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Effects of Exercise on Gut Health

It's well-established that exercise can boost cardiovascular function, mental health, and metabolism. For example, high-intensity interval training (HIIT) was shown to improve insulin sensitivity and increase muscle mitochondrial capacity in obese patients. Exercise normally reduces the risk of GI cancer, reflux, and the incidence of ulcers, fatty liver, IBS, and diverticulitis.[1, 2, 3] But how does exercise change the gut microbiota?

Meet your second brain and endocrine organ

The enteric nervous system, the network of neurons innervating the GI tract, has been called the second brain because it's the largest component of the autonomic nervous system, numbering around 100 million neurons. The vagus nerve runs from the brain stem to the heart, lungs, gut, and other organs.

Recently, some scientists have proposed calling the gut microbiota an endocrine organ because of its widespread interactions with host physiology. Gut microbes can produce neurotransmitters like serotonin and dopamine.[4] They can also neutralize carcinogens and control oxidative stress and inflammatory responses.[5]

6 General benefits of exercise on gut microbes & health

1. Exercise affects neurotransmitters, mood, and brain function

You may notice increased energy and mental clarity after a great workout. This is no coincidence: exercise increases serotonin and dopamine levels in the brain.[5] Rats that swam briefly and regularly had increased levels of serotonin in the brain stem and hypothalamus.[6] Running at low speed also increased brain serotonin and decreased depressive and anxious behavior in rats.[7]

2. Exercise affects appetite and satiety

Light to moderate exercise can make you feel less hungry, thanks to the interplay between gut microbes and hormones. Leptin (a satiety hormone) is associated with more Bifidobacterium and Lactobacillus; these same bacteria were increased in exercised groups. Meanwhile, ghrelin (a hunger hormone) was associated with increased Bacteroides and Prevotella[8, 9] Exercise was found to decrease ghrelin, insulin, IL-6, and VLDL secretion.[9]

3. Exercise keeps things moving, which improves intestinal integrity

Exercise reduces transient stool time, which minimizes contact between potential pathogens and the GI mucosa. This partly explains the decreased risk of colon cancer, diverticulosis, IBD, and hemorrhage in individuals who exercise.

4. Exercise kept villi thinner, a sign of lower gut inflammation

A Rutgers University study compared diet (normal vs. high-fat diet or HFD) and exercise (active vs. sedentary) to biomarkers of inflammation, gut integrity, and gut microbial ecology. They found obese (HFD) sedentary mice had twice the villi width of lean sedentary animals. A major cause of villi widening was an increase in inflammatory cells in lymph and plasma cells and an increase in fat cells. The HFD exercised animals had normal villi.[2]

5. Exercise reduced Cox2 expression in the gut

The same Rutgers study looked at the expression of an enzyme called Cox2 that produces prostaglandins, which promotes inflammation, pain, and fever. The groups ranked from highest to lowest Cox2 expression were: obese sedentary, lean sedentary, lean exercise, obese exercise.[2]

Three key takeaways from this study:

  • Being sedentary is a risk factor for inflammation

  • Exercise can make a huge difference for individuals eating high-fat diets

  • Just because you're lean, doesn't mean you're healthy

6. Exercise strengthens antioxidant capacity and boosts gut immunity

Exercise increased expression of antioxidant enzymes (like glutathione peroxidase and catalase), anti-inflammatory cytokine IL-10, and expression of anti-apoptotic protein Bcl-2 in intestinal lymphocytes, which promoted their survival and increased their numbers. By the same token, exercise decreased expression of pro-inflammatory cytokines TNF-alpha and IL-17, apoptotic proteins caspases 3 and 7, and reactive oxygen species (ROS) generation in intestinal lymphocytes.[10]

How do the gut microbes of athletes differ from those of sedentary individuals?

Exercise changes the composition of gut microbes. Here's 4 ways how.

1. Exercise enriches biodiversity

Low microbial diversity is associated with more adiposity, insulin resistance, and inflammation; it's also a risk factor for weight gain. Exercise such as running can enhance the number of beneficial microbial species and improve host health.[9, 11] HIIT was also found to increase alpha diversity in mice; this effect was more pronounced in the distal gut, where it makes a difference in colon health.[12]

2. Exercise increases levels of butyrate producing bacteria, an indicator of gut health

Certain bacteria convert plant-based carbohydrates (aka fiber) into short-chain fatty acids (SCFAs), an indicator of gut health. SCFAs like acetate, propionate, butyrate enhance barrier function, reduce inflammation, provide energy for colonocytes, prevent mucosal degradation, and overall protect the GI tract.[9]

SCFA-producing bacteria include Faecalibacterium prausnitzii, Lactobacillus, Bifidobacterium, Clostridium, Bacteroides, Roseburia, and Lachnospiraceae.[9] In particular, Lactobacillus and Bifidobacterium enhance absorption of vitamins and minerals.[13] Exercise, including cardio, has been found to increase numbers and diversity of these butyrate producers.[9, 14]

Higher Faecalibacterium prausnitzii was found in elite rugby players, as well as in female athletes.[11] Additionally, female athletes had more Roseburia hominis and Prevotella.[15] When levels of these bacteria increase, so do levels of SCFAs and their associated benefits.

3. Higher mucus-degrading bacteria in athletes promotes turnover

Athletes (both men and women) have higher mucus-degrading Akkermansia muciniphila,[16] which improves mucus turnover and helps to maintain the gut barrier.[15] Ample evidence suggests Akkermansia is a favorable gut microbe for mucosal homeostasis, with an exception being in multiple sclerosis. (In MS patients, elevated Akkermansia comes with a leaky gut.) Excessively thin mucus can enable leaky gut, while thick mucus can increase levels of pathogenic mucus degraders. When it comes to gut mucosa, it’s all about balance and homeostatic turnover.

