How Your Gut Health Impacts Your Gym Performance (And Vice Versa)

Written by Megan Falk: Experienced health and wellness journalist and editor. Megan is a graduate of Syracuse University’s S.I. Newhouse School of Public Communications, where she earned a bachelor’s degree in Magazine Journalism and a minor in Food Studies. She’s also a certified personal trainer through the American Council on Exercise.
Reviewed by Jennie O’Grady: Senior SciComms Specialist at Seed Health

Every time you work out, your gut microbes do too. During exercise, the trillions of bacteria and other microorganisms in your gastrointestinal tract can spring into action in ways that support your digestion, immunity, and brain function. That said, some forms of movement may be more advantageous for your microbial milieu than others.

Let’s take a deep dive into how exercise impacts gut functioning and explore what this means for athletes of all kinds. Along the way, we’ll read the poop of professional rugby players and martial artists, learn about a next-gen gym supplement powered by microbes, and cover why high-intensity training may send you straight to the bathroom.

Exercise and the Microbiome

Studies published over the last decade suggest exercise can increase the number of beneficial microbial species, enhance microflora diversity, and improve the development of commensal bacteria in the gut (which break down indigestible compounds and defend against pathogens).^1,2 One 2019 review found that exercise can alter the composition and functional capacity of gut microbiota—even regardless of diet.³ 

Let’s dig into why this happens, starting with the way exercise increases gut motility (read: how quickly food moves through your GI system). Your digestive tract contains a layer of muscle that, like other muscles in your body, are supported during exercise. This allows us to more quickly and efficiently break down food and transport it to its final destination (the toilet!) while also relieving gas that builds up during the digestive process. 

As for how this impacts the composition of microbes in your gut, researchers suspect that if your transit time is slow, your gut bacteria may be deprived of carbohydrates (their primary energy source) and start to feed on protein instead. Byproducts made from the breakdown of protein, such as ammonia and sulfur compounds, can have harmful effects on gut health, so there’s a distinct advantage to keeping things moving.⁴ 

Exercise also seems to upregulate anti-inflammatory cytokines (proteins) circulating throughout the body, which can help strengthen the gut barrier and maintain a strong and diverse microbiome.^5,6,7

These exercise-induced changes to the gut microbiome can enhance muscle mass, too, kicking off a positive feedback loop. 

A diverse, well-balanced microbiome can more effectively break down and absorb nutrients that are essential for muscle growth and maintenance, such as amino acids and vitamins.⁸ It also may ease inflammation—which can contribute to sarcopenia (muscle loss) in chronic conditions—via its upregulation of anti-inflammatory compounds.^9,10 

Plus, the microbiome can impact the production and regulation of hormones that affect muscle growth, including insulin-like growth factor 1. A balanced gut may support balanced levels of these hormones, which, in turn, can help curb muscle loss and increase hypertrophy (muscle growth).^11,12 

Movement may also bolster levels of certain bacteria and functional pathways that can enhance performance. Case in point: Exercise, specifically sustained aerobic training, has been shown to increase the production of short-chain fatty acids (SCFAs).^13,14 These metabolites are produced when your gut microbiota ferments certain dietary fibers, and they can be used for energy by your cells and intestinal microbiota.¹⁵ Over time, exercise can bump up the number of bacterial species that produce SCFAs.¹⁴ With more SCFAs being created, you may see gains in muscle mass, body composition, and physical functioning.¹⁶ 

Inside the Guts of High-Performance Athletes

While a rigorous study on the guts of different extreme athletes has yet to be conducted (though there’s an idea for the next Olympic Village), some research has been conducted on a sport-by-sport basis. 

Consider a small 2016 study, which found that professional rugby players had more carbohydrate metabolism pathways than control groups. This means their bodies were efficient at breaking down carbs (like sugars and starches) for energy during activity. The study authors also analyzed the athletes’ excrement (💩) and discovered SCFAs and other substances associated with enhanced muscle turnover.¹⁷ In other words, their poop showed signs that these athletes are able to efficiently replace old muscle proteins with new muscle, enhancing strength and hypertrophy.

It’s not just rugby, either. One study on high-performing elite martial arts athletes found they tended to have a more rich and diverse gut microbiome (as demonstrated via stool sampling) than less seasoned martial artists.¹⁸ Notably, their guts seemed to have higher levels of the genus Phascolarctobacterium, which can produce short-chain fatty acids, and contain more of the histidine (an amino acid) metabolism pathways required for protein synthesis.¹⁹

Other Benefits of Exercise

Of course, increasing gut bacterial diversity is far from the only reason to exercise. Here are a few more tangible ways that getting moving can support your whole body.

