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Gut Microbiome, Gut “Health” and the Athlete

This is a topic of much interest, as there is growing interest in the relationship between the gut microbiome and health (and the first principle of sports nutrition is health). Plus, we know that gut distress can impact many athletes, particularly endurance or nervous athletes, at some point in their training and competition career.

Gut Microbiome

Two thousand and eight witnessed the start of the human microbiome project which revealed just how many microbes find their home in our gut … something like 100 trillion!! Collectively, these microbes are known as the gut microbiota, existing in the gastrointestinal tract (GT). The collection of genomes from these microorganisms in the environment is known as the gut microbiome. We now understand that this diverse array of microbes may influence many aspects of human biology, including health.

Although the media can sometimes perpetuate the idea we have it all figured out with regards to gut health and the microbiome, the complexity of microbiome-host interactions means studying the microbiome is very multifaceted and complex and there is much we still need to learn. Our gut microbiota are highly individualised. Many factors including age, birth method, and antibiotic use as well as lifestyle factors such as diet and exercise shape the microbiota. The gut microbiome appears to be important for regulating mucosal immune activity, modulating host metabolic activity and harvesting energy. We also know the gut microbiome produces short chain fatty acids, enzymes and vitamins in the GT that may help to protect against intestinal infection, influence gastrointestinal health and have a role in the digestion of the foods we eat.

The interaction between exercise, the gut and the gut microbiota (including how exercise interacts with other stressors, restricted diets, environment to influence gut microbiota) is less understood. We know athlete (the recreational or the pro) physiology – from muscular strength, power, aerobic capacity, energy expenditure and heat production - differs to sedentary individuals. However, the potential role of the gut microbiota in influencing and / or being influenced by athletic performance remains unclear. This may be of interest to athletes in order to improve results and reduce recovery time.

Given this uncertainty, can we define what a ‘healthy gut’ looks like? In other words, do we know what microbes may benefit us all, and any that have a specific role for specific individuals (such as athletes, or those with a particular diet type, e.g. a vegan diet). The short answer is no. However, there are some things that we understand to be important in the gut … and this may be directly or indirectly related to the gut microbiome.

With nutrition as a focus there are a few areas we can look at.

The first are probiotics. These get a lot of coverage that may give the impression it is all figured out. But this is not the case. Probiotics are live bacteria that are part of the body’s normal digestive tract. Some evidence suggests taking specific probiotic supplements may support in certain illnesses, such as certain gastrointestinal and upper respiratory tract infections, as well as modulate some aspects of the immune system. However, in the absence of these symptoms and for a healthy individual with no gut symptoms, there is currently little evidence to suggest a supplement is effective. Particularly as a supplement will only provide a subset of the bacteria that may be living in the gut. But research is ongoing, and for sure we will have more information emerging as to when and where probiotic use might be appropriate over the coming years and decades.

Be careful not to confuse prebiotics and probiotics. Prebiotics include fibres and other resistant starches, like those found in fruit, veg, wholegrains and legumes. Fibres and resistant starches are forms of plant-based carbohydrate that are not digested in the small intestine (like the other carbohydrates we eat) and instead reach the large intestine undigested, where they are fermented by bacteria. Fibres have an array of roles, including supporting gut-transit time by bulking out and softening stools, impacting the levels of certain nutrients in the blood, and being a precursor to signalling molecules after fermentation by bacteria (like the short chain fatty acids I spoke about above). Eating a range of high fibre foods supports diversification of the gut microbiota by allowing different species to thrive and grow, because different species appear to prefer different foods (prebiotics). This may be beneficial, although cause and effect has not been established in research. But we do know that, in the absence of a disorder that means fibre and resistant starch intake must be limited, a diet that contains a variety of fibres is supportive of overall health … be it for the impact on the gut microbiome or other reasons!

Difficulty can lie with athletes here as high fibre intake can result in gastric emptying and gastrointestinal distress during exercise. But a diet low in fibre may reduce microbial diversity (which we think may be adverse) and have an impact on overall health. Therefore timing of fibre intake, particularly for endurance athletes, may be important. In short, avoiding high fibre intake immediately before or after heavy exercise. It is worth highlighting at this point that uncomfortable gut symptoms do not necessarily mean you have poor gut health. Symptoms such as bloating, and gas can mean microbes are doing their job and as a result, producing bi-products. The structure of fermentable carbohydrates (fibre) means when they ferment, gas is produced. They are also osmotic meaning they pull water into the intestine which may cause bloating. Such symptoms may be seen most frequently when fibre intake is rapidly increased. This is why it is often recommended that when adding more fibre to the diet, aim to do it slowly, perhaps a maximum of 5g fibre per day. As an athlete, it is also recommended to practice routines of food intake and timing before heavy training sessions or competition to test and then train the gut against distress.

It does seem that we must have a mutually beneficial (or at least not adverse) relationship with our gut microbiota … as neither of us have killed each other off yet!! And we know that many things that have a positive impact on health also influence the gut microbiome (like prebiotics), so there may be there are some cause and effect relationships there. But we just don’t have the research to prove it yet in most cases. So whilst taking a probiotic or prebiotic supplement and suddenly having great gut health sounds fantastic, we just don’t yet know a) if this is possible, b) if it is, what would be in that pro- or pre- biotic supplement, and c) how it would differ between individuals … including athletes and non athletes.

Other Aspects of Gut Function

Above we noted that high fibre, particularly immediately before heavy training, may cause some gut distress. Other ‘ingested’ factors that can cause gut distress are dehydration, which includes an appropriate electrolyte balance, high fat intake (as it is typically slow to digest), high volumes or spicy foods. The temperature of the environment and timing of food intake can impact the gut.

And then there is the training itself. In particular, heavy or prolonged training. Training induces a stress response, and the longer or heavier the training session the greater the stress induced. And the greater the stress the greater the impact on the gut, as blood is diverted away from the gut and the gut gradually reduces function. If an individual is dehydrated, gut function normally shuts down faster. And if an individual is still digesting food, this may cause sudden evacuation or digestion to stop. There is also some evidence this stress impacts the gut microbiome (and this may have further impacts on bodily function during or after exercise). As with most things gut related, there is significant individual variability in the response of the gut to training and so you must consider – and trial – carefully what works and does not work for you around such sessions and also in competition.

Competition is a particularly interesting one as you have the added complication of ‘nerves’, which in itself impacts gut function … usually in the form of more rapid evacuation of the gut!! During competition a lower fibre intake (intentionally) may help gut distress and gastric emptying. If attending a competition away from home, the environment and food availability are likely to be different too so that may mean the diet differs to normal. If an athlete knows their gut is typically sensitive, particularly with nerves, it may be wise to consider how to access foods that they know typically sit well around training. The key message is: be prepared!


In summary, we are all unique! It is clear that the function of our gut is important beyond ‘just’ the critical role of digesting the food we need to fuel and recover from life and training. The gut microbiome is clearly an intricate web within this. But the details of it all are still to be fully revealed. For now, we can say that we don’t know the perfect diet for the gut (if one exists!). We all have a number and type of different bacteria; we all have different bodies and guts. Our guts may respond in different ways to different foods and environmental factors. So as an athlete, practice changes in hydration and fuelling around training if you experience gut distress.It is often a case of trial and error to find what works for you.

Read more:

3. The Human Microbiome Project Consortium (2012)

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