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the athletic microbiome

Daybreak finds many a bicycle racer putting in grueling hours in the saddle, riding long distances through the sunrise and morning mist to build cardio endurance. On the hardest days, this baseline training is capped with sprint intervals or hill repeats, the extreme efforts to push riders into the red zone and challenge their muscles, which then rebuild better, stronger, faster on recovery days.

Plotting their training regimens, bike racers target their leg muscles, heart, and lungs. Mountain biker Lauren Petersen considered something more — her gut.

Petersen, who has a PhD in genetics, had a gut feeling that her microbiome may play a key role in her athletic performance. This hypothesis led her down a research path, which she detailed on the Nourish Balance Thrive podcast in 2017 and 2018.

The gut microbiome is the vast ecosystem of microorganisms and their genetic material inhabiting our gastrointestinal tracts. Not so long ago, we were taught to fear all contact with germs, wash our hands religiously, and liberally use antibiotics to protect ourselves. Now, in just two short decades since researchers began to understand the workings of the microbiome and the term became popular parlance, we’re learning to embrace many of those same germs.

Trailblazing researcher Alessio Fasano, MD, professor in the Department of Nutrition at the Harvard T. H. Chan School of Public Health, now hails the microbiome as an “invisible organ” that shapes our lives. Others call the microbiome a second brain.

We contain multitudes of bacteria, fungi, parasites, and viruses — as many as 100 trillion, in fact. Human cells actually make up only half of our bodies; the other half is composed of microbes. And, as Petersen learned, not only does the 21-foot-long gastrointestinal tract host a microbiome, but scientists are discovering microbiota in our eyes, skin, and mouth — and probably elsewhere.

So, what does the gut microbiome do? More — maybe much more — than we likely realize. Researchers now recognize that it plays a role in digestion and nutrition absorption, immune-system and brain function, and mental health.

Petersen suspected it also affected how well she rode her bicycle.

Her athleticism had been suffering. She contracted Lyme disease when she was 11 and spent the next 10 years taking “all the antibiotics that you could name,” she explained on Nourish Balance Thrive. By the time she was 21, she was finally cured of Lyme, but at a cost: She suffered chronic exhaustion and stomach issues so severe she could hardly digest food.

She searched for a cure during graduate school, still striving to train for racing but so worn down she could only muster the strength to ride her bicycle twice a week, at best. The blood tests and stool tests doctors ordered offered no clues.

“Everything was fine,” Petersen said. “But I knew something was wrong.”

While working toward her PhD, she learned about the American Gut Project at the University of California, San Diego, where researchers were attempting to map the human microbiome, an effort akin to the Human Genome Project’s sequencing of DNA. “This little green light went off in my head,” Petersen remembered.

She submitted a fecal sample and the results showed her microbiome was devoid of healthy bacteria. “It was shocking.”

By the time Petersen turned 31, in 2014, she decided there was only one solution: a fecal transplant of healthy bacteria. But the U.S. Food and Drug Administration had restricted the enema-like procedure in 2013; it was legal in the United States only when used to battle severe cases of Clostridium difficile infection, which causes diarrhea and colitis.

It was Petersen’s mom who suggested they do it themselves at home.

Copious research had warned Petersen of the potential dangers. But she recruited another athlete as a donor: an elite bike racer whose microbiome had been deemed healthy after a recent bout of salmonella. So, while writing her doctoral dissertation, Petersen scrubbed her system clean with antibiotics, then performed a DIY fecal transplant.

During the transplant process, human feces containing a balanced suite of beneficial microbes are transferred from a healthy individual to someone needing their gut flora replenished. A DIY transplant employs a sanitized kitchen blender and store-bought enema kit. [Editor’s note: DIY fecal transplants are not legal or recommended by medical doctors; rather than curing microbiome problems, they can cause them.]

“It’s very, very unpleasant,” Petersen recalled.

It was also simple and fast. And the effects manifested quickly.

Within a month, she was eating normally and experiencing no stomach discomfort for the first time in two decades. Two months later, she was back on her bike, training vigorously. She began to race again — and win.

Based on her experience, Petersen launched the Athlete Microbiome Project, studying athletes’ microbiota as part of the National Institutes of Health–funded Human Microbiome Project at The Jackson Laboratory for Genomic Medicine in Farmington, Conn.

It was while discussing her new research in 2017 that the story of Petersen’s fecal transplant broke in the mainstream press with sensationalized stories everywhere ­— from the Washington Post to ESPN — displaying all the glee of toddlers saying a naughty word out loud. As Bicycling magazine queried, “Is Poop Doping the Next Big Thing?”

Fellow scientists, including Jonathan A. Eisen, PhD, genomics professor at the University of California, Davis, were harsher, poo-pooing her DIY transplant.

