Why good gut health is critical for athletes

September 13, 2022
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For a lot of athletes, diet and training programs are at the forefront of their attention. That means doing whatever is necessary to achieve the best performance possible. But unfortunately for a lot of people, athletes included, they don’t give a second thought to the health of their organ systems, especially their gut. And with the gut being the literal epicentre of the body, an imbalanced microbiome can interfere with more than just your digestion.

I’ve done the research and I’m breaking down why good gut health is critical for athletes, why athletes are subject to more issues with gut health than the average person, and what you can do about it to keep your gut in an optimal working capacity.

What is the gut?

When most people hear the word gut, the stomach comes to mind. But the gut is more than just the stomach. The gastrointestinal tract encompasses the wide array of organs that are involved in the process of digesting, absorbing, and metabolizing food to supply the body with everything it needs to run.

We’re talking about:

  • Mouth
  • Pharynx (throat)
  • Oesophagus
  • Stomach
  • Small intestine
  • Large intestine
  • Rectum
  • Anus

Gut health, specifically, refers to the function and balance of bacteria residing throughout the gastrointestinal tract. Ideally, organisms in the oesophagus, stomach, and intestines all work synergistically to allow us to thrive. But for more than 70 million people in the US with digestive diseases [6], that’s not quite the case. Contrary to what most people think, an imbalance and unhealthy gut extend far beyond just the digestive tract. It can interfere with mood, immunity, glucose metabolism, and even your performance and recovery.

Why is gut health important?

Like I just mentioned, most people think that the health of the gut has everything to do with just your digestion–but it’s so much more. The gut extends beyond the GI tract and has interconnections with the brain and nervous system, the immune system, hormones and neurotransmitters, digestion, and more.

​​The microorganisms present in the gastrointestinal tract play an important role in nutrient uptake, vitamin synthesis, energy production, modulating inflammation, and host immune response, which collectively contribute to overall health and well-being [11]. For athletes specifically, a healthy gut plays a critical role in improving energy metabolism by supplying muscles with oxygen and nutrients during exercise, but also modulating levels of inflammation and expediting tissue repair after exercise improves performance and accelerate recovery [9].

Energy Production:

Intense exercise requires sufficient energy availability and limitations can severely interfere with work capacity. During prolonged or intenseWhy good gut health is critical for athletes article by PERFECT Sports exercise, the body taps into various energy sources to maintain or exceed load. When the microbiome is healthy and balanced, it contributes to this energy supply through the breakdown of foods into short-chain fatty acids (SCFAs), which act as a substrate for gluconeogenesis, the process that generates glucose for energy [1]. A 2021 review confirmed that SCFAs may be an important part of endurance performance. One of the risks that athletes run where gut health is concerned, and where they’re particularly vulnerable, is under fueling.


The bacteria in the gut also play an important role in mitigating inflammation, which is essential for athletic performance and recovery. HeavyWhy good gut health is critical for athletes article by PERFECT Sports exercise induces microtears in muscle fibres, which results in inflammation. During the repair process, blood flow increases to the affected area to replenish oxygen, bring in nutrients needed for repair, and clear out waste, ultimately allowing muscles to repair and grow. And while some level of inflammation is needed for the growth and recovery process, excessive inflammation can actually be detrimental to the immune system.

However, having a healthy gut helps to counteract the potential for excess inflammation brought on by intense physical activity. The SCFAs not only contribute to energy production, but they also can mitigate inflammation by reducing gut permeability and inhibiting the release of cytokines, a type of pro-inflammatory molecule [5]. As such, by modulating levels of inflammation, the gut can also help to delay fatigue and post-exercise soreness.

For both athletes and non, the health of the gut is also critical to immune function. More than 70% of the immune system resides in the gut and microbial balance is crucial for mounting appropriate immune responses. The gut microbiota that resides in the GI tract provides numerous health benefits to the host, and recently it has become obvious that the gut microbial communities can cause immune dysregulation, leading to the development of autoimmune disorders [19]. An abundance of research has confirmed that signals derived from gut microbiota are essential for the development of the immune system, as well as shaping both innate and adaptive immunity.

