“I’ll be the first to admit I eat a decent amount of ice cream,” says obstacle-course racer Amelia Boone. “Definitely more than I should.” (Chloe Crespi)
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Does Your Gut Hold the Secret to Performance?

The microbes in our digestive systems can affect everything from our mental health to our weight and vulnerability to disease. So why not athletic performance? New science is set to revolutionize the way we eat, train, and live.​

It’s never an easy thing, convincing a person to give you their feces.

The instructions are simple enough: defecate, swipe the provided swab across a wad of used toilet paper (no need to be aggressive—so long as the tip is brown, you’ll have enough material for analysis), pop the newly defiled cotton bud into its test tube, and wash up.

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Still, even if the donations are for science, the gross-out factor means that people tend to make excuses. They’re too busy or too tired, or their sample was “off” that morning. No matter. For Embriette Hyde, a scientist at the University of California at San Diego, the value of a fecal sample is too high to let a little thing like squeamishness get in the way. That’s why she has a spiel she’s honed in weight rooms across the squintingly sunny campus. We all have these microorganisms living inside of us, she tells the collegiate tennis players and point guards. What would you do if you knew you could use them to your advantage, to help you perform or recover better? We hope it’s true, but we still need to do the research to find out—she pauses for effect—and you can help by giving us your poop. Hyde grins. “The word poop goes over well with them.”

Hyde manages the American Gut Project at the university’s Knight Lab, which is five years into a deeply ambitious effort to map the average American’s bacterial makeup—what scientists call the human microbiome. But her pet project is studying whether athletes have different, healthier microbiomes than everybody else. And the best way to find out what’s happening inside a person, it turns out, is to analyze what comes out. So far she’s tested upwards of 150 samples from professional and amateur athletes. But if there’s a specific ­superbiome for performance, it has remained elusive.

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Hyde, who is as small and compact as you’d expect a weekend half-marathon addict to be, leads me by airtight chambers used to culture oxygen-phobic bacteria (most of your gut, I learn, is an anaerobic space), past pipetting lab techs and postdocs corralling data. Since it was founded by microbiologist Rob Knight in 2004, the lab has been responsible for some of the most exciting revelations in microbiome studies. Scientists here and elsewhere now believe that our personal microbial universes are intertwined with a host of conditions, including acne, allergies, obesity, anxiety, cardiovascular disease, irritable bowel syndrome, autoimmune disorders, and even cancer.

Only a decade or so into this young field, the connections can still astonish. The bacterial content of an autistic child’s gut looks significantly different from the general population’s. Bacteria found in multiple-­sclerosis patients may contribute to sending the immune system into overdrive and causing the disease’s devastating symptoms. And as Rob Knight himself helped discover in 2013, you can make a sterile rat gain weight simply by giving it bacteria from an obese human’s microbiome.


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“I can’t just be on a trip and think, I’m hungry—oh, there’s a hot dog,” says skier Cody Townsend. “I have to plan ahead.” (Peggy Sirota)

“Everyone responds to diet in their own way,” Knight says, thanks in part to their bacterial makeup. “Some people gain twenty pounds; some people lose ten pounds.” His work, exciting as it is on its face, has also elucidated a fundamental aspect of the microbiome: the bacterial community inside us is always changing—and we can influence it, too. As Knight says, “There’s a lot of potential in terms of being able to, I don’t want to say diagnose, but classify people according to their current level of performance and—more excitingly—their potential for future performance.”

That’s why Hyde’s eyes light up as she opens freezer number seven and pulls out a small tray with 96 individual wells, each containing the raw genetic contents of various athletes’ bacteria. This clear liquid, extracted from feces, could be the key that will one day make us run longer, recover faster, and stay fitter.


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To the uninitiated, the microbiome can be a difficult thing to come to terms with. In your colon, your mouth, your eyes, your skin, your genitalia, are trillions of microscopic bacteria. There are as many of these bugs—among them pill-shaped rods and spherical blobs so small that tens of millions of them are no larger than a grain of sand—as human cells. According to some metrics, in fact, you are as much host as human. Forty thousand different species of bacteria can call your gut home, along with smaller numbers of viruses and fungi. And on a genetic level, your microbial residents dwarf you. The human genome, the sum of all those snippets of DNA you get from your parents and pass along to your offspring, contains some 20,000 genes; your microbiome contains millions. To fully consider the microbiome, you first have to reconsider yourself.

