Does exercise change your gut microbiome?

Whether or not we get as much as we should, we all know that exercise is good for us.

It strengthens our muscles and bones and keeps our hearts and lungs healthy, while providing a raft of other health benefits.

Experts have also shown that exercise is linked to gut health. For instance, physical activity appears to reduce the risk of colon cancer. 

Plus, studies show that it may improve the quality of life and reduce symptoms for people with inflammatory bowel disease.

And exercise might reduce symptoms for people with irritable bowel syndrome, too.

According to the latest research, the links between physical activity and gut health could be partly explained by changes in your gut bacteria. In this article, we’ll look at the evidence of this intriguing link.

Gut bacteria and exercise

The earliest evidence that physical activity might influence gut bacteria came from animal studies.

Scientists compared rats that had access to a running wheel with sedentary rats and found significant differences in their gut microbiomes.

The active rats, which ran an impressive average of 2.2 miles (3.5 kilometers) a day, also had more butyrate in their guts.

Butyrate is a type of short-chain fatty acid (SCFA). These compounds, or metabolites, are produced by “good” gut bacteria and have a range of health benefits. Among other roles, SCFAs help nourish the lining of your gut.

Other rodent studies produced similar results — they showed significant differences between the gut microbiomes of animals that got regular exercise and those that didn’t. 

Follow-up work also found that shifts in rodent gut bacteria after exercise differed from changes associated with diet. So, exercise appears to drive change in the gut microbiome, regardless of diet.

But we must always be wary of animal studies. After all, there’s a fairly sizable difference between you and a mouse. However, as we’ll see, studies in humans have reached similar conclusions.

What about humans?

One of the first studies to investigate links between exercise and gut bacteria in humans was published in 2014. The scientists compared elite athletes — rugby players — with nonathletes. 

Of the two, the rugby players had the most diverse sets of gut bacteria.

This is important because experts consider diversity a sign of a healthy gut microbiome. By the same token, a less diverse microbiome is linked with poorer health outcomes.

Compared with the control group, the rugby players also had higher levels of Akkermansia muciniphila

What’s A. muciniphila?

These bacteria feed on a component of the mucus that lines your gut. They also produce SCFAs. 

Scientists believe that A. muciniphila help control inflammation. They may also help maintain gut barrier function, making sure unwanted compounds don’t leak from your gut into your blood, which some experts call "leaky gut."

A thriving community of A. muciniphila is linked to a lower risk of obesity, diabetes, inflammation, and metabolic disorders.

Before we get too excited about these results, we should remember that rugby players don’t just exercise more than nonathletes.

They also have different dietary habits, which could influence their gut microbiomes. 

Overall, the authors concluded that exercise influenced gut bacteria. But they highlighted that the relationship is complex and warrants further research.

Since then, researchers have carried out many more studies. And a number of these arrived at results broadly in line with the rugby player study. 

For instance, the authors of a 2020 review on the gut microbiomes of athletes concluded that, in general, athletes have:

  • more diverse gut microbiomes

  • more “good” gut bacteria

  • higher levels of gut bacteria metabolites, including SCFAs

  • more bacteria that protect gut health

Still, like the authors of the rugby player study, the authors of the review explain that it’s hard to figure out whether differences in gut bacteria between athletes and nonathletes stem from exercise or diet.

Disentangling diet

Following hot on the heels of the rugby research, another study tried to tease apart the roles of diet and exercise on the gut microbiome.

To do this, the team analyzed the poop of 39 people with different fitness levels. All participants had a similar BMI and, importantly, a similar diet.

The researchers assessed the participants’ fitness by measuring their peak oxygen uptake, which the team describes as “the gold-standard measure of cardiorespiratory fitness.”

The scientists found that the more fit an individual was, the more species of bacteria they had in their guts. 

In particular, they had more Clostridiales, Roseburia, Lachnospiraceae, and Erysipelotrichaceae bacteria. Notably, these bacteria produce butyrate, the SCFA that we met earlier.  

A similar study, which also assessed participants’ peak oxygen uptake, found that more physically fit individuals had significant differences in their gut microbiomes. 

Importantly, the scientists noted that differences in gut microbiomes between fit and less fit people weren’t associated with their diets.

So, it seems that exercise is driving the changes.

The bigger picture

All the studies we’ve mentioned have been observational. This means that they looked at people’s gut bacteria at one point in time. 

