Physical exercise is one of the most effective ways to achieve a healthy life. Exercise exerts beneficial effects on practically every organ and every aspect of your physiology. And now, new research is coming out that is exploring the relationship between the gut microbiome and exercise.

The gut microbiome comprises an enormous number of microbes and their genes that reside in your intestinal tract.

Weighing around 2 kg, your gut microbiome is both genetically and metabolically a powerhouse – consisting of over a thousand different microbial types and representing over three million unique genes.

microbiome fact infographic

A lot of recent scientific evidence shows the microbial composition of your intestine is indeed a very strong determinant of health, behavior and disease.

Scientists have been learning more and more about the well-established effects of exercise and the gut microbiome on health. And in recent years, scientists sought to answer two emerging questions:

  • How does the gut microbiome affect exercise motivation and performance?
  • How does physical exercise affect the gut microbiome of the host?

For the first question, we have a great article that goes into a lot of the research used to uncover the answer.

And in this article, we will see what science tells us about how exercise can affect our gut microbiome.

Specifically, we will look at three levels of data to answer this question, and we will discuss the potential mechanisms by which exercise is considered to alter the gut microbiome.

Article table of contents:

Physical exercise and effects on the gut microbiome: Animal studies

Physical exercise and effects on the gut microbiome: Human studies

Cross-sectional and longitudinal studies

Cross-sectional studies in humans

Longitudinal studies in humans

Potential mechanisms explaining exercise induced changes in the gut microbiome

Is there such a thing as too much exercise?

The take-home message


Physical exercise and effects on the gut microbiome: Animal studies

A research group in Japan, Megumi Matsumoto and colleagues were one of the first teams of scientists who showed, using rats, that a 5-week regimen of voluntary wheel running changed the gut microbiome composition compared to a sedentary lifestyle.

Further, the gut microbial metabolite butyrate was also increased in rats that exercised.

exercise and the gut microbiome - mouse study showing how a mouse exercises and it changes the gut microbiome profile.

To put things in perspective, butyrate is a short chain fatty acid (SCFA). SCFAs are considered metabolites produced by beneficial microbes in the gut, and these molecules mediate many of the positive effects of the gut microbiome on its host’s physiology.

Later studies from other research groups across the world have corroborated these findings. Indeed, exercise appears to alter the gut microbiome in lab animals in a way that increases the production of butyrate in the gut.

However, data from lab animals do have their limitations.

For instance, inconsistencies exist in the subjects in terms of diet, cage conditions, physical activity regimen, genetics, age, etc.

Also, very importantly, results from animal experiments may or may not be relevant to humans.

Because of this, using these findings from lab animals as a hypothetical steppingstone, scientists have tried to find similar observations in humans.

Here is what they’ve found.

Physical exercise and effects on the gut microbiome: Human studies

For a long time, scientists wanted to determine the effect of physical exercise on gut microbiota composition. For such analyses where the effect of one parameter on another parameter is studied, there are two approaches: cross-sectional and longitudinal methods.

Cross-sectional and longitudinal studies

In cross-sectional studies, data is collected from a pre-determined population at a specific time point.

Whereas with longitudinal studies, data is collected from the same study population regularly, at various time points.

This gives longitudinal studies more importance compared to cross-sectional data.

The importance of longitudinal studies is due to the fact that data on a specific parameter are collected at multiple time points, which gives the analysis more depth. This is because the collected data points are numerous, as opposed to just one in cross-sectional analyses.

Further, since the data are collected regularly from the same population, this eliminates any population-related variables that might influence the analysis.

Nevertheless, the first evidences about the effects of physical exercise on the gut microbiome came from cross-sectional studies.

list of some things that positively change in the gut microbiome after routine exercise

Cross-sectional studies in humans

A team of scientists in Ireland published their research in the journal Gut, which showed professional athletes like rugby players have higher microbial diversity in their guts compared to sedentary but lean individuals who were studied as the control (Clarke et al., 2014).

While it is generally accepted that higher gut microbial biodiversity is associated with positive health outcomes, cross-sectional studies like this one have limitations.

For instance, athletes consume different diets compared to the general population of age-matched controls, especially in terms of proteins eaten.

So, it is difficult to conclusively consider that the observed differences in gut microbiome composition between athletes and non-athletes are solely due to exercise or whether other factors such as diet are also involved.

Notwithstanding such caveats, some other studies have also reported findings that align similarly to this cross-sectional study.

For example, a team of scientists found that women who are physically active for a minimum of three hours per week have higher proportions of some specific microbial strains compared to women who do not exercise (Bressa et al., 2017).

Interestingly, the microbial species found in higher abundance in the guts of these physically active women were reported by other scientists to be SCFA producers and to be associated with better metabolic indices and BMI indices in the host.

Longitudinal studies in humans

In 2018, professor Jacob Allen published the first well-controlled longitudinal study on this topic.

Thirty-two adults comprised the study population. The subjects were classified either as lean or obese based on their BMI. Diet was rigorously controlled so the effects of differential eating could not offset the effects of exercising.

The exercise regimen included 30-60 minutes of endurance activity, performed three times per week.

In this controlled study, the results were similar to those observed in cross-sectional studies. For instance, in this study, researchers also found exercise increased SCFA-producing microbes in the guts of the host.

However, the research group reported two additional remarkable findings.

First, baseline BMI of the study subjects seemed to determine, to some extent, how much of an effect exercise had on the gut microbiome. Specifically, lean subjects appeared to benefit more than obese individuals in terms of beneficial shifts in their gut microbial populations following exercise.

