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Yes, Where Do I Start?

Can Exercise Improve Your Gut Microbiome?

How Exercise and the Gut Microbiome Go Hand in Hand

Key Takeaways:
  • Consistent exercise, as long as it’s not overly strenuous, appears to be one of the best things you can do to improve and maintain your gut health.
  • Research shows that exercise can improve leaky gut, gut dysbiosis, constipation, gut motility, IBS, and IBD.
  • When you stop exercising for a time, the gut microbiome appears to lose any positive gains from consistent exercise, but positive changes in gut health can be regained by resuming exercise. 
  • Find your optimal exercise load that’s challenging but not overwhelming for you or your gut.
  • An evidence-based exercise program for gut health includes 3–5 sessions of cardio or strength training per week at 30–60 minutes per session.

You’ll never find me questioning the importance of a healthy diet for a healthy gut. But that doesn’t mean other factors can’t be just as important for resilient gut health. The research tells us that one of those non-dietary factors is consistent, moderate- to high-intensity exercise. 

Exercise can be an amazing and low- or no-cost tool for improving the balance of bacteria in the gut microbiome and reducing chronic symptoms related to gut health imbalances. These positive outcomes may largely occur by helping to reduce inflammation and improve immune system function. In turn, a less reactive immune system reduces leaky gut, dysbiosis, IBS symptoms, and more. 

In this article, I’ll explore the relationship between exercise and the gut microbiome, review what happens to your gut when you stop exercising, and propose an evidence-based exercise protocol for optimal gut health. 

Exercise is Great for Your Gut: A Review of the Evidence

A consistent exercise routine appears to be one of the best things you can do to improve and maintain your gut health. Let’s review some of the areas where exercise can make a difference to your gut health. 

Leaky Gut

Following these guidelines may help protect your gut from cell damage and leakiness [1]:

  • Engage in moderate exercise for an hour or less.
  • While exercising, avoid high heat.
  • Stay well hydrated before, during, and after exercise.

In contrast, studies show that exercising intensely, especially in a hot environment, might temporarily harm the lining of your gut and make it more permeable [2]. 

This happens because, during intense exercise, blood flow moves away from the gut, which can lead to reduced oxygen and higher stress for the gut lining. The cell damage could affect nutrient absorption, and larger gaps between the tight junctions of gut cells can make it easier for harmful bacteria to enter the bloodstream and cause widespread inflammation. Luckily, this effect seems to be short-lived and usually goes away a few hours after intense exercise [2].

Dr. R tip: If you’re currently healing a leaky gut, you may want to stick to more moderate exercise while you focus on recovery. Then, you can work on increasing your exercise load as your gut is able to handle more stress. As always, listen to your body.


High-quality evidence shows that regular, moderate-intensity exercise with short bouts of high-intensity exercise (30–90 minutes, 3 times a week, for 8 or more weeks) positively affects the gut microbiome in both healthy and unhealthy people [3]. Intense exercise in fit people may initially cause inflammation, but they often have more diverse gut microbes that may promote better metabolic health and offset the inflammation [4]. 

Does this mean that exercise can resolve a chronic viral or fungal imbalance in your gut? For some, it’s possible, but others may need additional probiotics or antimicrobial support to correct the imbalance. In any case, once you get closer to a state of equilibrium with your gut, a consistent exercise routine will help you keep it more balanced in the future. 

Constipation and Gut Motility

Some clinical evidence suggests that 4–12 weeks of light aerobic exercise, like walking or Qigong, can improve constipation symptoms to a clinically meaningful extent [5]. This type of exercise seems to help move stool toward the rectum by enhancing motility (digestive movement) in the large intestine. In other words, light exercise helps relieve constipation by improving motility and transit time (how long it takes for poo to move through) and stimulating abdominal muscles. More reasons to get your daily steps!


If you suffer from irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD), certain kinds of exercise may act as a salve. A meta-analysis showed that engaging in moderate physical activity, such as yoga or treadmill exercise, for 6–24 weeks may have a large positive effect on IBS symptoms (except abdominal pain) [6]. Another analysis showed evidence that physical activity, whether it’s aerobic exercise or strength training at different intensities, can help reduce disease activity in people with IBD [7]. 

Of course, with a condition like IBD, you’ll want to modulate your exercise depending on how severe your symptoms are and whether your condition is flaring or in remission. But, especially if high stress leads to a flare-up, exercise can be a valuable tool to increase feel-good chemicals like serotonin and dopamine, and calm the nervous system at the same time [8]. 