They were missing the point.

Poop doping wasn’t the next big thing; the future was something far simpler. What they overlooked was the prescient message that Petersen delivered: She was thinking big by thinking microscopic.

Petersen predicted that someday soon athletes would be able to pop a pill containing specially formulated doses of probiotics — beneficial living microorganisms — to “train” their microbiomes for athletic performance.

Gut Check

It seems fitting that the first study of athletes’ microbiomes would be connected to a sport offering plenty of opportunities to get down and dirty with germs. Professor Fergus Shanahan, MD, at Ireland’s University College Cork, asked Michael Molloy, a former team doctor for Ireland’s famed national rugby team, if he could help him study the squad’s feces to assess their microbiomes.

“We had to sell it to [the players],” Molloy told Outside magazine. “But when we talked about possibly improving performance — well, you know, they’d eat cow dung to increase performance.”

In groundbreaking research published in 2014 in the journal Gut, Shanahan, Molloy, and their academic team found that the 40 rugby players had lower inflammatory and improved metabolic markers, plus dramatically more diverse microbiota than two nonathlete control groups. In particular, their microbiomes boasted significantly elevated levels of Akkermansia bacteria, which other studies have shown to improve metabolic function and enhance gut-barrier function.

Shanahan and Molloy concluded that exercise and diet improve gut microbial diversity — and a more diverse microbiota improves athletic performance. “Diversity is important in all ecosystems to promote stability and performance,” the study authors wrote. And they ­predicted that “microbiota diversity may become a new biomarker or indicator of health.”

Their study was the first of many in what has become a flourishing field of research. In 2017, Petersen’s Athlete Microbiome Project published its exploratory pilot study in Microbiome. They assessed the fecal DNA in the microbiota of a small selection of elite cyclists — just 33 people.

A number of the elite cyclists had a surfeit of Methanobrevibacter smithii, which the study authors suggest may spur “metabolic efficiency.” “Theoretically, this could lead to reduced recovery time from intense exercise and may even influence race performance,” Petersen concluded.

They also had a host of Prevotella, which boosts biosynthesis of branched-chain amino acids; BCAAs may not enhance performance, but they do promote muscle-protein synthesis and decrease muscle fatigue.

Oddly, Prevotella is rare in American adults’ microbiomes. It’s connected with diets high in fiber and carbohydrates and more often found in people from central Asia and Africa. This sparked Petersen to ask:

Which came first — the chicken or the egg? Does athletic training nurture microbial diversity in the gut, or does a special mix of microbes foster athletic superpowers?

“Our results raise several questions,” Petersen wrote. “Would a given cyclist have an increased chance of becoming a professional athlete if they were colonized by M. smithii due to increased metabolism of the gut microbiome? Or would a lifetime of training, competition, and a diet high in complex carbohydrates somehow influence a better niche for M. smithii to thrive where the gut is constantly subjected to physiological perturbations?”

Further studies followed, involving America’s Cup sailors, bodybuilders, elite distance runners, Olympic rowers, ultramarathoners, and participants from other disciplines. But many of the studies were based on small pools of participants, such as both Shanahan’s and Petersen’s; could not control for all dietary elements, like ­Shanahan’s; or were observational.

“A big issue is drawing causation from observational, cross-sectional studies,” Arizona State University nutrition scientist Alex Mohr, PhD, told Nature. “We really need some longitudinal and, importantly, experimental work.”

In a 2020 Journal of the International Society of Sports Nutrition review of all these studies to date, the authors concluded that “the gut microbiota, with its ability to harvest energy, modulate the immune system, and influence gastrointestinal health, likely plays an important role in athlete health, well-being, and sports performance.”

The race was now on to pinpoint the beneficial bacteria to create a probiotic performance pill.

The New Frontier of Fitness?

“When we first started thinking about [a probiotic for athletes], I was asked whether we could use genomics to predict the next Michael Jordan,” says Jonathan Scheiman, PhD, then a research fellow at Harvard Medical School and Harvard University’s Wyss Institute for Biologically Inspired Engineering. “But my response was that a better question is: Can you extract Jordan’s biology and give it to others to help make the next Michael Jordan?”

Scheiman, himself a former Division I college basketballer, made his comments prior to a 2017 meeting of the American Chemical Society at which he presented a longitudinal — yet still small — study subsequently published in Nature Medicine. For the research, he spent two weeks collecting stool samples from 20 Boston Marathon runners and keeping them on dry ice in his car so he could study their microbiomes from before and after the race.

“Can you extract Jordan’s biology and give it to others to help make the next Michael Jordan?”

