human gut microbiome and exercise

Exercise And Its Effect On The Human Gut

Exercise And Its Effect On The Human Gut

Physical activity keeps you a lean, mean fighting machine. It also keeps your gut bacteria whipped into good shape, too. Gut health and exercise go together like peanut butter and jelly. Exercise promotes the production of gut-healing short-chain fatty acids (SCFAs) and metabolites, supports a more diverse microbial composition to prevent bacterial overgrowth, and prevents weight gain because…well, who doesn’t like a trim bod? Let’s discuss the connection between exercise and the human gut microbiome!

What Is the Gut Microbiome?

The gut microbiota is the collective microbial community housed within the lumen (the space inside the tubular structure) of our intestinal tract. There is a growing body of evidence on the capability of microorganisms within our gut microbiome to respond to dietary, environmental, pathological, and genetic factors.

The gastrointestinal (GI) microbiome represents a complex network of trillions of microbes, mainly consisting of bacteria. Gut microbes coordinate in a bidirectional way to affect our general state of health.

The effect of diet and potential therapies (prebiotics and probiotics), in improving gut health, have been extensively studied. Recently, the role of environmental factors, such as exercise training, is also being understood to affect our gut microbiota profile 1.

Exercise for A Healthier Gut

benefits of exercise for gut health

Combining physical activity with proper diet and strain-specific probiotic supplementation will help boost microbial diversity in your gut. With a wider spectrum of bacteria, you will have better digestive health, meet your weight loss goals, and boost your mood. Let’s discuss the positive impact of exercise on the gut microbiome.

Better Overall Health

Exercise has been widely recognized as a useful therapy for a range of diseases, including:

  • Cardiovascular Disease
  • Cancer
  • Depression
  • Anxiety
  • Diabetes
  • Systemic Inflammation

The processes through which exercise can have a therapeutic effect on human diseases have been extensively studied and found to be many and also interconnected.

Most of your immune system cells reside in your gut. They help modulate inflammation along the gut barrier. When we endure chronic inflammation, it compromises our gut bacteria, immune system, and overall health and wellbeing.

Studies show that exercise helps improve your immune system naturally 2. Physical activity burns fat, promotes metabolite-producing bacterial growth, and lowers stress. All of these benefits improve blood flow, regulate bowel movements, reduce inflammation, and ultimately, the development of many chronic illnesses.

Weight Loss

Exercise isn't just about building abdominal muscles made of steel. It's about improving your overall health.

Obesity is ranked as the most prevalent preventable health-related disease globally. Current estimates suggest that there are approximately 1.9 billion obese humans worldwide 3.

These rates are alarming, as evidence suggests that obesity can cause metabolic health issues, heart disease, and type 2 diabetes.

Recently, scientists have tied a lack of Faecalibacterium prausnitzii and Akkermansia as markers for gut dysbiosis 5. Inversely, the host becomes more susceptible to inflammation and weight gain.

Researchers also noted that those with weight issues might have elevated levels of Proteobacteria. This finding further cements the importance of bacterial diversity.

Improves Bacterial Diversity

In this study, mice were made to undergo endurance exercise and had their gut microbiomes compared to sedentary counterparts. The goal was to see if physical activity increased alpha diversity within their microbiota. Researchers observed a change in over 2,000 bacterial taxa!

Research has already established the role of gut microbiota in the metabolic health of skeletal growth. In mice, exercise may increase the prevalence of the Lactobacillus species and decrease bacteria from the Tenericutes phylum 6.

Exercise is like a personal trainer for your gut bacteria! In one of the few studies which involved humans, athletic rugby players and healthy controls were compared based on their microbiota composition. Athletes showed more than twice as many bacterial species compared to their non-athletic counterparts 7.

Prevents Leaky Gut, IBS, and IBD

Another study involving humans noted that physically active people tend to have more taxa, such as:

  • Clostridiales
  • Roseburia
  • Lachnospiraceae
  • Erysipelotrichaceae

These probiotic bacteria are known to produce a significant amount of butyrate 8. Butyrate is a beneficial short-chain fatty acid that helps repair the digestive tract. It has strong anti-inflammatory effects to prevent the degradation of the intestinal lining that might cause Leaky Gut Syndrome, Inflammatory Bowel Disease (IBD) or Irritable Bowel Syndrome (IBS).

Another recent study noted that endurance exercise also promotes the production of acetate 9, especially in the large intestine (colon). Exercise expedites this process by encouraging fermentation of large intestine bacteria.

Acetate is the most prevalent SCFAs in the body. It is essential for metabolizing lipids, cholesterol, proteins, and amino acids.

Boosts Mood

Exercise stimulates our vagus nerve. This series of nerves serve as a communication line between our gut bacteria and brain. When specific bacteria take over the system, it disrupts homeostasis. Ultimately, the vagus nerve picks up on the problems and it alters hormone production to influence our mood.

Exercise creates new diversity. It helps break up the dominance of one particular bacterial species that might be overstaying its welcome and causing you mental health issues.

Lactococcus lactis and Lactobacillus plantarum and two Lactobacilli strains under the Firmicutes phylum. They are known to activate 5-hydroxytryptamine receptors (5HT) 11. This physiological process is the precursor to serotonin production. 

