Exercise Increases Good Gut Bacteria

By Ross Pelton

RPh, PhD, CCN
Scientific Director, Essential Formulas

Ross Pelton is a pharmacist, nutritionist, author and a health educator who is widely recognized as the world’s leading authority on drug-induced nutrient depletions. He was named one of the top 50 most influential pharmacists in the United States by American Druggist magazine for his work in Natural Medicine.

By Ross Pelton, RPh, PhD, CCN
Scientific Director, Essential Formulas

Original Post Date:

December 20, 2021


There is increasing evidence that regular exercise promotes the growth of beneficial bacteria in the colon. This is important because over 99.9% of the probiotic bacteria in the human gut microbiome reside in the colon’s anaerobic (non-oxygen) environment. This is where the vast majority of your all-important postbiotic metabolites are created when your probiotic bacteria ferment the fibers and polyphenols contained in the foods you eat.

An increasing body of scientific evidence indicates that postbiotic metabolites function in multiple ways to promote and regulate your health. Conversely, poor diet and lifestyle factors encourage the growth of harmful bacteria in the microbiome, increasing the risk of heart attacks, strokes, diabetes, autoimmune diseases, and colon cancer.

Two new studies, one in mice and one in humans, report that exercise promotes the growth of beneficial bacteria in your colon and reduces the number of bad ones.

Exercise & Gut Bacteria in Mice

Researchers transplanted material from a group of exercising and sedentary mice into the colons of germ-free mice (mice with no bacteria in their intestinal tract). The germ-free mice developed the same species of colon bacteria that they received from each donor group. Recipient mice that received fecal samples from the exercising mice developed much higher levels of beneficial bacteria that produce high levels of short-chain fatty acids, which are known to help promote healthy cholesterol levels and provide other important health benefits.(1)

The recipient mice were then given a chemical that causes irritation and damage in the intestinal tract. Mice that received bacteria from the exercising mice had far less damage to cells lining the colon, and exhibited much faster recovery times than those who had received bacteria from the sedentary mice.

Exercise & Gut Bacteria in Humans

Investigators monitored 18 lean and 14 obese female subjects in a supervised, endurance-based exercise program for 30 to 60 minutes, three days/week for six weeks. They were then instructed not to exercise for six weeks. After six weeks of exercise, both the lean and obese subjects increased the number of beneficial colon bacteria that produce short-chain fatty acids, which are known to provides a number of important health benefits 

The lean subjects had the most significant increase in good bacteria after exercising, while the obese subjects had a more modest increase in good bacteria. Also, it was revealed that the exercise-induced changes in the microbiota were reversed once exercise training was discontinued.(2) 

These studies add to the body of scientific studies that indicate that regular exercise is a vital lifestyle factor contributing to maintaining a healthy microbiome.


i Allen JM. The effects of exercise training on the gut microbiota, microbial metabolites and microbial-host interactions in mice and humans. 2017. https://www.ideals.illinois.edu/handle/2142/97726
ii Allen JM, et al. Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans. Med Sci Sports Exerc. 2018 Apr;50(4):747-757.

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By Ross Pelton, RPh, PhD, CCN
Scientific Director, Essential Formulas

Ross Pelton is a pharmacist, nutritionist, author and a health educator who is widely recognized as the world’s leading authority on drug-induced nutrient depletions. He was named one of the top 50 most influential pharmacists in the United States by American Druggist magazine for his work in Natural Medicine.

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