“The bugs in our gut affect our energy metabolism, making it easier to break down carbohydrates, protein, and fiber,” Scheiman says. “They are also involved in inflammation and neurological function. So perhaps the microbiome could be relevant for applications in endurance, recovery, and maybe even mental toughness.”

In particular, Scheiman’s team found a prevalence of Veillonella in the marathoners’ guts. The bug speeds the breakdown of lactic acid; when injected into mice, Veillonella upped the amount of time they could run on a treadmill by a potentially game-changing 13 percent.

“The study provides one of the most compelling examples of ‘metabolic symbiosis’ between the human host and microbiome that could be broadly harnessed as a probiotic strategy not only for athletes but also to improve health in patients,” concluded study coauthor George Church, PhD, a professor of health sciences and technology at Harvard University and MIT and leader of the Wyss Institute’s Synthetic Biology platform.

Scheiman and colleagues then launched a startup company, Fitbiomics, to boldly enter what they call “the new frontier of fitness.” In 2021, Fitbiomics unveiled Nella, a probiotic pill derived from elite athletes to provide “next-generation wellness for everyone.” Other such probiotics are also debuting, backed by their own research. In fact, the flurry of flora now on store shelves would fall under what the UC Davis’s Eisen has dubbed “microbiomania.”

Most of the research to date agrees that the gut microbiome and exercise have an intimate and symbiotic relationship. But if there’s one consistent finding, it’s that studies pinpoint different bacteria in the microbiomes of different types of athletes.

Do we even know for sure what a healthy, “normal” human microbiome comprises?

This raises a larger question: Do we even know for sure what a healthy, “normal” human microbiome comprises?

A decade on, the American Gut Project continues its work, now as the Microsetta Initiative, but with trillions of bacteria to map, the science remains in its infancy. And neither the chicken-egg cycle nor causation are fully understood.

Functional-medicine trailblazer Frank Lipman, MD, warns that our understanding of the microbiome has a long way to go. “You can’t take this probiotic for this result. People simplify the microbiome; it’s such a complicated organ system.”

Others caution against expecting the microbiome to unleash true athletic superpowers. Old Dominion University exercise science professor Patrick Wilson, PhD, RD, author of The Athlete’s Gut, contends that the various studies so far are small and “the mechanisms to explain these supposed improvements in performance are ­pretty speculative.”

At this stage, the athlete’s microbiome remains a frontier — and it’s likely that we don’t even know what we don’t know.

Feed Your Gut

When we think of athleticism, we tend to think of powerful muscles, a strong heart, and mental smarts. But we may not be thinking small enough: A multitude of studies have found that a diverse microbiota in our gut feeds our performance.

In addition, the microbiome can boost performance in other ways, such as keeping you from getting sick and missing out on training. “It may seem odd that bugs in your gut can impact your respiratory tract, but the presence of certain microorganisms in your gut leads to an uptick in the production and activity of immune cells and compounds that offer protection from respiratory infections,” notes Patrick Wilson, PhD, RD, author of The Athlete’s Gut. This, in turn, can improve your availability — the amount of time you’re fit to train and compete.

Experts offer advice on how you can keep your gut in top form.

⋅ Eat plenty of plants. “Building the foundation of your diet on plants is key for building the best foundation for good health and optimum performance,” says exercise physiologist and nutrition scientist Stacy Sims, MSC, PhD.

The more plant types a person eats, the higher the microbial diversity of their gut, noted the American Gut Project, now called the Microsetta Initiative. A plant-centric diet is anti-inflammatory and good for your gut, aiding digestion and providing lots of fiber.

It also helps balance hormones. The microbiome is “so instrumental in managing sex hormones that recent research has suggested the concept of a ‘microgenderome’ to indicate the interplay between the gut microbiome and sex hormones,” Sims says.

⋅ Prioritize protein. Athletes need sufficient protein to build and maintain muscles, Sims says. (For advice on how much protein you may need, see “Protein Power: What You Need to Know“; for sources of plant-based protein, see “How to Get Enough Protein From a Plant-Based Diet.”)

⋅ Get your probiotics. While there are still questions about how probiotics may affect your athletic performance, it’s clear that the healthy bacteria in probiotic foods are good for your microbiome as a whole. The best sources are fermented foods, such as yogurt, kimchi, sauerkraut, and kefir.

You can also supplement with probiotic capsules, which contain billions of live bacteria. “Probiotic supplements are sources of microorganisms that can shift the microbial balance of the lower intestine,” explains Paul Kriegler, RD, Life Time’s nutrition program manager.

Whichever probiotic you choose, ­Wilson advises a trial period of at least one to two weeks prior to a competition to make certain it doesn’t cause unwanted side effects, such as gas, bloating, or loose stools. (For more on probiotic foods and supplements, see “Everything You Need to Know About Probiotics.”)

