Exercise, gut health and gastrointestinal issues
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Exercise, gut health and gastrointestinal issues

Exercise is generally regarded as beneficial for health. Gut health is not an exception, athletes tend to have microbiomes with increased composition and/or function. However, too much exercise can be detrimental. This is an overview on exercise, gut health and gastrointestinal issues.

Exercise and gut health

Most people will agree that exercising is beneficial for health. When comparing the microbiomes of exercising individuals (including athletes) with those of sedentary individuals, scientists have found:

  • More bacterial diversity and/or richness, generally regarded as beneficial to health
  • More short-chain fatty acid (SCFA) metabolic pathways, important for intestinal integrity and other aspects of health
  • Increased metabolic pathways of amino acids (including branched-chain amino acid, important for recovery) and carbohydrates (1, 2, 3)

It is important to note that these results are not consistent and it is likely that a combination of factors including exercise, genetics and diet is responsible for the observed results. Moreover, the type of exercise may influence whether an athlete’s microbiome is more diverse in terms of bacterial composition or in terms of bacterial function (2).

Scientists have found that measures of aerobic fitness (e.g. VO2max) can predict a more robust gut microbiome (2).

The benefits of exercise are not exclusive to athletes as several interventions have shown to improve the microbiome composition of the general population. However, ceasing to exercise reverts the microbiome to its original state (1).

Exercise and gastrointestinal issues

Gastrointestinal symptoms are common in athletes, particularly endurance athletes. Symptoms may include acid reflux, nausea, vomiting, abdominal cramping, diarrhoea and ischaemic colitis (3, 4).

Symptoms can go from mild (e.g. discomfort) to severe, sometimes requiring surgery. Depending on severity, they can impact performance (both in training and competition), recovery from exercise and general health (4).

Risk factors

Gastrointestinal symptoms seem to be very individual and not exclusive of a specific type of sport. However, it is well known that individuals participating in endurance events tend to report this type of symptoms than other exercisers. In fact, studies report that 30-93% of individuals participating in exhausting endurance and ultra-endurance events have reported gastrointestinal symptoms. Factors that influence the prevalence include the type of event (e.g. duration and intensity), environmental conditions and athletic level of the participant (4).

Causes of gastrointestinal issues in athletes

Redirection of blood flow

During physical activity, blood is diverted from the gastrointestinal organs to the exercising muscles (4). At the same time, the tight junctions between intestinal cells may become loose, leading to intestinal permeability (1, 4) (a.k.a. “leaky gut”). This is especially true when overtraining, which unfortunately is part of many elite and professional athlete’s life.

Besides gastrointestinal symptoms, increased intestinal permeability, may also increase the risk of upper respiratory tract infections, increase inflammation due to the leakage of bacterial toxins, decrease immune function and contribute to depression and anxiety (1, 3).

Changes in motility

Exercise also reduces motility in the oesophagus and relaxes the gastro-oesophageal sphincter, potentially leading to reflux. Also, intense exercise, exercising in extreme heat or when dehydrated can all slow down gastric emptying, which can lead to some of the aforementioned symptoms (4).

Impact and posture

High impact sports (e.g. running) and those that require postures that increase abdominal pressure (e.g. cycling) may increase the prevalence of gastrointestinal symptoms (4).


In general, foods that slow down gastric emptying (which is a good thing for things like weight management and metabolic health) may cause gastrointestinal symptoms. These include foods high in dietary fibre, fat and protein (4). Also, concentrated carbohydrate solutions as required for some endurance events may cause gastrointestinal distress due to shifts of fluids in the gut (4).

On the topic of carbohydrate, fructose has been reported as a source of gastrointestinal distress. However, it seems that fructose itself is not the culprit, but rather a large amount of a single type of carbohydrate. This is justified by the fact that beverages containing more than one type of sugar (e.g. fructose + glucose) tend to be better tolerated than those containing a single sugar source (4).


Non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen can increase the risk of upper gastrointestinal symptoms (4).

Exercise, gut health and gastrointestinal issues

The strategies below can help athletes improve their gut health and prevent gastrointestinal symptoms, with the ultimate benefit of increased performance and long-term health.


Although evidence is not conclusive, probiotic supplementation may improve gut health, therefore improving the signs and symptoms of overtraining (1, 3). It seems that multi-strain formulations are more effective than single-strain ones (3).

Pre-competition meal(s)

Before a competition, and potentially before intense training sessions:

  • Avoid foods high in dietary fibre, fat and protein
  • Avoid taking NSAIDs if not absolutely necessary
  • Avoid fluids with high concentration of carbohydrate
  • Avoid foods and fluids with excess fructose (4)

Summary and recommendations

The relationship between exercise, gut health and gastrointestinal issues is dose-dependent and individual. Adequate exercise is important for many aspects of health. Intense exercise and overtraining, on the other hand, can cause gastrointestinal issues that can hinder performance.

Probiotics and pre-competition food manipulation as specified above can help prevent the onset of those symptoms.

Because each body is different, it is very important for athletes to know how their bodies react to particular foods, fluids, supplements, medications, environmental conditions, stress, exercise intensity, etc. The optimal time for testing things out is as far away from competition as possible.


  1. Wosinska L, Cotter PD, O’Sullivan O, Guinane C. The Potential Impact of Probiotics on the Gut Microbiome of Athletes. Nutrients. 2019/09/25. 2019;11(10).
  2. Mohr AE, Jäger R, Carpenter KC, Kerksick CM, Purpura M, Townsend JR, et al. The athletic gut microbiota. J Int Soc Sports Nutr [Internet]. 2020;17(1):24. Available from: https://doi.org/10.1186/s12970-020-00353-w
  3. Jäger R, Mohr AE, Carpenter KC, Kerksick CM, Purpura M, Moussa A, et al. International Society of Sports Nutrition Position Stand: Probiotics. J Int Soc Sport Nutr. 2019/12/23. 2019;16(1):62.
  4. de Oliveira EP, Burini RC, Jeukendrup A. Gastrointestinal complaints during exercise: prevalence, etiology, and nutritional recommendations. Sport Med. 2014/05/06. 2014;44 Suppl 1(Suppl 1):S79-85.

[Photo by Miguel A. Amutio on Unsplash]

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