Studies show that perturbation of the gut microbiome by external factors (antibiotics, diet, changes in geography, etc.), impaired host-microbiome interfaces, or changes to the immune system can result in systemic alteration of microbial balance, increased susceptibility to illness and infection, and abnormal immune responses [20]. Along with that, the microbiome-immune interaction is also implicated in a number of ‘non-communicable gastrointestinal diseases such as inflammatory bowel disease (IBD), and celiac disease, along with rheumatoid arthritis, metabolic syndrome, and neurodegenerative disorders.

While the immune-microbiome relationship is rather complex, it’s important to know that supporting your gut and maintaining that delicate balance within the microbiome is critical for the optimal function of the immune system.

What contributes to poor gut health?

Most people aren’t aware that things they do on a daily basis can alter the composition of the gut and disrupt the delicate balance needed to maintain health. Some of the biggest hitters that influence gut health include:Why good gut health is critical for athletes article by PERFECT Sports

Symptoms that your gut might be an imbalance

Dysbiosis is probably a lot more common than you think, and the bloating that you get after eating meals may not be from the sheer amount you’ve eaten but rather your gut telling you that something isn’t quite right. Or maybe it’s the fatigue you’re dealing with even though you feel like you’ve slept well. Watch out for the symptoms indicating that you may have microbial imbalances:

  • Chronic fatigue
  • Digestive issues
  • Constipation
  • Diarrhea
  • Bloating
  • Skin rash or redness
  • Bad breath
  • Brain fog
  • Difficulty concentrating
  • Anxiety or depression

How your gut affects your athletic performance

The link between gut health and athletes is bidirectional, meaning that gut health can affect athletic performance, but exercise can also affect gut health. Studies have shown that gut microbiome diversity (a marker of a healthy gut) has a great composition in people who are active compared to those who are sedentary [x]. While research is still uncovering more about the link between exercise and gut health, researchers have found multiple possible mechanisms by which exercise may influence gut health, including [11]:

  • Higher amounts of beneficial gut bacteria
  • Increased diversity of microbial strains
  • Increased metabolic capacity
  • Improved GI barrier function
  • Improved mucosal immune function

But that’s not it. Touching a little bit more on what we talked about earlier, gut bacteria are intricately involved in your physical performance for a few other reasons:

Improved Energy Output:

In addition to what I mentioned before, a healthy gut microbiome is also essential for [9, 13, 5, 4]:

  • Reducing fatigue via more efficient lactic acid breakdownWhy good gut health is critical for athletes article by PERFECT Sports
  • Controlling redox function, which can delay symptoms of fatigue
  • Increasing ATP production
  • Modulating metabolism
  • Supplying essential metabolites to mitochondria, the powerhouses of your cells
  • Regulating energy harvest, storage, and expenditure

Improving Mental Strength:

How many times have you lacked the motivation and focus to get through your workout? As it turns out, the composition of your gut may have something to do with that. Your gut microbes communicate with your brain via the vagus nerve (10th cranial nerve) and have a huge influence on the state of your mental health. Dysbiosis has been known to contribute to mental health issues, but a healthy gut can also contribute to mental toughness, as the gut has profound influences on [12]:

  • MoodWhy good gut health is critical for athletes article by PERFECT Sports
  • Pain threshold
  • Cognitive performance
  • Behaviour
  • Mental clarity
  • Attitude

Supports Body Composition:

Athletes come in all shapes and sizes, but the thing that most can agree on is that fat mass isn’t exactly functional and can be an impedance to performance. But when you’re in a sport that relies on strength and speed, the gut microbiome can help the body run more efficiently. This is because it influences [5]:

  • Body composition (muscle vs. fat)Why good gut health is critical for athletes article by PERFECT Sports
  • White vs. brown fat
  • Blood glucose response

Nutrient Absorption and Utilization:

Every athlete knows that diet affects their performance, but your performance is dictated not only by what you eat but alsoWhy good gut health is critical for athletes article by PERFECT Sports by what you actually absorb. Your body’s ability to effectively metabolize and use nutrients is key for optimal body function and athletic performance–and it’s the guts job to do that.

