016/j.cmet.2014.07.003.

Yatsunenko, T., et al. 2012. Human gut microbiome viewed across age and geography. Nature, 486 (7402), 222–27. doi: 10.1038/nature11053.


Concerned about your place in the new fitness industry? We have 40 years of experience supporting pros just like you! Let’s create a new wellness paradigm together—IDEAfit+ is the extra edge you need. Once you team up with IDEA, be sure to take full advantage of all the benefits of membership.

Sanna Delmonico, MS, RDS, CHES

"Sanna Delmonico, MS, RDN, CHE, is an associate professor at the Culinary Institute of America where she teaches food safety and nutrition. She previously led programming for the CIA Healthy Kids Collaborative and the CIA-Harvard Healthy Kitchens, Healthy Lives Continuing Medical Education Conference. Prior to joining the CIA, she was an instructor at Santa Rosa Junior College where she co-coordinated the dietetic technician program. Sanna develops delicious, seasonal recipes and writes about food and nutrition for publications, including IDEA Fitness Journal. She lives in Napa, California, and is a home winemaker."

When you buy something using the retail links in our content, we may earn a small commission. IDEA Health and Fitness Association does not accept money for editorial reviews. Read more about our Terms & Conditions and our Privacy Policy.


Subscribe to our Newsletter

Stay up tp date with our latest news and products.