Everything You Ever Wanted To Know About The Microbiome (But Were Afraid To Ask)

The microorganisms in your gut microbiome can affect how well you train and race. Learn the latest science on the athlete's microbiome, plus ways that you can make it work harder for you.

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Here’s some food for thought: In some ways, you are more bacteria than human. You are host to so many microscopic organisms that if you counted each one, you’d find they equal the number of human cells in your body. Sounds disturbing, but it’s actually a good thing – especially if you’re an athlete.

As scientists discover more about the microorganisms in your body, they’re uncovering important information about how influential it could be to athletes. As it turns out, the balance of bacteria inside of you can have just as much impact on health and performance – if not more – than your genetics. Read on to learn about the potential role the microorganisms in your gut microbiome play in how well you train and race, and ways that you can make the microbiome work harder for you.

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What exactly is your microbiome?

These days, most people have heard the word “microbiome,” yet few understand what it actually is. In short, the human microbiome is composed of communities of bacteria (and viruses and fungi) and their genes that live on our bodies and inside us – an estimated 100 trillion microbes, the bulk of which live in our gut. This is the area that is most often studied.

But the gut isn’t the only place where these organisms live. Various organs have distinct microbial inhabitants, too. Did you know that your mouth has its own distinct microbiome? It’s true, and its unique makeup equals unique effects. Helpful bacteria on the back of your tongue convert nitrate in foods like beets into a form of the compound that makes aerobic exercise more efficient. (Think of that the next time you are chugging back beet juice in the hopes of gaining an edge, and thank your microbiome.)

No matter what area we’re talking about, however, the microbiome is looking to play a numbers game. For better health, the goal is that the good bacteria (called probiotics) exist in a proportion that can counterbalance the disruptive bad bacteria. In recent years, probiotic balance has been linked to everything from improved cholesterol levels, to better brain functioning, to immune system resilience. An international team of scientists recently found associations between particular gut bacterial species, some of which were new to science, and metabolic risk factors (inflammation, blood sugar, etc.) for conditions such as diabetes, heart disease, and obesity. The microbes were determined to be more strongly associated with a person’s risk of certain illnesses than their genetics.

RELATED: How the Microbiome Might Affect Motivation and Performance

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The athlete’s microbiome

It’s not just your cardiovascular system and muscles you should be training to make you a better athlete, but also your gut microbiome.Some intriguing evidence suggests that the composition of the gut microbiota could contribute or hinder athletic performance by influencing microbial metabolite production, gastrointestinal physiology, and immune modulation. Who would have thought that certain bugs could influence your split times?

Currently, there is no consensus in the scientific community on what true impact a “healthy gut” microbiome has on athletic performance. But there is some promising research to suggest that it might fairly significant. A University of Tasmania study found that runners performed better on a treadmill in 95-degree heat after taking a multistrain probiotic for four weeks which, in theory, should have improved the composition of their microbiome. This 2022 investigation in the International Journal of Environmental Research and Public Health showed that cyclists who consumed a multistrain probiotic of beneficial bacteria for four months increased their aerobic exercise capacity. Investigators in Taiwan discovered that fertilizing the gut with a particular strain of Lactobacillus bacteria increased physical adaptations to training in athletes in a way that could improve endurance performance. Members of the genus Veillonella in the microbiome have been discovered to aid in themetabolic conversion of exercise-induced lactate into propionate, a short-chain fatty acid believed to improve exercise capacity.

RELATED: 6 Probiotic Foods for Runners

With this said, we are still a long, long way off from fully understanding the role the human microbiome plays in exercise performance. We are only in the early stages of uncovering which microbiota species impact athletes most and how to best alter the microbiome to glean the greatest benefit. Do athletes need to take supplements, or can an optimal microbiome for performance be achieved through diet alone? Despite what advertising or influencers try to tell you, we simply don’t have enough scientific evidence to say for sure.

It’s unlikely that the gut microbiome and probiotics provide any direct ergogenic benefits for athletes. However, they could indirectly promote better fitness through several measures including increasing immunity, improving GI function, producing beneficial metabolites, and allowing you to better utilize nutrients from food.

Let’s take a closer look at a few of the possible ways that a robust microbiome can help athletes rise to the occasion.

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A happier gut (and fewer port-o-john stops in your race)

Multiple studies and plenty of anecdotal evidence show that gastrointestinal issues like bloating, nausea, cramping, and diarrhea are common in athletes—particularly those who engage in endurance events, and these issues understandably often impair performance.

