Top 4 Reasons to Exercise for Your Gut Microbiome

Have you found your wellness ambitions crumble at the sight of a chocolate cookie? A healthy lifestyle includes both diet and exercise. Now, research has highlighted just how impactful exercise can actually be, going as far to enhance our microbial diversity. Turns out there’s more reason than ever to schedule in that morning run. 

By Lena Baumann

It can sometimes be all too easy to overlook the simplest of truths: eat healthy, exercise regularly – what’s new? Well, when it comes to our gut health and microbiome, we’re finding out exactly how influential and important establishing these healthy routines can be; from improving our digestion to lowering risk of various inflammatory and chronic diseases, such as asthma, inflammatory bowel disease (IBD) and cardiovascular disease2

Whether you’re already active, or looking to get moving now, here are the top 4 reasons you should be exercising – for your gut!


Researchers have associated regular exercise with higher gut microbial diversity but also an increased abundance of healthy bacteria, like Prevotella3. Moreover, a recent randomized controlled trial by scientists at Copenhagen University confirmed that exercise changes the gut microbiome. In this study, 88 overweight or obese participants were randomized into either habitual living, an active lifestyle (biking) or moderate or vigorous leisure-time exercise for 6 months. Faecal samples revealed increased diversity of the gut microbiota in the exercise groups4.

A recent study showed increases in the number of intestinal Bacteroids by 4.8% (p < .05) after a 12-week training program including moderate aerobic exercise.

So in fact, with exercise your microbial diversity can be restored and the number and metabolic activity of beneficial bacteria (i.e. Bacteroids) improved. 


If you have constipation, exercise can help speed things up. According to researchers, exercise has been shown to increase peristalsis, transit times and help  accelerate the clearance of accumulated gas. Often, one of the key contributing factors for constipation is inactivity. When we move our bodies, we lower the time it takes for food to move through the large intestine, this, in turn, limits the amount of water absorbed from the stool. If you think about it, hard, dry stools are tricky to pass – the smoother our transits, the more moisture that remains, and the easier it is! Add to that how aerobic exercise speeds up your breathing and heart rate. This helps stimulate our natural squeezing muscles in our intestines – when they’re stronger we move stools out more quickly. 


With greater diversity, your microbiome is more efficient in producing short-chain fatty acids (SCFA). Those are produced through the fermentation of dietary fiber by our friendly microbiome. SCFA are used as an energy source by the cells in your colon, as signalling molecules and they even improve lipid metabolism and metabolic health5. As a result, your glucose homeostasis, insulin sensitivity and inflammation improves. An additional nice effect: SCFAs influence your appetite by stimulating the satiety centre within your brain (arcuate nucleus in the hypothalamus). Therefore, you may feel full and satiated for longer. Naturally, this makes it easier to dietary goals and lose that extra padding. Weight loss, in turn, supports your microbial diversity and overall health2, 6-10. It really is a full circle win-win!


A more diverse microbiome improves your immune function, lowers susceptibility to infections, reduces oxidative stress, induces tissue repair and improves the inflammatory responses within your body3. According to researchers, exercise decreases inflammation, improves our immune system, as well as the composition of microbes within our gut 2, 6-9. Your immune system is responsible for defending our body from pathogens and infections. Even in people with Irritable Bowel Disease, researchers have reported that moderate-intensity exercise was able to reduce their inflammatory markers11. Consequently, they recommend that patients with IBD regularly exercise at a moderate level in order to suppress inflammation and improve their disease management. 

According to researchers, exercise decreases inflammation, improves our immune system, as well as the composition of microbes within our gut.

Previous studies showed clear improvements in this essential ability with regular exercise and improved microbial composition. In short: the “good” bacteria within your gastrointestinal tract regulate immune functions, compete with pathogens for nutrients and maintain barrier functions. As a conclusion: you want to increase the amount of good bacteria, like Bifidobacteria or Bacteroids, in your gut.