Short-Chain Fatty Acids

Exercise seems to help the gut microbiome make more short-chain fatty acids (SCFAs), like butyrate, which fuels the cells of the gut lining. Specifically, exercise that’s moderate in intensity and duration, plus better fitness overall, may lead to more diverse gut bacteria, like Bifidobacteria species, Akkermansia muciniphila, and Faecalibacterium prausnitzii. Many of these bacteria produce short-chain fatty acids, which have multiple known benefits [9]

SCFAs like butyrate appear to reduce inflammation, support immune system function, and provide us and our muscles with energy [3, 9, 10]. These observations suggest a complementary cycle between the gut and skeletal muscle—a gut-muscle axis—in which each supports the other in a continuous feedback loop.

We still don’t know much about this gut-muscle axis, but it’s possible that when skeletal muscles contract during exercise, they release anti-inflammatory substances called myokines. In turn, some myokines may help the gut release a hormone called GLP-1 that’s important for metabolism. In the other direction, from gut to muscles, SCFAs made in the gut can help regulate how our muscles use energy, and they may improve our ability to use glucose (carbs) [9]. 

What Happens to Your Gut When You Stop Exercising?

When it comes to the effects of stopping exercise, we have less research. But what we do have suggests that it only takes 1–3 weeks for a lack of exercise to revert your gut microbiome to its status before you started exercising regularly [11]. 

This doesn’t necessarily mean that your intestinal microbiome goes from being healthy to unhealthy if you stop exercising. If it was already healthy when you started exercising regularly, and then became healthier during your exercise program, your gut microbiome may just go back to being as healthy as it was before you started exercising. Plus, you can regain those improvements once you start exercising again.

I mention this because we all have times when we fall off the wagon and drop our consistent exercise routine for a while, no matter how dedicated we are. But take heart: whether it’s a planned hiatus or not, when we return to consistent exercise, we can regain any improvements we previously saw in our gut health. 

Your brain may be tempted into all-or-nothing thinking when it comes to physical activity, but remember that some is better than none, and returning to a consistent routine after a break is part of the process for just about everyone. 

Find Your Optimal Exercise Load

I mentioned earlier that overtraining can be rough on your gut health, and I can speak to this from personal experience. At one point, I was doing three, pretty intense weight-training sessions and three long, moderate to intense bouts of cardio exercise per week, as well as sauna and cold plunges every day. In addition to spending 35 hours per week doing high-demand cognitive work, this load on my body eventually led to a number of unpleasant symptoms, including poor sleep, low mood, and loose bowels. It was nothing drastic, but I definitely noticed a difference in my gut health. 

Once I dialed back my exercise routine a little bit and made sure to include enough rest and recovery time, my gut health and other symptoms normalized. The lesson here is: more is not always better. Finding the right intensity and frequency of exercise that pushes you but doesn’t exhaust you is key to stimulating positive changes in your microbiome as well as skeletal muscle growth. 

An Evidence-Based Exercise Protocol for Optimal Gut Health

So, what is a good exercise schedule to follow in order to improve your gut health? The research suggests 3–5 exercise sessions per week consisting of [3]:

  • 30–60 minutes
  • A mix of cardio and strength training (can be in the same session or different sessions) 
  • Moderate to high intensity 

Doing this consistently for at least 8 weeks should impart beneficial impacts on your gut health [3]. 

The most important thing is to move your body regularly. That means that even if you don’t feel up to doing cardio or strength on a given day, taking a walk or doing yoga is much better than nothing. You’ll build up your exercise tolerance over time and slowly be able to increase your number of sessions per week.

Just remember that regularly doing high-intensity exercise for more than an hour may be bad for the gut. This doesn’t mean you can’t push yourself or participate in active sports for longer than an hour, but be mindful to balance out your longer training days with more restorative exercise to keep your gut happy. 

Moderate vs. High Intensity

Not sure what moderate-intensity or high-intensity exercise looks like? Here are a few examples. 

Moderate-Intensity ActivitiesHigh-Intensity Activities
Brisk walking, biking, light jogging, swimming, hiking, weight trainingRunning, jumping rope, cycling, high-intensity interval training (HIIT), team sports, hiking uphill

Make Exercise Part of Your Protocol for Gut Health

Consistent exercise has the power to modulate gut microbiota composition, lower inflammation, and boost short-chain fatty acid production. All of these outcomes are really good for gut health! And a healthy gut may, in a cyclic fashion, support muscle growth and step up processes like metabolism and glucose regulation that help us continue to exercise. 