Improves Sleep:

Sleep is quite possibly one of the most important things an athlete can do for their performance, and research suggests that the compositionWhy good gut health is critical for athletes article by PERFECT Sports and health of the microbiome may play a role in regulating sleep by helping create important chemical messengers in the brain, including serotonin and dopamine. Studies show that total microbiome diversity was positively associated with increased sleep efficiency and total sleep time, and negatively correlated with wake after sleep onset [16]. Sleep deficiency in athletes has been associated with not only impaired cognitive function but also affects reaction time, accuracy, speed, decision making, injury risk, and fatigue onset.

Supports Antioxidant Defences:

Because virtually all metabolic processes produce free radicals as a byproduct of normal function, having a strong antioxidant defence system is critical to keeping the body healthy. And for athletes whose muscles are constantly working overtime, that need is even greater. But the health of that system partially relies on the health of the gut. A recent study found that ​ gut microbiota plays a role in regulating glutathione and amino acid metabolism of the host [x]; glutathione is the body’s most powerful antioxidant and the main detoxifying agent that plays an essential role in enabling the immune system, nutrient metabolism, and regulation of other important cellular events. A deficiency of this antioxidant is known to contribute to oxidative stress, which plays a major role in the mechanisms of several chronic diseases. A healthy antioxidant defence system is associated with:

  • Prevents of tissue damage from intense exerciseWhy good gut health is critical for athletes article by PERFECT Sports
  • Protects against intense exercise-induced oxidative damage and inflammation
  • Reduces physical fatigue
  • Improves exercise performance
  • Accelerates tissue repair and recovery
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Why athletes are more susceptible to poor gut health

While it may seem a little unjust, the reality is that athletes are exposed to significantly higher stress levels and altered lifestyle practices than the vast majority of the population. While they may not be downing cheeseburgers and poutine every other day, they’re engaging in practices that push their bodies to the max and sometimes functions become compromised because of that, so most athletes will experience gut complaints at some point. For some athletes, it’s sporadic and comes every once in a blue moon and has minimal consequences, while for other athletes it’s a chronic thing that becomes repetitive, frustrating, debilitating, and can lead to more serious health complications.

But what actually causes these gut issues in a large percentage of athletes?

​​Exercise-induced gut imbalances usually arise from normal physiological changes that happen to the GI tract and immune system in response to exercise [3]. There’s a good size body of evidence linking changes in both blood flow and the stress response when initiating exercise to various gut complaints [2]. But there is also some evidence to suggest that physiological changes in mechanical aspects like foot strike, jolting, and sudden impact may also be linked to changes in the microbiome.


Let’s dig into each of those:

Changes in blood flow

During exercise, the body diverts blood away from “unnecessary” processes and increases blood flow to working muscles to supply oxygen and nutrients, as well as the skin to help with thermoregulation. In doing so, blood flow to the gut is reduced. If this becomes chronic, as with athletes who are undergoing intense training schedules, it can start to damage the barrier of the GI tract and it becomes increasingly more permeable to unwanted and pathogenic microorganisms. The localized damage along with the permeability allows particles to enter the bloodstream and prompt a local and/or systemic immune response, which induces inflammation. Eventually, this can turn into a condition called leaky gut syndrome.

Stress response

There’s no denying that exercise is a big stress on the body, and the stress response that ensues from exercise promotes a decrease in overall gut function, including reduced gastrointestinal motility, nutrient digestion, and absorption. As such, there is an increased risk of nutrient malabsorption, which naturally impedes an athlete’s ability to nourish and hydrate their body. ​​

Mechanical effects 

The mechanisms aspects of intense training can put strain on the physical barrier function of the gut and can contribute to intestinal damage.

But it’s important to remember these three mechanisms that contribute to athlete gut issues don’t occur independently of each other. They’re constantly interacting in a dynamic fashion.

