Exercise and the Microbiome

March 6th, 2023 | Posted in Info

The Microbiome ~ It’s Not Just What You Eat

The gastrointestinal tract contains trillions of microbes, known as the gut microbiota or microbiome. The balance and diversity of specific families of bacteria support many aspects of health, while other organisms are associated with adverse health outcomes.  When gut bacterial diversity diminishes there may be many consequences to health. Whilst we all know that diet affects the composition of the microbiome there are other lifestyle factors that can also affect our gut organisms.

In this month’s blog posts we’ll look at the effects of non-dietary factors on the microbiome.

Exercise and the Microbiome

There are numerous studies showing that exercise is good for the gut microbiome. Exercise appears to enhance the number and diversity of beneficial microbial species, as well as enhancing short chain fatty acid synthesis and carbohydrate metabolism (1).

Physical exercise may also augment intestinal microbial diversity through promotion of an anti-inflammatory state  (2).

Short Chain Fatty Acids

In some cases it’s the by-products of certain bacteria that are beneficial to health. These beneficial by-products include short chain fatty acids (SCFAs).

One major study investigated the microbiomes of 40 professional international rugby union players compared to control groups of people of similar age with either high or low BMI. It found that the athletes had significantly greater intestinal microbial diversity as well as higher levels of short chain fatty acids. SCFAs are beneficial compounds produced by gut bacteria when they digest plant fibres. SCFAs provide fuel for the cells of the gut lining, helping to maintain its integrity thus preventing metabolites from entering the bloodstream. They also have anti-inflammatory effects.

Certain bacterial populations are correlated with body fat, muscle mass, and physical activity. These include F. prausnitzii and Roseburia hominis, which are known for producing the SCFA, butyrate, and Akkermansia muciniphila that is abundant in athletes, low levels of which are associated with obesity and diabetes.

Chicken or Egg

It’s pertinent to ask whether physical exercise transforms the microbiota, or if having a healthy microbiota makes you more inclined to be active. Dysbiosis can cause inflammation and depressive symptoms that might make exercise less likely. But studies do seem to show that exercise actually changes the gut ecosystem.

An important factor affecting our engagement in exercise is the pleasure derived from physical activity, which is triggered by exercise-induced neurochemical changes in the brain – commonly called endorphins. It turns out that the microbiome affects the production of endocannabinoid metabolites in the gut which elevate dopamine levels during exercise. Stimulation of this pathway improves running performance, whereas microbiome depletion reduces exercise capacity. These findings indicate that the rewarding properties of exercise are influenced by the gut microbiome and that molecules that stimulate the transmission of gut-derived signals to the brain may enhance the motivation to exercise (3).

What Type of Exercise is Best?

Physical activity can be divided into two main categories, strength and endurance:

Strength exercises require high-intensity effort, like weight lifting, sprinting, and boxing. These sports build muscle mass by exercising your cells’ anaerobic pathways. That means that your muscles use their glycogen stores to create ATP (the fuel for your muscles) without oxygen.

Endurance exercise, aerobic or cardio exercise, includes activities that are performed at a lower intensity but for longer, like long distance running, walking, dancing, cycling, swimming and rowing. Such activities are considered aerobic because the muscles use oxygen to transform fats and sugars into ATP for energy.

The NHS recommendations for physical activity in adults are (4):

  • 150 minutes of moderate aerobic activity a week, such as cycling or brisk walking. This equates to 30 minutes a day 5 days a week
  • Strength exercises on 2 or more days a week that work all the major muscles: legs, hips, back, abdomen, chest, shoulders, and arms.


  • 75 minutes of vigorous aerobic activity a week, such as running
  • Strength exercises on 2 or more days a week as above.


  • A mix of moderate and vigorous aerobic activity every week – for example, two 30-minute runs plus 30 minutes of brisk walking equates to 150 minutes of moderate aerobic activity


  • Strength exercises on 2 or more days a week as above.

Don’t Overdo It

Although exercise is good for you it is always worth remembering that too much exercise can be detrimental to health. Training to exhaustion may be associated with dysbiosis of the intestinal microbiome, promoting inflammation and negative metabolic consequences (5).


  1. 1. Exerc Sport Sci Rev. 2019 Apr;47(2):75-85. Exercise and the Gut Microbiome: A Review of the Evidence, Potential Mechanisms, and Implications for Human Health. Mailing LJ et al.
  2. 2. Dig Liver Dis. 2018 Apr;50(4):331-341. Exercise has the guts: How physical activity may positively modulate gut microbiota in chronic and immune-based diseases. Codella R et
  3. 3. 2022 Dec;612(7941):739-747. A microbiome-dependent gut-brain pathway regulates motivation for exercise. Dohnalova L et al.
  4. 4. https://www.nhs.uk/live-well/exercise/exercise-guidelines/physical-activity-guidelines-for-adults-aged-19-to-64/
  5. 5. Exerc Immunol Rev. 2019;25:84-95. Exercise and immune system as modulators of intestinal microbiome: implications for the gut-muscle axis hypothesis. Ticinesi A et al.