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Jennifer Bouron

You Are What You Eat

Or, more precisely, you are what you eat eats. Here we explore the wild and diverse world of your gut microbiome and its critical role in your total body health—from head to toe.
May 04, 2018

At a recent dinner party to celebrate a friend's birthday, I met a gregarious German woman in her 60s who had just tried one of those DNA testing kits to learn about her family history. "Everyone is doing it," she said, smiling and laughing, speaking in a thick accent. "You just spit into a tube, swoosh it around, and drop it in the mail! Then you receive an email with your results. It's fun!"

I immediately wanted to tell her about the mail-order test-tube kit that I'd just tried, but my husband intervened. "Wait," he said, "people are still eating."

Intestinal bacteria, stool samples, and bowel movements are hardly polite dinner conversation. When the dishes were all cleared, I shared that I'd recently done something similar to those DNA kits, but instead of spitting into a tube, I swabbed a piece of used toilet paper. I was testing my gut microbiome, not only for curiosity but also because I was hoping to collect a few clues about some health issues.

Blank stares suggested I'd better explain that the microbiome is the community of trillions of bacteria and other organisms living in and on us. The majority of those invisible organisms are in our intestinal tract, the gut, where they are capable of influencing virtually every aspect of our health. These microbes are like factory workers keeping the body's operations running smoothly, playing essential roles in digestion, revving up the immune system, protecting us from pathogens, and regulating metabolism. They produce certain important vitamins, including K2, good for strong bones, and folate, key for healthy cell development. They can alter how we store fat and balance sugar levels in the blood. Remarkably, the gut contains some 100 million neurons, specialized cells that transmit nerve impulses—as many as the spinal cord and more than the peripheral nervous system, which means intestinal microbes have a direct line to our body's command center. A "gut feeling" isn't just cliché—many experts refer to the gut as the body's "second brain."

Jennifer Bouron

"These little guys in the gut are literally pulling all the levers on every bit of our health," says Jeff Leach, director of the Terlingua, Texas–based Human Food Project, an effort to understand the coevolution of humans and the trillions of microbes that live in and on our bodies. That's why experts believe it's essential to create an environment where those microbes can thrive, largely by choosing nurturing foods and living in environments that encourage microbial diversity.

You Need More than Probiotics

People have pondered the importance of eating foods containing beneficial bacteria for over a century, ever since Nobel laureate Élie Metchnikoff theorized in the early 1900s that Bulgarian peasants who ate yogurt lived longer. Today, that quest represents a more than $37 billion global industry in probiotic drinks, foods, and pills—from kefir shakes and apple cider vinegar "gut shots" to sauerkraut chips and dietary supplements (see "Your Shopping Guide to Probiotic Foods").

Though probiotics are a promising field of research, there is not enough science to support their widespread use. Claims like "supports good digestive health" are smart marketing. According to some scientists, the probiotics that are sold to consumers usually don't contain the all-star bacteria that are especially good at providing health benefits. What's more, dietary supplements do not undergo the same level of scrutiny for efficacy and safety as medicines because they are not tested and approved by the U.S. Food and Drug Administration.

Experts say that above all else, it is paramount that you live a lifestyle and consume a diet that nurture a diverse community of microbes—which is a far more comprehensive approach than popping a probiotic supplement. Like a forest filled with wildlife, the gut is an ecosystem. "If you reduce the diversity," Leach says, "you reduce resiliency." There are a lot of modern-day practices that reduce diversity, he explains, some of which are more controllable than others. Elective cesarean sections, using formula instead of breast milk, obsessive cleanliness, and spending the majority of time indoors all inhibit us from being exposed to germs, viruses, and bacteria. As a result, microbial diversity can be stifled. Some studies show such limited diversity in babies and young children can ultimately lead to higher rates of certain diseases like asthma.

The bacteria in your gut microbiome are like factory workers keeping your body’s systems running smoothly—from digestion to your immune system to metabolism. They produce vitamins, alter fat storage, and even impact blood sugar.
Jennifer Bouron

Food plays a crucial role, too. However, the phrase "You are what you eat" isn't exactly correct, Leach says. "It's more accurate to say ‘you are what you eat eats.'" That's because bacteria "eat" by fermenting fiber in our diets.