There are also several factors that can aggravate or prevent gut complaints during and after exercise that are dependant on the magnitude of exposure and how they’re managed. These include:

  • Exercise intensity
  • Duration
  • Modality
  • Ambient conditions (climate, environmental conditions)
  • Circadian variation
  • Hydration status
  • Pre-exercise diary patterns
  • Pharmaceuticals
  • Genetic predisposition to gut disease/disorders
  • Gut microbiota composition

How to avoid gut issues as an athlete

Over the last handful of years, there has been a lot of research into prevention and management strategies for athletes dealing with gut complications and complaints, and here are some of the most promising strategies:

  1. Eat carbs before and during exercise: Carbohydrate consumption before and during exercise, within tolerable limits, has been shown to prevent exercise-induced damage to cells in the Gi tract and doesn’t appear to accentuate gut discomfort [17]. Protein in the form of a whey-based protein powder may also ameliorate gut damage, although it can cause gut discomfort for some athletes.
  2. Gut-training: It may seem like an odd practice, but challenging the gut with high content and volume of carbs may improve carbohydrate malabsorption, improve glucose availability into the blood, and substantially reduce gut discomfort [3].
  3. FODMAPs: Cutting back on fermentable oligo- di- mono-saccharides and polyols, more commonly referred to as FODMAPs, may help in reducing gut issues in athletes. Research found that a 24-hour low FODMAP (2g/day) compared with a high FODMAP (47g) diet (energy and nutrient matched), was sufficient for reducing gut complications during endurance running in the heat due to reducing the degree of carbohydrate malabsorption before starting exercise [x]. But what’s interesting is that studies find that a low FODMAP diet may actually induce a higher degree of gut cell injury and greater disturbance to the gut-blood barrier compared with a high FODMAP diet. These protective effects of a high FODMAP diet on gut cells and gut-blood barrier may be the result of its influence on altering gut microbiota composition [7].

Other tips for boosting gut health

Load up on fermented foods

Fermented foods are rich in probiotic bacteria that have been shown to promote all sorts of health benefits, including weight loss, better gut health, and stronger immunity. Research finds that a diet high in fermented food promotes increased microbial diversity along with better immune cell activation. Wondering what to eat? Try these:

  • Kefir
  • Tempeh
  • Miso
  • Sauerkraut
  • Kimchi
  • Kombucha
  • Pickles (naturally fermented)

However, you want to keep in mind that because these bacteria are live species, all products containing them should be refrigerated. If you find a product on the shelf, chances are it’s not naturally fermented and doesn’t contain the probiotic bacteria you’re looking for.

Why good gut health is critical for athletes article by PERFECT Sports

Manage your stress

Stress is disastrous for virtually the entire body, but it does a real number on the gut and digestion. This is due to the influence of stress in reshaping gut bacteria composition through stress hormones, inflammation, and autonomic alterations [10]. Both chronic and acute stressors can shift the gut bacteria in several regions of the body, and studies actually demonstrate that catecholamines (the hormones released during stress) can elevate certain bacterial levels 10 000-fold and intensify their infectiousness in just 14 hours.

As such, implementing good stress management practices is key to keeping stress hormones down and maintaining gut microbial balance. Here are some ideas:

  • Do deep breathing
  • Go for a walk outside
  • Exercise
  • Meditate
  • Listen to music
  • Go in the sauna
  • Talk to a friend
  • Journal

Why good gut health is critical for athletes article by PERFECT Sports

Get enough sleep

As athletes, you’re probably well aware of the nasty effects that come with sleep deprivation, like brain fog, fatigue, delayed reaction time, headaches, and more. But did you know that poor sleep can also influence gut bacteria composition? It actually goes both ways. Sleep can affect gut health, and the health of your gut can influence sleep patterns.