As long as we don’t overdo it, exercise training can be a great partner to an anti-inflammatory diet for promoting homeostasis (a fairly stable balance) in the human gut. When it comes to managing or preventing gut conditions from developing, exercise can be a key (and free!) part of your gut health routine. 

If you want to learn more about the effects of exercise, how to get the most out of your exercise performance, and all things gut health, check out my YouTube channel

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➕ References

  1. Ribeiro FM, Petriz B, Marques G, Kamilla LH, Franco OL. Is There an Exercise-Intensity Threshold Capable of Avoiding the Leaky Gut? Front Nutr. 2021 Mar 8;8:627289. DOI: 10.3389/fnut.2021.627289. PMID: 33763441. PMCID: PMC7982409.
  2. Chantler S, Griffiths A, Matu J, Davison G, Jones B, Deighton K. The Effects of Exercise on Indirect Markers of Gut Damage and Permeability: A Systematic Review and Meta-analysis. Sports Med. 2021 Jan;51(1):113–24. DOI: 10.1007/s40279-020-01348-y. PMID: 33201454. PMCID: PMC7806566.
  3. Boytar AN, Skinner TL, Wallen RE, Jenkins DG, Dekker Nitert M. The Effect of Exercise Prescription on the Human Gut Microbiota and Comparison between Clinical and Apparently Healthy Populations: A Systematic Review. Nutrients. 2023 Mar 22;15(6). DOI: 10.3390/nu15061534. PMID: 36986264. PMCID: PMC10054511.
  4. Clauss M, Gérard P, Mosca A, Leclerc M. Interplay between exercise and gut microbiome in the context of human health and performance. Front Nutr. 2021 Jun 10;8:637010. DOI: 10.3389/fnut.2021.637010. PMID: 34179053. PMCID: PMC8222532.
  5. Gao R, Tao Y, Zhou C, Li J, Wang X, Chen L, et al. Exercise therapy in patients with constipation: a systematic review and meta-analysis of randomized controlled trials. Scand J Gastroenterol. 2019 Feb;54(2):169–77. DOI: 10.1080/00365521.2019.1568544. PMID: 30843436.
  6. Nunan D, Cai T, Gardener AD, Ordóñez-Mena JM, Roberts NW, Thomas ET, et al. Physical activity for treatment of irritable bowel syndrome. Cochrane Database Syst Rev. 2022 Jun 29;6(6):CD011497. DOI: 10.1002/14651858.CD011497.pub2. PMID: 35766861. PMCID: PMC9243367.
  7. Jones K, Kimble R, Baker K, Tew GA. Effects of structured exercise programmes on physiological and psychological outcomes in adults with inflammatory bowel disease (IBD): A systematic review and meta-analysis. PLoS ONE. 2022 Dec 1;17(12):e0278480. DOI: 10.1371/journal.pone.0278480. PMID: 36454911. PMCID: PMC9714897.
  8. Marques A, Marconcin P, Werneck AO, Ferrari G, Gouveia ÉR, Kliegel M, et al. Bidirectional Association between Physical Activity and Dopamine Across Adulthood-A Systematic Review. Brain Sci. 2021 Jun 23;11(7). DOI: 10.3390/brainsci11070829. PMID: 34201523. PMCID: PMC8301978.
  9. Ortiz-Alvarez L, Xu H, Martinez-Tellez B. Influence of exercise on the human gut microbiota of healthy adults: A systematic review. Clin Transl Gastroenterol. 2020 Feb;11(2):e00126. DOI: 10.14309/ctg.0000000000000126. PMID: 32463624. PMCID: PMC7145029.
  10. Tarracchini C, Fontana F, Lugli GA, Mancabelli L, Alessandri G, Turroni F, et al. Investigation of the Ecological Link between Recurrent Microbial Human Gut Communities and Physical Activity. Microbiol Spectr. 2022 Apr 27;10(2):e0042022. DOI: 10.1128/spectrum.00420-22. PMID: 35377222. PMCID: PMC9045144.
  11. Bycura D, Santos AC, Shiffer A, Kyman S, Winfree K, Sutliffe J, et al. Impact of different exercise modalities on the human gut microbiome. Sports (Basel). 2021 Jan 21;9(2). DOI: 10.3390/sports9020014. PMID: 33494210. PMCID: PMC7909775.

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