The studies so far have been useful, but they can’t prove cause and effect, only associations.

To find out if exercise causes a shift in bacteria, let's turn to longitudinal studies, where scientists track participants over time.

One such study followed 14 people with obesity and 32 people with healthy weights. All the participants had relatively sedentary lifestyles at the start of the study.

During the study, they followed a program that involved doing endurance exercise 3 days a week for 6 weeks.

The scientists analyzed the participants' gut bacteria at the start of the study and at the end of the 6 weeks. Then, 6 weeks after the exercise program had ended, they took a final sample.

What did they find?

As with much of the research into gut bacteria, the results were complex. 

For people with healthy weights, exercise increased levels of SCFAs in their poop. But not for those with obesity.

The two groups also had different changes in their gut microbiomes. 

Those with healthy weights had increased levels of Faecalibacterium, a “good” gut bug that reduces inflammation. But in the participants with obesity, the numbers of these bacteria had dropped.

Conversely, levels of Bacteroides dropped in people with healthy weights and increased in those with obesity.

As we’ve seen in previous studies, there was also an increase in butyrate-producing bacteria, but only for individuals with healthy weights.

Interestingly, 6 weeks after the exercise program, most of the changes were reversed. So, these exercise-related alterations to the gut microbiome seem to be short-lived if a person doesn’t carry on exercising.

Another longitudinal study followed 19 sedentary women with overweight. The researchers had them do 6 weeks of endurance exercise.

The team found an increase in the “good” bacteria A. muciniphila and a decrease in Proteobacteria, which are considered “bad” gut bugs.

According to the authors of a review that looked into exercise and the gut microbiome, “longer-duration or higher-intensity aerobic training” might be needed to create substantial changes to your gut microbiome. 

They also write that the microbiomes of people with healthy weights might be more responsive to exercise. As you can see, there are still a lot of questions to be answered.

Overall, though, the authors of the review conclude: “Increasing evidence suggests that regular aerobic exercise confers benefits to the gut microbiota, which may be partially responsible for the widespread benefits of regular physical activity on human health.”

What should you do?

It seems increasingly likely that being active might help keep your “good” gut bugs happy.

However, to fully understand how exercise influences your gut and why not everyone’s gut bacteria respond in the same way, scientists need to do a lot more research.

With that said, there are reams of evidence that exercise is good for your brain, heart, and gut health. 

So, whether physical activity affects your gut microbiome or not, try and get the recommended amount of exercise every week.

You don’t have to run a marathon every day, but making space in your schedule to get your blood pumping a few times a week can make a real difference to your overall health, including your gut health.


Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions. Microbiome. (2016). 

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. PNAS. (2013). 

Does physical activity affect quality of life, disease symptoms and immune measures in patients with inflammatory bowel disease? A systematic review. The Journal of Sports Medicine and Physical Fitness. (2010). 

Exercise and associated dietary extremes impact on gut microbial diversity. Gut. (2014). 

Exercise and the gut microbiome: A review of the evidence, potential mechanisms, and implications for human health. Exercise and Sport Sciences Reviews. (2019). 

Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity. PLOS One. (2014). 

Exercise therapy of patients with irritable bowel syndrome: A systematic review of randomized controlled trials. Neurogastroenterology & Motility. (2018). 

Gut dysbiosis is associated with poorer long-term prognosis in cirrhosis. World Journal of Hepatology. (2021). 

Gut microbiota composition is related to cardiorespiratory fitness in healthy young adults. International Journal of Sport Nutrition and Exercise Metabolism. (2019). 

Low diversity gut microbiota dysbiosis: Drivers, functional implications and recovery. Current Opinion in Microbiology. (2018). 

Six-week endurance exercise alters gut metagenome that is not reflected in systemic metabolism in overweight women. Frontiers in Microbiology. (2018). 

Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies. Journal of Functional Foods. (2017). 

The athletic gut microbiota. Journal of the International Society of Sports Nutrition. (2020). 

The effect of diet and exercise on intestinal integrity and microbial diversity in mice. PLOS One. (2016). 

Timing and intensity of recreational physical activity and the risk of subsite-specific colorectal cancer. Cancer Causes and Control. (2011). 

Voluntary running exercise alters microbiota composition and increases n-butyrate concentration in the rat cecum. Bioscience, Biotechnology, and Biochemistry. (2008).