⋅ Feed the bacteria with prebiotics. Ample fiber is key to feeding those healthy bacteria. Prebiotic foods include apples, asparagus, onions, garlic, leeks, oatmeal, and legumes. (For more on prebiotics, see “Why Prebiotics Are as Important as Probiotics“; for more on fiber, see “Why You Need to Eat Fiber.”)

⋅ Just say no to ultraprocessed foods. Those irresistible, lab-engineered processed foods don’t help your athleticism at all. Refined sugary foods promote bad bacteria, which can lead to inflammation, Sims explains.

Processed foods contain fewer nutrients and can hamper your immune system. Recent research suggests they can also promote anxiety, depression, and other mental health concerns.

Skip the NSAIDs. “Nonsteroidal anti-inflammatory drugs can directly impact the composition and function of the gut microbiota, and can lead to dysbiosis, or an imbalance of microorganisms in our microbiome,” says Sims.

Be careful with antibiotics. Antibiotics can dramatically harm the gut’s microbial diversity, according to the Microsetta Initiative. And we often unknowingly consume antibiotics in the meat we eat, a good reason to opt for organic meats.

Soothe Your Gut

Most athletes occasionally experience some sort of gut problems during training or competition, says Patrick Wilson, PhD, RD. Nausea, abdominal cramping, bloating, diarrhea — any one of these “can quickly kill a solid performance.”

“Gut issues can be caused by a wide variety of different things, and I’d advocate for trying to identify the underlying cause,” he advises.

If you’re dealing with gut ­dysbiosis — disruption of the gut microbiome — none of our experts recommend a fecal transplant. Rather, they focus on several common causes, along with mitigation strategies.

⋅ Race-day indigestion: As running legend Bill Rodgers once famously warned, “More marathons are won or lost in the porta-toilets than at the dinner table!” When you compete, your body typically shuts down your digestive system and diverts the energy to powering your limbs and muscles. The reduction of blood flow to the gut can cause tummy troubles, from mild to dramatic — side stitches, diarrhea, reflux, nausea, and more.

You can strive to prevent this with several simple tactics:

Eat only familiar foods leading up to an event.

Don’t eat for an hour or two before a race.

Keep well hydrated but consume sugary sports drinks or energy gels in moderation.

“Most people feel best limiting their intake to liquids or low-fiber foods within two hours of the start of an exercise session,” explains Life Time master trainer and dietitian Samantha McKinney, RDN, LD. “Using something like essential amino acids — which are the building blocks to protein and easily digested — can be helpful. If you know you’re going to need to eat, try having nut butter on either a banana or rice cake. Anything heavy or higher in fiber can cause distress during exercise.”

⋅ Food reactivity: A food intolerance, sensitivity, or allergy can disrupt your whole life, not just a 5K race. Food reactivity can cause diarrhea or constipation, gas and bloating, irritable bowel syndrome, leaky-gut syndrome, and more.

Testing can determine food reactivity, and an elimination diet is one strategy that could help put your system back on track. Over-the-counter digestive enzymes can also help. (For more on food reactivity, see “Allergy, Sensitivity, or Intolerance? A Guide to Food-Reactivity Issues.”)

⋅ Bacterial infection: Bacterial invaders from contaminated water or food or a virus can disrupt the best-laid training plans. Check with your healthcare provider to determine whether it’s food poisoning. Often, you will have to wait for your system to purge the bad bugs. Keep well hydrated.

⋅ Anxiety or stress: Stress can stem from your daily life or, ironically, the thrill of a race. “Exercise is considered a ‘good’ stress, but if you’re living a stressed-out lifestyle and adding in high-intensity exercise, it’s possible to get too much of a good thing,” explains ­McKinney. “An overload of stress can cause imbalances in cortisol, which can trigger digestive upset.”

“For someone with anxiety and gut issues, engaging in activities that incorporate mindfulness and stress reduction may be helpful,” Wilson adds. Deep breathing, listening to music, or mindfulness meditation; acupuncture or hypnosis; or sessions of cognitive behavioral therapy may help.

Learn More

The gut microbiome plays a crucial role in our overall well-being, from digestion and immune function to mood and mental health. You can learn more about the importance of gut health by exploring our collection of articles.

This article originally appeared as “No Guts, No Glory” in the May 2023 issue of Experience Life.

Michael Dregni

Michael Dregni is an Experience Life deputy editor.

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  1. Great article. Very well written and informative. I have been studying gut health for more than 30 years, having written the first book for patients with irritable bowel syndrome back in 1989. Everything we do starts with “healing and sealing the gut.” Thanks. —Gerard L. Guillory MD

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