It can be unnerving for a person raised with a healthy fear of pathogens to embrace the idea of a legion of foreigners inside us. But despite any experiences you may have had with members of the genus Salmonella, the vast majority of microbes that inhabit your body do you no harm. They’ve taken up residence for their own reasons—to eat mucus or feed off fiber or break down resistant starch (found in foods like lentils or cold potatoes that don’t break down in the small intestine). And humans and our bacteria, we go way back. Over the millennia, we have evolved together, our bodies offshoring jobs to our bugs, finding it easier for, say, Helicobacter pylori to help regulate hunger hormones than to do it all by ourselves.

“People call the microbiome the forgotten organ,” says Erica Sonnenburg, a micro­biologist at Stanford University who has made big strides connecting the microbiome and the immune system. “These organisms aren’t reactive. They’re holding some of the reins themselves.” And their composition in your gut—which species are most prevalent at any given moment—is critical to daily function. “They affect how our bodies work,” says Jack Gilbert, director of the Microbiome Center at the University of Chicago. “Our immune systems, our hormone levels, our neurocognition, how we behave—things that you wouldn’t even consider. How much brown fat versus white fat you have in your body, your insulin levels, the functioning of your kidneys and liver…”

The more discoveries we make, the more we realize how little we know. Thus far the American Gut Project has found our digestive tracts to be so diverse in microbial content, and so unique to us and our individual lifestyles, that researchers really can’t yet say what a “normal” gut should look like—let alone an elite athlete’s gut.

What we do know: of those trillions of bacteria, a small core of species rule our ecosystems. The vast majority of people have guts dominated by two big phyla. Bacteroidetes break down complex indigestible plant matter into stuff our body needs, like nutrients or fatty acids; Firmicutes, the other big phylum, are even better at turning fibrous and starchy foods into beneficial things such as anti-inflammatory butyrates. Like greedy kids holding up the line at the buffet, these bugs’ dominance may keep other malicious bacteria from gaining a foothold in our guts. But despite the good flora in the phylum Firmicutes, some studies have shown that obese people are more likely to have guts dominated by these bacteria than by Bacteroidetes. Frustratingly, nobody is entirely sure why it plays out this way. Scientists still don’t have enough evidence to tell people how to eat for a “skinny” gut, but most told me that they personally eat a diet high in fiber—close to double the amount the average American eats—as well as loads of plants and grains.

But in their quest to figure out just what the hell a healthy gut looks like, researchers realized that most of their subjects looked a lot alike: middle-class, white, desk job. (In other words, people you can easily find walking around a university campus.) So they sought samples from other populations—Inuits, hunter-gatherer tribes in remote parts of East Africa and the Amazon, the young and the old.

It was almost inevitable that as researchers learned more about the gut and our health, they started to wonder what was going on inside the superhumans scoring goals on TV and breaking records in their sports.


One of the first scientists to really target the link between the microbiome and performance was Fergus Shanahan, director of an interdisciplinary group at Ireland’s University College Cork. Shanahan’s colleague Mick Molloy had been a team doctor for the national rugby team, and in 2011 Shanahan asked him, “What do you suppose the microbiome of a professional athlete looks like?” Molloy made some calls, and the team agreed to help the researchers find out. (“We had to sell it to them,” Molloy remembers. “But when we talked about possibly improving performance—well, you know, they’d eat cow dung to increase performance.”)

The men in green went on to lose the Rugby World Cup that year, but Shanahan’s research team won big. “We stayed with them for days on end. We photographed their food, and we got their stool samples,” he says. The scientists found that the players’ gut biomes boasted dramatic diversity—an African savanna compared with the frozen tundra of the couch-potato control group—with double the number of phyla represented. Firmicutes were higher than average, which made sense for men with a high body-mass index burning lots of energy; and the quantity of Akkermansia mucini­phila (a bacterium often found in skinny folk but not obese people) was exceptional.

Shanahan and his team inadvertently birthed a whole subfield of microbiome studies, and it has professional teams salivating. In the lead-up to the America’s Cup last summer, Scott Tindal, the nutritionist and physiotherapist for Oracle Team USA—the yacht-racing syndicate that represents the United States—was running the numbers on the crew’s health. Perhaps unsurprising for a team sponsored by a tech company that has made billions selling database software, Oracle Team USA prides itself on metrics. Sailors’ lives were being analyzed down to the hour, with nutrients tracked, heartbeats per minute monitored, and calories uploaded. But Tindal was obsessed with a more obscure data point, something the trainers called availability—the amount of time the crew was fit to train.

Studies have shown that elite athletes get sick more often than average healthy people. Marathoners, for instance, are two to six times more likely to come down with something after a race. Furthermore, research suggests that athletes who get sick within two months of a competition rarely match their training bests. “Being available to train and sail is a massive marker of their ability to perform,” Tindal says. From January to August 2016, he tracked 17 different infections among the crew, which led to 50 days of missed training and 40 days of lost sailing. It was a dispiriting total. “We were in the gym six days a week and on the water at least four days, and quite often five or six,” remembers Andrew Campbell, a sailor on Team USA. “There was an obvious correlation. You’d spend two cold weeks fully ripping into the training, and guys would get sick. You see the cause and effect.”