It's common knowledge that fiber is essential for our good health, yet less than 10% of Americans consume the recommended daily amount (from 19g to 38g per day, with men requiring the most). Nineteen grams of fiber is the amount found in about 2 1/2 cups of raspberries, 1 1/8 cup of black beans, or 29 cups of raw spinach. The typical Western diet—low in fiber, high in refined sugars and refined carbohydrates—provides about half that.

Such fiber deficiencies are concerning because they're associated with a higher risk of certain types of disease, including colon cancer. "Studies show a strong association between a diet rich in red meat and poor in fiber intake and a higher risk of colon cancer," says Jacques Izard, a professor at the University of Nebraska–Lincoln's Food Science and Technology Department, "while a regular intake of fiber-rich vegetables, like broccoli, decreases the risk."


The gut microbiome requires fiber—and it has a particular affinity for types that are sturdy enough to survive the long, winding journey from the stomach to the large intestine, where bacteria congregate. Only two fibers have what it takes to go that distance. The first is nondigestible cellulose fiber. Although all fruits, vegetables, nuts, whole grains, beans, and seeds contain cellulose, some are better stocked than others. They're the foods we tend to chuck: broccoli and asparagus stalks, carrot peels, stringy celery, wheat bran. Because you don't digest it, cellulose plays a crucial role in keeping things moving along the intestinal tract, helping to prevent constipation and irregularity.

The other essential source is the soluble fiber fructan, which has a prebiotic effect on the gut, meaning it feeds your healthy bacteria. Good sources of soluble fiber include artichokes, asparagus, bananas, garlic, leeks, onions, and whole wheat.

In addition to eating more fiber, experts say consuming natural probiotics in the form of fermented foods containing bacteria (sauerkraut, kimchi, yogurt, raw milk cheese) helps the gut produce certain molecules that can fight inflammation often associated with illness. "The scientific community has shown that there is an interaction between these probiotics and the immune system," Izard says. "It directly involves the stimulation of the immune system in a beneficial way." Experts also recommend limiting artificial sweeteners; red meat; and highly processed foods, such crackers, cookies, and cold cuts, to nurture a diverse microbiome.

This Is the Next Frontier in Medicine

Researchers are learning more about the human microbiome by mining data (stool samples) collected by outfits like uBiome, which provided the "SmartGut" test kit that I tried. (uBiome has only one other major competitor, American Gut, an academic project co-founded by Leach and microbiologist Rob Knight, professor and principal investigator for the Knight Lab at the University of California, San Diego). The goal of these DIY tests is to use the knowledge gained to better diagnose and treat illness, though we are really at the infancy of this understanding. Knight says the gut microbiome represents the next great frontier in life-saving medicine: "A better understanding of these links could help us develop fundamentally new therapies for many of the chronic diseases that are currently intractable and cost society billions of dollars a year."

Jennifer Bouron

There have been some surprising findings about links between certain diseases and gastrointestinal ailments. There is widely accepted evidence that 75% of Parkinson's disease patients suffer gastrointestinal illnesses, particularly constipation, as long as 10 years before the onset of hallmark motor symptoms: tremors, difficulty walking, and brain inflammation. Scientists at the California Institute of Technology theorize that people with certain types of gut bacteria might be more at risk of developing Parkinson's. If that's the case, future treatments might involve specifically targeting those bacteria with antibiotics or other treatments to prevent the onset of a disease that plagues 1 million Americans.

The composition of gut bacteria also appears to be strongly associated with colon cancer, which is partly why I was curious enough to go to the trouble of swabbing a stool sample. When I was 27 years old, a doctor plucked from my colon a kumquat-size precancerous polyp that was "twice as large as what should have become cancer," according to my gastroenterologist. Why a young woman with no family history of colon cancer would start developing such a threatening growth, I'll probably never know. But because researchers studying the microbiome are finding connections between the bacterial makeup of a person's gut and the development of intestinal diseases, I thought it would be interesting to see if uBiome's test kit might reveal anything enlightening about my microbes.

After receiving an email announcing that the results were ready, I logged onto my account and downloaded a 10-page report. Not surprisingly, I tested negative for the pathogens, including Salmonella enterica, Campylobacter, and E. coli, all related to foodborne illness; Clostridium difficile, associated with life-threatening inflammation in the colon; and Vibrio cholerae, contracted from contaminated drinking water. Everything else appeared to be within normal range, but reading the list of names—Akkermansia muciniphila, Barnesiella, Butyrivibrio crossotus, Collinsella aerofaciens—was like reading a foreign language.