An unhappy gut often makes for an unhappy set of miles. It’s not entirely clear what exactly causes these loathed issues, or how they can be prevented, but a handful of preliminary studies (including this one) suggests that populating the digestive tract with more probiotics could serve to reduce thefrequency or severity of symptoms during workouts.

Some scientists believe probiotics help by making the gut lining healthier, thereby increasing tolerance to the stress of exercise and also improving how your digestive tract handles sports drinks and other nutrition products. Carb malabsorption in the digestive tract during exercise is thought to be a big contributor to stomach woes, and probiotics may be something that can help the gut process the influx of carbs from sport nutrition while in motion.

But not all research has shown that probiotics are the answer to bidding adieu to GI issues. There are simply too many variables that can influence results, including strains used, and what level of exposure is required. The background diet of an individual athlete is also important, since this can impact what type of microbiome they are starting out with. We should expect a lot of individual variability among athletes.

Fewer cases of the “taper flu”

Trail runner’s strenuous training can erode their immunity, making them more vulnerable to catching viruses that lead to colds and flus, especially during peak training periods (which is why so many athletes fall ill after their heaviest training periods or post-race). But a daily dose of “good” bacteria could bring your immune systems back up to speed. This is according to a study in the British Journal of Sports Medicine, which reported that runners taking the probiotic Lactobacillus fermentum cut their incidence of respiratory illness in half during a four-month winter training block. A similar result has been found in some competitive cyclists. A 2022 review study also found that there is enough reasonable evidence to say that probiotics could help athletes reduce the risk of developing the sniffles as well as reduce the severity of symptoms.

A better balance of bacteria in the gut microbiome through certain dietary and supplementation measures may improve mucosal immunity, or the ability of cells in the body’s mucous membranes to fight off infection throughout the body during periods of training. In other words, a healthy gut may make you a more resilient athlete. However, it still remains to be determined how impactful this is on your chances of getting sick, and if some bacterial strains are more powerful than others.

Better muscle functioning

The gut-brain axis is the two-way biochemical signaling that takes place between the gastrointestinal tract and the central nervous system, linking emotional and cognitive centers of the brain with intestinal functions – which is why you notice your appetite changes with your mood, or why your nervous pre-race butterflies make you feel nauseous. Now, some researchers are speculating that a gut-muscle axis exists.

In this case, an optimal intestinal microbiota composition would benefit an athlete by impacting everything from muscle protein synthesis (i.e., making new muscle) to energy generation within muscle cells to muscle inflammation following exercise to glycogen storage levels. A study in mice who were administered antibiotics (which skews the balance of bacteria in the gut) indicates that a disrupted gut microbiome could impair muscle growth in response to exercise.

It’s thought that microbial-derived metabolites can work their way to skeletal muscle, where they can regulate how it functions – in other words, how your gut speaks with your muscles. Some believe that if we can fine-tune this gut-muscle axis, we can produce super-athletes and also help older individuals maintain better muscle functionality.

There is a long way to go before the finer points of this process are uncovered by science (to say studies are scarce would be accurate), but the idea that a healthy microbiome can make our muscles perform better and also better handle the rigors of training is certainly intriguing.

More energy in the tank

The composition of our gut microbes appears to influence how much energy we extract from the food we eat. Some athletes are at an advantage by having a microbiome containing more bacteria, particularly Bacteroides, that are more effective at extracting energy from food which can be used to meet training needs. The makeup of your microbiome may allow you to clean more carbohydrate calories from your pasta which in turn will help power your muscles when you’re on the move.

On the flip side, microbiome makeup might be why some people are more prone to putting on weight than others – more calories are available for the human host from the same amount of food.

Better processing of vitamin D

Once consumed in the diet or generated in the skin from sun exposure, a precursor form of vitamin D must be converted into its active form for it to have a biological effect in the body. We have evidence that sufficient amounts of active vitamin D can be important for improving endurance performance, though it’s not clear why.

Scientists at the University of California San Diego discovered that microbiome diversity – the variety of bacteria types in a person’s gut – was closely associated with someone’s levels of active vitamin D in the body. Subjects with 12 particular types of bacteria in their gut microbiomes had lots of active vitamin D. It might be that certain species of bacteria in a healthy microbiome play an important role in this conversion.

