Although both diet and medications together have been documented to be the main exogenous factor that modulates the gut microbiota composition and functional diversity, previous research in professional athletes has found that physical activity status correlates with gut microbiota composition. However, no intervention studies have yet been investigated the effects of endurance-based exercise training on the composition, functional capacity and gut microbial metabolites.

A new study, led by Dr. Jeffrey Woods from the Department of Kinesiology and Community Health and Division of Nutritional Sciences at the University of Illinois at Urbana-Champaign (Urbana, Illinois), has found that exercise training induces both compositional and functional changes in the human gut microbiota that are independent of diet and related to the maintenance of exercise.

The researchers enrolled 18 lean and 14 obese sedentary adults and started them on an exercise program during which they performed supervised cardiovascular exercise -which progressed from moderate (60% of heart rate reserve) to vigorous intensity (75% of heart rate reserve)- for 30-60 minutes/day three times a week for 6 weeks. Their faecal samples for gut microbiome analysis were collected before and after 6 weeks of exercise, as well as after another 6 weeks of sedentary behaviour (washout period). On the whole, in this longitudinal study changes in the composition of the gut microbiota were tracked in participants as they changed from a sedentary lifestyle to a more active one and back again to a sedentary state.

Participants’ usual diets were maintained during the whole study. Besides diet, the researchers controlled for other factors that transiently affect the gut microbiota including obesity status and antibiotic use.

Exercise training increased faecal concentrations of the three most abundant short-chain fatty acids (SCFAs), acetate, propionate and butyrate in lean participants -the effect was dependent on body mass index as the change in both acetate and butyrate was observed primarily in the lean participants. Interestingly, exercise-related changes in microbial metabolites correlated with changes in the proportion of SCFA-producing taxa (Faecalibacterium spp. and Lachnospira spp.) and levels of acetate Coenzyme A (CoA) transferase gene (BcoAT) -a gene involved in regulating butyrate production- that were more substantial in lean versus obese participants. Indeed, exercise-induced increases in faecal BcoAT and SCFA levels also strongly paralleled increases in lean mass. However, their levels decreased again once exercise training finished.

In a second study in mice, the same researchers transplanted cecal contents from exercised (n= 19) and sedentary (n = 10) mice into the colon of sedentary germ-free (GF) mice. As happened with the previous longitudinal study in humans, GF mouse recipients of the exercised mouse microbiota exhibited a higher proportion of butyrate-producing taxa. In a second experimental cohort of GF mice colonized by the exercised-gut microbiota and then treated with dextran-sodium-sulfate, gut microbiota transfer from exercise-trained mice led to altered gut microbiota composition, increased anti-inflammatory gene expression and attenuated histological parameters in colons of recipient mice -which was evidenced by reduced colon shortening, attenuated mucus depletion and increased expression of cytokines involved in tissue regeneration.

In conclusion, the findings in the human study suggest that exercise training induces compositional and functional changes in the gut microbiome that relies on obesity status and the sustainment of exercise but are independent of diet. Regarding the mouse study, these data show that exercise-induced modifications in the gut microbiota can directly affect host responses to gut microbiota colonization and chemically-induced colitis. Further research is needed in order to depict a clear picture regarding diet-exercise-host interactions.

According to Prof. Jeffrey Woods: “These are the first studies to show that exercise can have an effect on your gut independent of diet or other factors.” He adds, “The bottom line is that there are clear differences in how the microbiome of somebody who is obese versus somebody who is lean responds to exercise. We have more work to do to determine why that is.”




Allen JM, Mailing LJ, Niemiro GM, et al. Exercise alters gut microbiota composition and function in lean and obese humans. Med Sci Sports Exerc. 2017; doi: 10.1249/MSS.0000000000001495.

Allen JM, Mailing LJ, Cohrs J, et al. Exercise training-induced modification of the gut microbiota persists after microbiota colonization and attenuates the response to chemically-induced colitis in gnotobiotic mice. Gut Microbes. 2017; 1-16. doi: 10.1080/19490976.2017.1372077.