Second, if there was a sedentary period following an exercise routine, in this case 6 weeks, the positive changes in the gut microbiome seen as an effect of the exercise regimen, might get reversed (Allen et al. 2018).

Unfortunately, being the “weekend warrior” at the gym, likely will not have a similar benefit.

Potential mechanisms explaining exercise induced changes in the gut microbiome

In a very well-cited review published in 2019, Lucy Mailing (from the Jeffery Woods lab at the University of Illinois at Urbana-Champaign) attempted to summarize the physiological mechanisms she thought might explain the effects of exercise on gut microbiome changes.

Gut associated lymphoid tissue (GALT) contains about 70% of our immune repertoire and is situated across the gut. The gut associated lymphoid tissue has profound effects on intestinal microbes.

Exercise greatly alters immune metabolism and signaling. As those effects reach the GALT, the altered immune responses reverberate across your intestines and affect the microbiome there.

Exercise also induces heat generation in your body, as well as short phases of normal and transient ischemia when you’re exercising hard. Both effects may have a positive or negative impact on your gut microbes.

Our gut mucus is also affected by exercise. Since mucus quality and quantity affects microbes in a large way, this ultimately ends up having huge implications for your gut microbiome.

In similar lines, exercise also impacts the permeability of gut lining. The more permeable our gut lining is, the higher the chances are for immune cells to get in closer contact with the gut microbes, impacting them more - and vice versa.

Scientists think this might be one way exercise might be affecting gut microbial compositions.

Another reason that scientists think physical exercise affects gut microbiota composition is that some digestive chemicals in your gut, most prominently bile acids, are affected by exercise.

Since your gut microbes live in that chemical environment after all, these chemicals, in turn, largely shape your gut microbial population.

For example, Kakiyama et al. 2013 showed that in mice with high cholesterol, exercising on a running wheel improved bile acid secretion and bile acid levels in their feces compared to those mice that did not exercise.

Further, bile acid levels have been shown to be a key determinant of gut microbial composition.

Finally, have you ever noticed the urge to have a bowel movement after a good walk? That is because exercise affects gut transit time and muscle contractions in your intestines. Such mechanical reasons likely also play a role in shaping your gut microbiome as a downstream effect of exercise.

Is there such a thing as too much exercise?

After reading this far, perhaps you’re thinking, “I should run. My gut microbiome needs it.”

But some studies found excessive exercise is also not good if you want a healthy gut microbiome.

As scientific evidence, a systematic review is considered heavily.

A systematic review lays out a clear pre-determined protocol by which the authors systematically screen all scientific publications available on a topic in scholarly databases such as PubMED. And then, the data obtained is reviewed, appraised and presented.

Because a systematic review screens and reviews all scientific articles on a topic based on given criteria, this kind of a study is considered very robust and comprehensive. And it also eliminates any author bias, for the most part, due to the pre-determined inclusion-exclusion criteria for screening data.

Such a systematic review by a group of scientists in Poland thoroughly reported the effects of physical activity on the gut microbiome in humans.

This study reported that too much intense exercise, both in terms of intensity and duration, might not be good for your gut microbiome .

When you overexert yourself, either with exercise intensity or duration, the gut is affected by what the authors called “exercise-induced gastrointestinal syndrome.” Some symptoms of exercise-induced gastrointestinal syndrome include diarrhea and nausea, and a general feeling of gastrointestinal discomfort (Dziewiecka et al., 2022).

Not surprising, this occurs more with athletes than with the general population.

The other effects that you may not easily perceive is that too much exercise can disrupt the healthy immune system of the gut, causing inflammation, and may negatively affect gut permeability.

These alterations are bad for your gut microbiota composition and can lead to dysbiosis.

In the literature, dysbiosis is defined as “the loss of commensal bacteria with possible beneficial metabolic activity and the overgrowth of opportunistic pathogens, as well as reduced biodiversity (Dziewiecka et al., 2022).”

The take-home message

Scientists are becoming more and more convinced that regular exercise has a positive health effect that was not known to us earlier in that it ultimately makes your gut microbiome healthier.

The key to harnessing that benefit is sticking to a regular exercise routine, but not pushing yourself too hard.

Keep at it, and your gut and body will thank you in ways you perhaps couldn’t imagine!


Allen, J. M., Mailing, L. J., Niemiro, G. M., Moore, R., Cook, M. D., White, B. A., ... & Woods, J. A. (2018). Exercise alters gut microbiota composition and function in lean and obese humans. Med Sci Sports Exerc, 50(4), 747-57.

Bressa et al. 2017. Differences in gut microbiome profile between women with active lifestyle and sedentary women. PLoS One. 12(2)

Clarke et al. 2014. Exercise and associated dietary extremes impact on gut microbial diversity. Gut. 63(12): 1913-20

Dziewiecka et al. 2022. Physical activity induced alterations of gut microbiome in humans: a systematic review. BMC Sports Science, Medicine and Rehabilitation

Kakiyama et al. 2013. Modulation of the fecal bile acid profile by gut microbiota in cirrhosis. J Hepatol. 58(5): 949-55

Mailing, L. et al. 2019. Exercise and the Gut Microbiome: A Review of the Evidence, Potential Mechanisms, and Implications for Human Health. Exercise and sports sciences reviews. 47(2):p 75-85

Matsumoto et al. 2008. Voluntary running exercise alters microbiome composition and increases n-butyrate concentration in the rat cecum. Biosci Biotechnol Biochem. 72(2): 572-6

Weigierska et al. 2022. The Connection Between Physical Exercise and Gut Microbiome: Implications for Competitive Sports Athletes. Sports Med. 52(10):2355-2369