More motivation to train

When it comes to training, motivation is huge. When you are feeling down in the dumps, the chances that you’re going to be jazzed to go for a long run are rather slim. But this isn’t solely a psychological phenomenon – your microbiome might also play a role in keeping your stoke levels high.

Of all the many ways the teeming ecosystem of microbes in your might affect health, its potential influence on the brain may be the most provocative. A study of two large groups of Europeans has found several species of gut bacteria including the Coprococcus and Dialister strains are missing in people with depression but not so for those who were more upbeat. The researchers can’t say whether the absence is a cause or an effect of the illness, but the study did show that some bacteria affect nerve cell function in the brain, impacting mood. For instance, Coprococcus seems to have a pathway related to dopamine, a key brain signal involved in mood. The same microorganism also makes an anti-inflammatory substance called butyrate, and increased inflammation in the brain is implicated in depression.

Further, an investigation in the journal Nature found that of all the factors tested in mice (including genetics), gut bacteria composition influenced the desire to exercise the most. It does this by activating the gut-brain axis and influencing the regions of the brain that control motivation. The researchers found that mice with certain gut bacteria (in this case, Eubacterium rectale and Coprococcus eutactus) had better running performance. The microorganisms produce small molecules known as fatty acid amides that stimulate gut nerve receptors, which connect directly up the spine to the brain. There, they influence motivation by increasing the release of the neurotransmitter dopamine. Keep in mind that this was an animal study, so we’re not positive that the same association would apply to bipedal athletes, but it’s certainly possible this microbiome-brain connection puts a new spin on the sports saying performance “is all mental.”

But we still have way more questions than answers when it comes to how the microbiome and probiotic consumption could impact performance. Until we understand more about the mechanisms by which microbes work, it’s too premature to declare the microbiome an athlete’s best friend. But if you’re one of those athletes who are always on the hunt for an edge, it’s understandable why you would be eager to keep your microbiome in tip-top shape.

RELATED: Are Gut Problems In Your Head?

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Five tips for optimizing your microbiome

When you eat, you are not just nourishing your body – you are feeding the trillions of microbes that live inside your gut, too. When now have a growing body of scientific evidence that dietary patterns have a profound impact on microbial composition in the gut, in turn affecting a range of metabolic, hormonal, and neurological processes that are involved in health outcomes and performance.

None of what we have discussed so far has established a definitive link between improving your microbiota composition and finding a spot on the podium at your next race. Still, if you’re a serious athlete, it seems clear that you should pay attention to what is going on in your gut. It’s important that the good bacteria in your microbiome keep the bad guys in check. Scientists are discovering the critters in our digestive tracts are affected greatly by the way we treat them, namely the dietary choices you make each day shapes your inner ecology. Diet is widely recognized as one of the main modifiable drivers of gut microbiota health and variability, and its influence on microbiota composition is a very active area of investigation. Here are a few ways that you can show your microbiome some love:

1. Eat more of the good stuff

Research is pretty clear that an overall healthy dietary pattern can do your microbiome some good. This large-scale population-based study published in the American Journal of Clinical Nutrition determined that the usual consumption of foods most often considered to be “healthy” such as fish and fruits were associated with a greater microbiome diversity of desirable bacteria whereas less desirable food items like sugary drinks, processed meats, and fried foods were negatively associated with microbiome diversity.

According to research published in the journal Nature Medicine, your gut microbiome thrives when your diet includes more vegetables, nuts, eggs, and seafood as these appear to feed the good bacteria in your gut, while sweetened beverages and highly refined grains feed the bad bacteria thereby allowing these nefarious fellows to thrive. Another study discovered that greater adherence to the Healthy Eating Index, a measure of diet quality used to assess how well a set of foods aligns with key recommendations of the Dietary Guidelines for Americans, was significantly associated with increased abundance of potentially beneficial bacteria but decreased harmful ones in the digestive tract of individuals. One investigation suggests eating too much added sugar can directly deter beneficial microbes from gaining a foothold in our guts. And a study with 1,425 people in the Netherlands showed that those who consumed a diet high in processed and animal-derived fatty foods (in other words, many fast foods), had greater levels of destructive bacteria that produce toxins that harm the gut.

All this is to say is that focusing mainly on eating whole foods and fewer ultra-processed ones will do your microbiome some good. And that could end up giving you a competitive edge.