There’s ​​a fair bit of evidence suggesting that the gut microbiome not only affects digestion, metabolism, and immune function but also regulates host sleep and mental states via the microbiome-gut-brain axis [8]. Studies also find that total microbiome diversity is positively correlated with increased sleep efficiency and total sleep time, and negatively correlated with waking after sleep. They also found a positive correlation between total microbiome diversity and interleukin-6, which is a cytokine that’s known for its effects on sleep [16].

While getting good quality sleep can be challenging for the best of us, it’s key to practice good sleep hygiene. That means:

  • Avoiding electronic use 2-3 hours before bed
  • Sleeping in a cool environment
  • Limiting external light exposure
  • Limiting caffeine consumption after 2 pm
  • Avoiding large meals 3 hours before bed
  • Implementing a bedtime routine

Why good gut health is critical for athletes article by PERFECT Sports

Limit toxin exposure

Chemical and environmental toxicity isn’t something that a lot of people think about but it;’s something we’re constantly exposed to. Whether it’s fumes from vehicles or toxins from cleaning and self-care products, the list is virtually endless. And while you may be thinking you are safe from harm’s way, the chemicals emitted by many of these things are subtly interfering with the health of your gut. Studies have shown that ​​exposure to certain xenobiotics leads to functional perturbation in the gut microbiome, which can have far-reaching effects on overall health and well being [18]. But these chemicals also damage the liver, which is responsible for detoxification.

But where do these toxins come from?

  • Food (check out the EWG for more information on pesticides in food)
  • Cleaning products
  • Houseware items (beds, couches, carpets in the form of off-gassing)
  • Vehicle exhaust
  • Cosmetics and self-care products
  • Cookware
  • Plastic products
  • Drinking water

Why good gut health is critical for athletes article by PERFECT Sports

Limit refined sugar and carbohydrates

We all love the taste of sugar and unfortunately for us, so do the bad bacteria in the gut. When you give them what they need to thrive, they can quickly overtake the good guys and leave you dealing with severe dysbiosis. Research has shown that a diet high in sugar increases the relative abundance of Proteobacteria in the gut, while simultaneously decreasing the abundance of Bacteroidetes that play a role in mitigating the effects of endotoxins, along with reinforcing gut barrier function [15]. As such, a high sugar diet can shift the balance of microbiota towards pro-inflammatory properties and decrease the capacity to regulate epithelial integrity and mucosal immunity. As a result, there’s an increased tendency to promote metabolic endotoxemia, systemic (low grade) inflammation, and the development of metabolic dysregulation.

While limiting consumption of added sugars may be easy to do, sugar is sneaky and hides under more than 51 different names, so reading labels and knowing the ingredients in your foods is key to avoiding it.

Why good gut health is critical for athletes article by PERFECT Sports

Avoid using antibiotics

While taking antibiotics to target a bad bacteria in your body may get the job done, antibiotics don’t differentiate between good and bad bacteria–they kill everything in their path, which means that you’re left with an altered gut composition and the potential for dysbiosis. Evidence suggests that antibiotic use can have several negative effects on the gut microbiota, including reduced species diversity, altered metabolic activity, and the selection of antibiotic-resistant organisms, which can lead to antibiotic-associated diarrhoea and recurrent C. difficile infections. There is also evidence suggesting that exposure to antibiotics in childhood can lead to several gastrointestinal, immunologic, and neurocognitive conditions [14].

If a dose of antibiotics is necessary, ensure you’re always loading up on a heavy dose of probiotics after completion. Some people make the mistake of taking probiotics while on antibiotics, but the antibiotics will kill the probiotics as long as you’re taking them, so it’s best to save them until the dose is completed.

Why good gut health is critical for athletes article by PERFECT Sports

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Shea Pierre – Coach and Owner of Pierre’s Elite Performance

A Father & Loving Husband First, Sports Performance Coach, Former Professional Football Player, Entrepreneur and Motivator second. Shea went from training athletes in his basement, to being a head college strength and conditioning coach to then become the head strength and conditioning coach of the Toronto Argonauts in the CFL. He has now spread his knowledge to 50,000+ elite athletes worldwide and continues to be a go-to strength coach for professional athletes.


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