4. Sedentary lifestyle increases acidification and inflammation in the gut

Sedentary individuals may have higher levels of pathogenic, inflammation-causing Proteobacteria compared to active individuals.[17] Acidobacteria was also found to be higher in sedentary women.[15] Additionally, the beneficial butyrate-producing bacteria, Faecalibacterium prausnitzii, was high in active mice but not found in sedentary mice.[2] Overall, poor diet, sedentary lifestyle, antibiotics, and other factors can lower biodiversity, which increases risk of pathogenic bacteria dominating the gut.

When intense exercise becomes gut stress & when to not exercise

Running is known for its adrenaline rush. But prolonged stressful, fight-or-flight situations release norepinephrine and cortisol, which have inhibitory effects on the gut. Endurance cardio increases blood flow to the muscles, heart, and lungs and decreases blood flow to the small and large intestines. This decreased blood flow to the gut can increase tight junction opening, resulting in leaky gut. Leaky gut, potentially caused by dehydration, allows bacterial LPS translocation, which triggers the host's immune system to release inflammatory molecules like TNF-a, IFN-gamma, IL-1b, histamine, and proteases.[18, 19] The process can continue and lead to endotoxemia. In fact, marathon runners and triathletes frequently report symptoms like nausea, cramping, vomiting, or diarrhea.[5] However, it is possible that this effect could be mitigated with adequate training. Decreased blood flow to the gut was shown in foxhounds to wear off after 8-12 weeks of training.[20]

Exercising to exhaustion is not recommended because it temporarily weakens the immune system and increases inflammation.[5] This is why individuals fighting a cold are advised to wait about 48 hours for recovery before returning to the gym. Patients with chronic fatigue syndrome show worsening gut dysbiosis, inflammation, pain, and mood following exercise.[21] Overall, the more strenuous the exercise and the more depleted the energy reserves, the greater the barrier disruption, due to changes in blood flow and insufficient removal of metabolites and delivery of nutrients.[2]

What kinds of exercise affect gut microbiota? What about resistance training, calisthenics, stretching, and yoga?

Type and intensity of exercise clearly matters, but to my knowledge, there are no published peer-reviewed studies on the effects of strength training on gut microbiota, indicating an open area for research. Muscle mass has previously correlated to several bacterial populations, so it's likely there's an effect. More clinical studies are needed to establish data relevant to humans and their diverse activities.[15]

Source: Dr. Peter Osborne, Gluten Free Society

Key takeaways

Gut microbiota are affected by infection, disease, diet, antibiotics, exercise, which can in turn modulate disease.

Early-life interventions have a profound effect. Beneficial effects of exercise on the gut and brain were more profound when started earlier in life.[22]

Recovery is necessary. It’s important to distinguish between physical and psychological stress in exercise, especially in endurance sports.

There is no one optimal diet. This is because of high interindividual variability in gut microbiota, genetics, exposure, and lifestyle. Despite this, functions carried out by these microbial species appear to be the same in everyone's GI tracts.[23] Therefore, it is possible to personalize a diet that is optimal for an individual at a given time.

Gut microbe research is in its infancy. Gut microbe research isn't cut and dry. We're still discovering new bacterial species, and certain species can be beneficial in one context and opportunistic pathogens in another. They can also evolve rapidly, giving rise to new strains.

We need diversity. Having a more diverse gut microbiota decreases the likelihood of illness, as they keep each other in check.

Diet still impacts gut microbes more than exercise does. But exercise can have profound effects on gut health and gut microbial composition as well.


  1. Little, J.P., et al., Low-volume high-intensity interval training reduces hyperglycemia and increases muscle mitochondrial capacity in patients with type 2 diabetes. J Appl Physiol (1985), 2011. 111(6): p. 1554-60.

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  3. Gillen, J.B., et al., Interval training in the fed or fasted state improves body composition and muscle oxidative capacity in overweight women. Obesity (Silver Spring), 2013. 21(11): p. 2249-55.

  4. Clarke, G., et al., Minireview: Gut microbiota: the neglected endocrine organ. Mol Endocrinol, 2014. 28(8): p. 1221-38.

  5. Clark, A. and N. Mach, Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes. J Int Soc Sports Nutr, 2016. 13: p. 43.

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  7. Otsuka, T., et al., Effects of acute treadmill running at different intensities on activities of serotonin and corticotropin-releasing factor neurons, and anxiety- and depressive-like behaviors in rats. Behav Brain Res, 2016. 298(Pt B): p. 44-51.

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  10. Hoffman-Goetz, L., N. Pervaiz, and J. Guan, Voluntary exercise training in mice increases the expression of antioxidant enzymes and decreases the expression of TNF-alpha in intestinal lymphocytes. Brain Behav Immun, 2009. 23(4): p. 498-506.

  11. Monda, V., et al., Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxid Med Cell Longev, 2017. 2017: p. 3831972.

  12. Denou, E., et al., High-intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity. Am J Physiol Endocrinol Metab, 2016. 310(11): p. E982-93.

  13. Cerda, B., et al., Gut Microbiota Modification: Another Piece in the Puzzle of the Benefits of Physical Exercise in Health? Front Physiol, 2016. 7: p. 51.

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  17. Munukka, E., et al., Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women. Front Microbiol, 2018. 9: p. 2323.

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