2. Power up on more plants

You don’t need to go full-on vegetarian or vegan to foster a robust microbiome, but putting more plants on your plate certainly is a path forward to a healthier gut. Research suggests that diets that feature more plant-based foods tend to result in a higher diversity of beneficial microbiota in the gut of people. And there is evidence that the composition of our microbiomes can change quickly in response to dietary shifts including eating more plant foods.

It’s also important to make it a point to eat as many different plant foods as possible. As part of the American Gut Project, University of California San Diego School of Medicine researchers discovered that people who ate more than 30 different types of plant-based foods per week had a greater diversity of gut microbiota than those who ate 10 or fewer types of plant foods in any given week. Similarly, this 2022 study in the American Journal of Clinical Nutrition determined that greater diet diversity is associated with a greater microbiome diversity and the production of potential health and performance-boosting bacterial-derived metabolites.

Certain components of plant-based foods like fiber and polyphenols found in items such as legumes and vegetables can serve as a fuel source for your microbiome so the helpful critters in there can become more abundant. In other words, plant foods act as prebiotics, which nourish the bacteria already in your body. In return, colonic microbial fermentation of plant components results in health-promoting and perhaps performance-enhancing metabolites.

On the flip side, some research suggests that a meat-heavy diet can shuffle around the types of microbes thriving in the gut to favor less beneficial types. Also, too much animal-based protein may promote microbial protein metabolism that generates potentially harmful byproducts that may sit in the gut, increasing the risk of negative health outcomes. A study in the journal Nature Microbiology found that certain gut microbes, found in greater quantities in people who eat red meat, may be responsible for turning the dietary nutrient carnitine into the chemical TMAO, which is linked to cardiovascular risks. So maybe consider going easy on the bacon and instead making sure your shopping cart is full of a variety of plant foods like whole grains, beans, lentils, vegetables, nuts, seeds, and fruits, and then work them into each of your meals and snacks. But in no way does this mean that a healthy omnivorous diet that includes plenty of plant-based foods and reasonable amounts of lesser processed meats is bad news for your microbiome.

RELATED: When Plant-based Eating Becomes Unhealthy

3. Learn to love fermented foods

It turns out one way we can give this colony of microorganisms a boost and, in turn, improve health and performance, is to feed it more not-so-fresh foods and the probiotics they contain. After analyzing blood and stool samples of 36 healthy adult participants, Stanford School of Medicine researchers discovered that a 10-week diet high in fermented foods including yogurt, kefir, kimchi, and sauerkraut (six servings daily) resulted in measurable improvements in microbiome diversity and decreases in markers of inflammation suggesting improved immune status. This is noteworthy since science has identified that healthy people and perhaps better performing athletes typically have a more diverse microbiome composition than those suffering from chronic conditions. Interestingly, a high-fermented food diet had more impact on the microbiome than a high-fiber diet, suggesting it may take longer for the latter to have a noticeable impact.

Fermentation is an anaerobic process in which microorganisms like yeast and bacteria break down food components (e.g., sugars such as glucose) into other products (e.g., organic acids or alcohol). Historically, this has been used to extend the shelf-life of items like vegetables and dairy. Beyond the potential probiotic effect of microorganisms, the fermentation process may bring about other important benefits including generating bioactive compounds in the food, as well as the reduction of anti-nutrients. It also generates new flavor compounds and explains why yogurt does not just taste like thick milk.

It’s absolutely a good idea to try to sneak more fermented foods into your training diet. This can include adding sauerkraut to sandwiches, kefir to smoothies, and miso to salad dressings. Swigs of kombucha is a good way to rehydrate after a training session while simultaneously fertilizing your gut. But seek out products that have not been heat treated (sometimes labelled “raw” or “unpasteurized”) to better assure the friendly bacteria are still alive. Yogurt with the “live active cultures” seal indicates it hasn’t been heated after fermentation and harbors at least 100 million cultures per gram.

Because probiotics in the gut can diminish unless reinforcements arrive, frequently eating fermented food is key. But if your system isn’t used to eating a lot of bug-laced foods you should start with small bites of fermented food to build up gut tolerance and limit unwelcome side effects like high amounts of gas.

4. Don’t skimp on carbs

Here’s a new way to think about how eating an insufficient amount of carbs when during high volume training can set your performance back: It upsets your microbiome. A groundbreaking study by scientists in the United Kingdom found that highly trained runners who were placed on a lower-carb diet (30% of calories from carbs) performed worse during fitness testing than those who were eating a higher carb diet (60% of calories from carbs). Nothing too surprising here, but what was interesting to learn was that the drop in performance on the lower carb diet was accompanied by a significantly reduced diversity and altered composition of the gut microbiome among the study participants. The increased stress of eating insufficient amounts of carbs to meet training needs may disturb microbial stasis in the gut that, in turn, could have a detrimental impact on performance. So if you are training hard be sure you’re putting enough carbs on your plate.