• It helps regulate our emotions: In helping to strengthen and diversify the gut microbiome, exercise can also influence gut-brain communication, helping to spur a positive emotional response and protect against psychological disorders like depression and anxiety.^20,21 
• It could promote improvements in brain function: Exercise increases blood flow, bringing more oxygen and nutrients to the brain. Movement’s impact on SCFA production may have an effect on the brain, too. Animal studies suggest the SCFA butyrate may help grow new nerve cells in a specific part of the brain that is important for memory and learning.²²
• It supports the immune system: Around 70-80% of your immune cells are stored in your gut tissue (!), and exercise can encourage the growth of bacteria to support them.²³ It can also improve barrier function, which plays a role in nutrient absorption and preventing the uptake of pathogens and harmful metabolites.^24,25 

Which Types of Exercise Are Best for the Gut?

For clues on which types of exercise are best for our guts (and overall well-being), we can look to our early ancestors. Before the days of weight racks and boutique fitness classes, we humans moved in order to pursue food and escape threats. When we weren’t doing either of these things, we rested to conserve our energy. As such, we’ve evolved to thrive on a combination of low- to moderate-intensity exercise—and our microbial hitchhikers have too.

Low-intensity workouts (like gardening and walking) can speed up gut transit time and increase the presence of certain health-promoting bacteria in the microbiota like Faecalibacterium prausnitzii, one of the main producers of the SCFA butyrate.^20,26,27

Similarly, moderate-intensity exercises (jogging, hiking—anything that gets you to about 50% to 70% of your maximum heart rate) can help reduce intestinal permeability, ease inflammation, and improve microbial diversity.^14,28

When exercise veers into the higher intensity zone, however, we risk harming—not helping—the gut.

Unlike more moderate-intensity movement, strenuous physical activity (particularly without proper rest) may increase intestinal permeability and reduce gut mucus thickness.^31,32

So why does this happen? As you train, your body diverts nutrient- and oxygen-rich blood toward your working muscles, redirecting it away from other organs that don’t immediately need it—like the gut. During vigorous exercise, this temporary reduction in blood flow can damage cells and their proteins that prevent pathogens from entering the bloodstream.^14,33 Compounding the problem: When the working muscles contract during vigorous exercise, pro-inflammatory chemicals like cytokines are released into the blood.³³

Almada says it’s useful to think of the cells of your gut lining like a net. Vigorous exercise can cause the net’s holes to become larger, allowing substances (in this case, pathogens and pro-inflammatory molecules) that wouldn’t normally fit through to become absorbed and enter the bloodstream.¹⁴ This gut barrier dysfunction is sometimes referred to as “leaky gut” and though you can’t feel it, it can last for several hours following exercise, says Almada.³⁴

Now, it’s worth noting that strenuous exercise isn’t inherently “bad” for your gut, especially if you enjoy it. It can actually be a form of hormesis (a short-term stressor that leads to resilience and positive adaptations in the long term) when paired with proper recovery.²⁴

An Athlete’s Guide to Training the Gut Microbiome

To support your gut as a high-performing athlete or HIIT workout lover, put these tips into action. 

1. Postpone your post-workout meal.

After exercise, the gut can’t digest protein and carbs as efficiently as usual. To better absorb the nutrients you’re consuming post-workout, you should wait for gut functioning to be restored, says Almada. Consider leaving at least 30 minutes after your workout before consuming a meal or snack.³⁵

2. Add a probiotic to your routine.

Probiotics—live microorganisms that, when administered in adequate amounts, confer a health benefit on the host—can be especially useful for athletes. Certain strains of bacteria can help improve the absorption of nutrients that play an essential role in performance, including amino acids, vitamins, and minerals.³⁶ What’s more, they may help support a protective inflammatory response and steady transit time—both of which are important for exercisers who are pushing their bodies to the limit.^37,38 (Curious if probiotics are right for you? Take this quiz to learn more about what they are and how they work.)

3. Don’t skip rest days.

As we now know, exercise places strain on many parts of the body—including the gut. Give yourself time to recover by taking adequate rest after tough workouts, prioritizing sleep, and balancing high-intensity exercises with gentler ones.

The Key Insight

Although your gut microbiome may not be top of mind when you’re lifting weights or taking your favorite cycling class, your workout does impact its bacterial diversity, barrier functioning, and metabolism pathways—all of which can ultimately influence your performance. 

Vigorous styles of physical activity may come with negative side effects. But remember: Your movement practice is just one component of the overall milieu of the gut. Your diet, stress, lifestyle, and age can all influence the microbiome, and studies may not account for those individual intricacies.²⁴