Then Tindal had a chance encounter with Erika Ebbel Angle, a Ph.D. biochemist and CEO of Ixcela, a startup that formulates supplements, including probiotics, based on your microbiome. “I was a bit skeptical,” Tindal says, but he was familiar with the growing research connecting the micro­biome to the immune system. Resident bacteria, he knew, help the immune system measure its response to invading bugs. And probiotics—as much as the term has been commandeered by yogurt, juice, and granola companies—do indeed impact resident microbes. Although studies are mixed, a few have been shown to provide real benefits to the immune system.

Tindal decided to take a chance and signed Team USA up for Ixcela’s supplements and a regimen of foods designed to promote microbial diversity. (“Things like kefir, which the guys had most mornings,” he says, “and sauerkraut, which all of them definitely did not.”) After nine months, he ran the numbers. “We saw a 30 percent reduc­tion in upper-respiratory incidents, a 47.5 per­cent reduction in sailing days lost, and a 54 percent reduction in full training days lost,” he says.

Many of the researchers I spoke with doubted the ability of any company to personalize probiotic regimens based on an at-home blood test. “I can’t do that here,” said Gilbert, of the University of Chicago’s Microbiome Center, adding, “There’s a lot of snake oil out there.” Ixcela, like many of the new microbiome companies, has not yet published peer-reviewed papers ­attesting to its products’ efficacy, though it does plan to publish a study about Team USA’s results. This doesn’t mean they don’t work. But it’s a common scenario in an exploding field where even seemingly simple things like proving causation versus correlation is still maddeningly hard.


And so we keep exploring. Change your diet and the bacterial population shifts; spend enough time in the dirt and your ­dominant bugs may switch. Remove a species and hopefully cure a disease. Add a new one and maybe improve your personal best. Is it really that easy?

That’s what Jonathan Scheiman wants to find out. For two weeks in 2015, he drove around Boston, chasing down runners who’d competed in the Boston Marathon to collect their fecal samples. “We want to understand what makes elite athletes elite—from a biological perspective—then extract that to benefit everyone. This isn’t just some scientists cooped up in a lab working on esoteric stuff. This has real-world applications,” he says, adding with a laugh, “I got my hands dirty for this project.”

Scheiman, a former Division I basketball player at St. John’s University in New York City, harbored dreams of going pro throughout his twenties. He couldn’t quite make it, though, so he settled for a Ph.D. in biomedical science from New York University and a life of research at the Wyss Institute at Harvard University. He’s now a postdoc working under George Church, one of the most famous geneticists alive. Church’s interests range from nanobots to bringing woolly mammoths back from extinction, but Scheiman’s focus is narrower. He’s built a veritable Augean stable at Harvard—he scooped up even more elite feces from Olympic hopefuls in the run-up to Rio—in search of a bug that will make people better athletes.

Early in his research, Scheiman discussed his work with someone affiliated with the NBA. “The first question he asked was, ‘Can we use gen­omics to predict the next Michael Jordan?’ My response was, ‘The better question is, can we extract Jordan’s biology and give it to other athletes to help make the next Michael Jordan?’ ”

He thinks he may have found just the microbe. In a meeting of the American Chemical Society in August, Scheiman told the world about a type of bacteria—one he wouldn’t name publicly—that he saw blooming in large numbers in marathoners shortly after they finished races. The bacteria accu­mulates in the bloodstream after strenuous exercise and appears to break down the ­metabolites associated with ­fatigue. The bug, which doesn’t show up at significant levels in sedentary subjects, ­almost appears to be a natural response to the buildup of lactic acid in our muscles during workouts—a recovery mechanism we may have outsourced to our microbiome mil­lennia ago.

Scheiman’s bacteria, as one hypothesis goes, may have been cultivated by these elite runners over years of intense training. By producing ­punishing, thigh-burning quantities of lactic acid throughout their lives, the marathoners created an ideal environment for the bugs to thrive. Lactic acid became a plentiful food source, and the bacteria most capable of breaking it down flourished. In a sense, the marathoners may have earned their ability to recover quickly.

Scheiman has already isolated the bacteria and is developing a startup called Fitbiomics. If all goes well, he hopes to sell a fatigue-busting, endurance-boosting probiotic to the public within two years of completing his research.