I dialed up uBiome co-founder Jessica Richman to talk about the results. At a glance, she said, "Your diversity is normal—but it's better if it's high." The test results suggested that it might be beneficial to tweak my diet a bit. "A doctor might tell you that you need more indigestible fiber," she said. "If you know that your diet is not as fiber-rich as it could be, eat more. And if you start to experience GI symptoms—pain, diarrhea, constipation—try a probiotic or a pre-probiotic combination [to help increase microbe diversity]."

She said that she would pay particular attention to A.muciniphila. "That's a really powerful bacteria that deserves more press," she said. "They say it's the ‘weight-loss bacteria' because it eats a lot of carbs. It's also a really good barometer of overall gut health because it calms inflammation." How do I get more Akkermansia? "Unfortunately it doesn't exist in pill form yet," but she explained that Akkermansia loves inulin, which is a type of prebiotic fructan fiber that you can find in health-food stores. Natural sources of inulin include leeks, onions, and asparagus. "Also, because bacteria live [in close association] with each other, a multi-strain probiotic can make your stomach more hospitable to Akkermansia," she said. But don't ramp up too fast, she warned: "You don't want to dump a ton of fertilizer on your garden—you'll just get a lot of gas."


Richman says that by identifying bacteria levels, at-home microbiome tests can help doctors and nutritionists shed light on whether specific foods and ingredients, such as gluten, dairy, nuts, and nightshades (tomatoes, potatoes, peppers), are contributing to patients' intestinal troubles. It's preliminary but promising, because more traditional medical tests aren't accurate enough yet.

For most people, though, the food author Michael Pollan's oft-quoted advice ("Eat food. Not too much. Mostly plants.") is usually the right course to nurture a healthier microbiome. (See "3-Day Gut Health Makeover" for an all-plants, high-fiber meal plan.)

It's Not Just What You Eat

Although each person's microbiome is as unique as a fingerprint, scientists find commonalities among cultural groups. Americans and Europeans, for example, tend to have fewer species in their gut compared to people in developing nations, probably due to diet, hygiene, sanitation, and antibiotic treatments. "[The Hadza] have nearly twice as many species of bacteria in their guts than the average American," Leach says. Leach spent the past five years studying the hunter-gatherers in Tanzania's Serengeti. Hadza have the most diverse microbiomes in the world, he says, which he considers a major factor in why they do not suffer obesity, diabetes, or many other chronic diseases common among Westerners. Unlike most of us, they eat a fiber-rich diet of foraged foods such as tubers, fruits, and foliage, with occasional wild game and honey.

Like a forest filled with wildlife, your gut is an ecosystem. If you reduce your microbial diversity, you reduce your resiliency. Your diet influences diversity, but so do some common practices, such as obsessive cleanliness and spending the majority of time indoors.
Jennifer Bouron

However, Leach has come to believe that diet is only part of the equation. The bigger factor, he says, is likely their overall lifestyle. Urbanites live and work in sterile houses and offices while Hadza live in what by Western standards is a dirty environment, sleeping on the ground, drinking unfiltered water from sources that can be contaminated by animal waste, hunting meat, cooking over a fire, all the while bearing children naturally and breastfeeding toddlers. "There's a microbial superhighway moving through the Hadza gut," Leach says. "Why do we have half the diversity of these hunter-gatherers? It's not because we eat Häagen-Dazs, McDonald's, or too much olive oil; it's because of our environment."

The pharmaceutical companies will try to figure out how to bottle some of that microbial diversity that can be acquired naturally, he says: "But then you'll have to take a pill for the rest of your life." The best caplet-free alternative is spending more time getting dirty outdoors. "You can lick your finger and be better off than by taking a probiotic," he says.

That might not be the most polite etiquette at dinner parties either, but then again, it beats talking about poop.

Rene Ebersole writes about science, health, and the environment for many outlets, including National Geographic, Prevention, Popular Science, Outside, The Nation, and Audubon. This story was produced in collaboration with the Food & Environment Reporting Network, a nonprofit investigative news organization.