Action steps for you 

You may ask, how you can increase the diversity of your microbiome. The answer is, go outside and do some sports. When you lack motivation to go running the next time (we all do sometimes), you should consider the changes it induces in your gut microbiota and how it improves your well-being. It might not even enjoy the fresh air and calm atmosphere during running early morning. Sedentary behaviour and an unhealthy diet, on the other hand, may not only put on some extra kilos but also increases your risk of inflammatory diseases8, 9. Think about it this way: TV, chips, guilt and bloating vs. happiness, improved microbial composition, a strong immune system and good gut feelings – clearly there’s a winner?!

And… if you’re looking for getting an even greater boost, we have another tip for you! According to recent research, probiotics can actually improve exercise performance. These live bacteria, such as Bifidobacteria and Lactobacilli, offer numerous health benefits. Maybe it’s time to try creating your own probiotic-rich foods, such as Sauerkraut, Tempeh or Kimchi3.

Closing thoughts

Overall, a healthy lifestyle might be efficient to get your symptoms in check, and feel your gut best. Be aware, this includes a healthy diet and regular physical activity. Although much more remains to be be seen regarding exercise and our gut microbiome, what we do know is that working out induces several health benefits. So, embrace an extra run, dance, or badminton friendly, and you’ll be supporting your heart, immunity and a lot more. Physical activity really is the spice of life, particularly when it elongates ours! 


  1. Hess AL, Benitez-Paez A, Blaedel T, Larsen LH, Iglesias JR, Madera C, et al. The effect of inulin and resistant maltodextrin on weight loss during energy restriction: a randomised, placebo-controlled, double-blinded intervention. Eur J Nutr. 2019.
  2. Cerda B, Perez M, Perez-Santiago JD, Tornero-Aguilera JF, Gonzalez-Soltero R, Larrosa M. Gut Microbiota Modification: Another Piece in the Puzzle of the Benefits of Physical Exercise in Health? Front Physiol. 2016;7:51
  3. Wosinska L, Cotter PD, O’Sullivan O, Guinane C. The Potential Impact of Probiotics on the Gut Microbiome of Athletes. Nutrients. 2019;11(10).
  4. Kern T, Blond MB, Hansen TH, Rosenkilde M, Quist JS, Gram AS, et al. Structured exercise alters the gut microbiota in humans with overweight and obesity-A randomized controlled trial. Int J Obes (Lond). 2019.
  5. Yu C, Liu S, Chen L, Shen J, Niu Y, Wang T, et al. Effect of exercise and butyrate supplementation on microbiota composition and lipid metabolism. J Endocrinol. 2019.
  6. Monda V, Villano I, Messina A, Valenzano A, Esposito T, Moscatelli F, et al. Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxid Med Cell Longev. 2017.
  7. Cronin O, Molloy MG, Shanahan F. Exercise, fitness, and the gut. Curr Opin Gastroenterol. 2016;67-73.
  8. Cook MD, Allen JM, Pence BD, Wallig MA, Gaskins HR, White BA, et al. Exercise and gut immune function: evidence of alterations in colon immune cell homeostasis and microbiome characteristics with exercise training. Immunol Cell Biol. 2016;158-63.
  9. Morita E, Yokoyama H, Imai D, Takeda R, Ota A, Kawai E, et al. Aerobic Exercise Training with Brisk Walking Increases Intestinal Bacteroides in Healthy Elderly Women. Nutrients. 2019;11.
  10. Allen JM, Mailing LJ, Niemiro GM, Moore R, Cook MD, White BA, et al. Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans. Med Sci Sports Exerc. 2018;747-57.
  11. Legeret, Corinne & Mählmann, et al. (2019). Favorable impact of long-term exercise on disease symptoms in pediatric patients with Inflammatory Bowel Disease. BMC Pediatrics. 19. 10.1186/s12887-019-1680-7.


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