Once you are awake to the bugs crawling around inside you, the drone of people trying to sell a cure for whatever ails your micro­biome becomes a roaring din. Dr. Oz and his rotating cast of telegenic TV physicians promise the secret to weight loss through the latest “gut diet.” A company called Mother Dirt claims that its AO+ Mist can improve your skin and “restore the essential bacteria” that modern hygiene has removed from your face. In the snack aisle at a fancy grocery store in Venice Beach, California, a $4 bag of fermented Kraut Krisps promises “one billion probiotics” per serving. We have entered an era of what University of California at Davis researcher Jonathan Eisen calls microbiomania.

Many of these promises are empty. Researchers can’t say with any confidence that there’s a take-home test that’ll help improve your health. Hyde and her team at the American Gut Project will analyze your microbiome for about a hundred bucks, but she stresses that the test is not diagnostic. You can learn a little about yourself, but mostly you’ll be contributing to citizen science. There are many tests out there on the Web that promise to improve your gut, but like Ixcela, the advice they offer isn’t yet peer-reviewed.

Still, there are encouraging anecdotal results. In Australia, Nicholas West, a researcher at Queensland’s Griffith University, has been meticulously testing publicly available probiotics on national-team athletes, based on their personal microbiomes, to help ward off pre-competition illness. He’s had some success and says he’s now working to “get an athlete on the podium, in that number-one spot—and to make sure that person is Australian.”

The Mayo Clinic recently invested in DayTwo, an Israeli startup cofounded by a computational biologist and marathon runner named Eran Segal that uses the microbiome to explore how foods affect different people’s blood-glucose levels. The research focuses on diabetics, but the Israeli national basketball team is already altering players’ diets based on DayTwo’s results, as is Omri Casspi, an Israeli member of the Golden State Warriors, in the hopes of crafting diets that keep athletes from crashing. “I used to do a lot of carbohydrate loading before runs, and I would still feel tired,” Segal says. Then he changed his diet based on his microbiome. Now, he tells me, “I can do a 20-mile run and be active hours later. And I ended up doing a sub-three-hour marathon.”

So where does it all lead? Last summer, during an interview with Bicycling, Lauren Petersen, a young researcher at the Maine-based Jackson ­Laboratory’s Connecticut branch, made explicit an idea that plenty of people had only whispered. “I think I can say with confidence,” the magazine quoted her saying, “that bacterial doping—call it poop doping, if you must—is coming soon.” Petersen, an enduro racer, has published papers on the microbiome of cyclists and is deeply interested in the role Prevotella plays in endurance athletes’ guts. The Bicy­cling story (“Is Poop Doping the Next Big Thing?”) ricocheted around the Internet and was picked up by publications as widely read as The Washington Post.

The backlash was overwhelming. The success of fecal transplants has, of course, thrilled researchers ever since 2013, when scientists proved that altering the gut biome could cure the deadly infection Clostridium difficile. But the idea of poop doping for athletic gain—even if Petersen wasn’t endorsing it—was too much. That’s because in addition to curing C. difficile, a transplant of someone else’s microbiome could result in a whole new set of problems. There are strong correlations between the bugs in your gut and a number of mental conditions, including depression and anxiety. (Clinical trials are investigating whether fecal transplants from healthy donors could help alleviate these conditions.) If a cyclist, seeking bacteria that could boost her body’s ability to, say, extract energy from carbohydrates, doped with the feces from a person suffering from severe depression, the doper could in theory become “infected.”

It’s a frightening prospect—but that doesn’t mean people won’t try. “Professional athletes will do anything to get a tiny margin of gain over competitors,” says Shanahan, the Irish researcher. At the Rio Games, the margin between gold and fifth place in the 200-meter men’s freestyle—from the top of the podium to nothing at all—was less than a second. Last year a runner came within a half-­minute of achieving a sub-two-hour marathon. Shanahan doesn’t recommend poop doping, and there’s no evidence it would even work. But, he says, “We’re talking about something completely legal. It’s not so daft, really.”

Embriette Hyde was particularly horrified by the poop-doping story. But she gets why people are interested. The microbiome is a beguiling thing; we know just enough about it for our hopes to rise. That’s part of the reason why she is now leaving the American Gut Project to become a science writer—to help explain this stuff to a confused public.

So far it appears unlikely that there is a Unified Athlete’s Gut, some mystical bacterial composition that appears across pro surfers, mountaineers, and runners. Hyde is skeptical of any easy fix, any ­yogurt or bio-drink that will turn you into Michael Jordan. But that doesn’t make her collection of samples any less intoxicating.

David Ferry (@ferryin140) lives in San Francisco and writes for ­Outside, The Atlantic, Mother Jones, and WIRED.

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