Serotonin is an important neurotransmitter that regulates so many crucial functions, including our sleep-wake cycle, appetite, and overall mood. There is enough literature to confirm the therapeutic role of exercise in promoting good health. 

The mechanisms by which the gut microbiota influences our energy, metabolism, and satiety are being studied extensively and researchers have established the unique relationship of exercise in shaping our microbiome independent of the diet. 

Thus, exercise alters the gut microbial population quantitatively and qualitatively which benefits the host aka us. As we mentioned earlier, exercise also boosts the presence of butyrate-producing bacteria. Studies suggest that butyrate also influences serotonin production 12.

Exercise and Gut Health Side Effects

Now, we shouldn’t be sedentary women and men. However, there is too much of a good thing. Too much exercise can cause wear and tear on the body and negatively impact the gut biome. Plus, it might cause injury or hyperextension when you overexert. 

Additionally, excessive exercise can cause stress. In turn, too much endurance training or high-intensity exercises can exacerbate GI problems, including IBS.

Don’t push yourself too hard every day. Break up your exercise routine with lighter workouts, including walking or yoga.

Exercise for Good Gut Health

Exercise leads to the enrichment of microflora diversity, contributing to reducing weight, obesity, and gastrointestinal disorders. Working out also helps in stimulating the growth of bacteria that are capable of producing substances that protect us against colon cancer and gastrointestinal diseases.

So, now you know how your gym routine, your morning jog, or the many other forms of exercises, are interconnected with the concept of human health in terms of your gut. Get moving!

exercise and gut health for healthy metabolism

Check to see if your exercise routine is helping with gut diversity. Get your gut tested with Ombre. We’ll let you know which bacteria you need, which are too abundant, and the foods you need to balance your microbiome!


  • 1 Hughes, Riley L. “A Review of the Role of the Gut Microbiome in Personalized Sports Nutrition.” Frontiers, Frontiers, 12 Dec. 2019, www.frontiersin.org/articles/10.3389/fnut.2019.00191/full.
  • 2 Nieman, David C., and Laurel M. Wentz. “The Compelling Link between Physical Activity and the Body’s Defense System.” Journal of Sport and Health Science, Elsevier, 16 Nov. 2018, www.sciencedirect.com/science/article/pii/S2095254618301005.
  • 3 “Obesity and Overweight.” World Health Organization, World Health Organization, 1 Apr. 2020, www.who.int/news-room/fact-sheets/detail/obesity-and-overweight.
  • 4 Dabke, Kruttika, et al. “The Gut Microbiome and Metabolic Syndrome.” The Journal of Clinical Investigation, American Society for Clinical Investigation, 1 Oct. 2019, www.jci.org/articles/view/129194.
  • 5 Magne, F., Gotteland, M., Gauthier, L., Zazueta, A., Pesoa, S., Navarrete, P., & Balamurugan, R. (2020). The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients?. Nutrients, 12(5), 1474. https://doi.org/10.3390/nu12051474. 
  • 6 Clarke, S. F., Murphy, E. F., Nilaweera, K., Ross, P. R., Shanahan, F., O’Toole, P. W., & Cotter, P. D. (2012). The gut microbiota and its relationship to diet and obesity: new insights. Gut microbes, 3(3), 186–202. https://doi.org/10.4161/gmic.20168.
  • 7 Mohr, Alex E., et al. “The Athletic Gut Microbiota.” Journal of the International Society of Sports Nutrition, BioMed Central, 12 May 2020, jissn.biomedcentral.com/articles/10.1186/s12970-020-00353-w#Sec19.
  • 8 Estaki, M., Pither, J., Baumeister, P., Little, J. P., Gill, S. K., Ghosh, S., Ahmadi-Vand, Z., Marsden, K. R., & Gibson, D. L. (2016). Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions. Microbiome, 4(1), 42. https://doi.org/10.1186/s40168-016-0189-7. 
  • 9 Okamoto, Takuya, et al. “Microbiome Potentiates Endurance Exercise through Intestinal Acetate Production.” American Journal of Physiology-Endocrinology and Metabolism, 8 May 2019, journals.physiology.org/doi/full/10.1152/ajpendo.00510.2018.
  • 10 Quiroga, Rocío, et al. “Exercise Training Modulates the Gut Microbiota Profile and Impairs Inflammatory Signaling Pathways in Obese Children.” Nature News, Nature Publishing Group, 6 July 2020, www.nature.com/articles/s12276-020-0459-0.
  • 11 Dalton, A., Mermier, C., & Zuhl, M. (2019). Exercise influence on the microbiome-gut-brain axis. Gut microbes, 10(5), 555–568. https://doi.org/10.1080/19490976.2018.1562268. 
  • 12 Reigstad, C. S., Salmonson, C. E., Rainey, J. F., 3rd, Szurszewski, J. H., Linden, D. R., Sonnenburg, J. L., Farrugia, G., & Kashyap, P. C. (2015). Gut microbes promote colonic serotonin production through an effect of short-chain fatty acids on enterochromaffin cells. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 29(4), 1395–1403. https://doi.org/10.1096/fj.14-259598.

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