RELATED: More Carbs Correlates With Less GI Distress in Runners

5. Keep your body (and microbiome) moving

It’s worth noting that the very act of performing physical efforts appears to alter the microbiome in a way that can benefit health and also improve exercise tolerance. Research shows that the microbiome of an athlete may be quite different from that of a sedentary person, and in a good way. For instance, Irish researchers compared the gut microbial composition of 40 professional rugby players with nonathlete controls and found that the rugby players had, on average, twice the microbial diversity. And this study review in Medicine and Science in Sports and Exercise says that it appears exercise is associated with a positive shift in gut microbial composition (higher levels of bugs that produce the beneficial compound butyrate) and this is independent of diet. But the study authors stress that at this point evidence in humans is limited.

For now, it’s unclear whether it is training, diet, or something else that accounts for most of the difference in the gut microbiome of athletes and nonathletes, but exercise likely has a certain measurable effect on the variety of a person’s microbes. That should be additional motivation to regularly work up a sweat.

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Are probiotic-fortified foods good for athletes?

If you’ve wandered the aisles of the supermarket recently, you’ve probably noticed that probiotics are the trend du jour. Everything – granola, protein powders, fruit juices, and cottage cheese – are being fortified with probiotics, all in an attempt for manufacturers to capitalize on the probiotic buzz.

While these products certainly can’t hurt (especially for those who don’t like naturally probiotic-rich foods like yogurt) keep in mind that there is very little data to indicate that probiotic-fortified foods have a noticeable impact on the microorganism quality of our guts. The benefits of probiotic ingestion vary from person to person, so the strain in that probiotic-fortified cereal needs to match the bacterial strain your gut is lacking. While there’s no harm in trying the latest energy bar pumped with probiotics, it might not be giving your body what it needs.

What’s more, it’s often not possible to know how many probiotics you are actually getting in those fortified foods, and if they are at levels shown to be of benefit. There is no guarantee the strains of microbes are still “alive” in a product and able to help you out once consumed. Vague label claims like “supports good digestive health” are fairly meaningless. You need to keep in mind the overall nutritional profile, and watch out for fortified foods that contain high amounts of added sugar, refined grains and unhealthy fats that will cancel out any probiotic benefit.

Overall, you are better served by focusing on more proven ways to bolster your microbiome such as going bigger on whole foods, not simply heavily processed items that have been dusted with strains of bugs.

Should athletes take probiotic supplements?

With all the hoopla about probiotics, it might be tempting to think that you can pop a pill to get your way to microbiome bliss. But you should heed the following supplement pitfalls:

  • A lack of high-quality data supporting benefits from taking these supplements
  • Concerns about industry-supported studies and reviews
  • A lack of regulation by any government agency on the production and sale of probiotics
  • Poor understanding about what strains of probiotics are most useful to each individual.

If turning to a supplement, go with one containing multiple bacterial strains – to better mimic the diversity of our guts – numbering at least five billion colony forming units. Lactobacillus and Bifidobacterium are two heavily studied strains. On the label there should be the genus, species, and strain of each microorganism in the product as well as the colony forming units (CFUs) which tells you how many live microorganisms are in each dose. Pay attention to use-by dates and storage instructions as well.

Now, this doesn’t mean they don’t work. A probiotic supplement can be a rather inexpensive way to help optimize the microbiome.And the right ones can be an easy way to load up on certain probiotics in doses not found in foods.

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The bottom line

It’s crucial to remember that each athlete’s microbiome is completely unique. This makes it difficult for one supplement or food to be effective for everyone, and even more difficult to figure out which one will work for you best. While certain strains of probiotics can help improve GI issues during a race or aid in fending off a cold during peak training times, those aren’t always the ones found in a particular supplement. The onus is on the consumer to look for products containing the strains they need, but that requires some digging through the research.

Ultimately, an ounce of prevention is worth a pound of cure when it comes to the athlete’s microbiome. Following a healthy diet and the advice above will go a long way in creating and maintaining a healthy, balanced microbiome, rather than waiting for things to get out of whack.