Justin and Erica Sonnenburg with their children, Claire (right) and Camille, and dog, Louis, in their home in Redwood City, California. Photo: Cody Pickens

Cute Family. And You Should See Their Bacteria. The scientific clan bringing microbe diversity to the dinner table. Justin and Erica Sonnenburg with their children, Claire (right) and Camille, and dog, Louis, in their home in Redwood City, California. Photographs by Cody Pickens

On a Saturday evening in late March, as the sun ducked behind the ridges separating Redwood City from the Pacific, I stood on the porch of an unassuming bungalow holding a bag of my own feces. I was to be a dinner guest of Justin and Erica Sonnenburg, Stanford scientists who study the microbiota, the ecosystem of microbial organisms that live inside us and may have a role to play in preventing maladies such as obesity, irritable ­bowel syndrome, and diabetes. Earlier in the day, I’d helped Justin, Erica, and their two young daughters harvest lacinato and curly kale from their front-yard-garden beds, then spread a fresh layer of turkey manure for the next round of plantings. Afterward, as I drank a refreshing kale-and-pear smoothie Erica had prepared as a reward for our efforts, Justin sidled up to me with a proposition. “You’ve embarked on an exciting new endeavor,” he said. “No pressure at all, but if you want to document it” — he pulled from his shirt pocket a test tube with a miniature plastic spoon inside. A few hours later, I stood on Justin and Erica’s front steps holding the now-burdened tube, which I’d tactfully concealed in a Starbucks cup, then packed in a clear plastic bag of hotel ice.

Our colons are home to 100 trillion bacteria, representing some 1,200 different species, which have evolved in symbiosis with their hosts over the course of millennia. Their cells outnumber our own by a factor of ten, but much of the microbiota remains terra incognita, and the precise ways in which it affects our health are still dimly understood. The Sonnenburgs believe, however, that the root of many Western diseases can be traced to our languishing guts, which we’ve done about as good a job looking after as we have the rain forests and the whales. The American diet is high in processed foods digested in the stomach and small intestine, leaving little fuel for the microbes in our large intestine. The result, they say, has been a “mass extinction event,” in which species of bacteria that have lived in our bodies for most of human history have died off, making it harder for our microbiota to perform its role in tuning our immune system and regulating inflammation.

I’d recently started an experiment in living according to the precepts of the Sonnenburgs’ new book, The Good Gut, which attempts to correct this seemingly dire state of affairs by offering suggestions for how to nurture a thriving community of bacteria. Much of their advice comes down to two basic ideas: (1) Stop trying to sterilize your home as if it were a surgical theater, which kills off more good bacteria than bad, and (2) eat lots and lots and lots of fiber, which is digested in the lower intestine.

I was just a few weeks into the gut diet when I met the Sonnenburgs, and my bacteria were surely still in an impoverished state, thanks to a diet heretofore deficient in fiber and rich in Chinese takeout and Bugles. Justin suggested I have my stool sequenced now, so that I could get the microbial equivalent of the “before” picture in a weight-loss ad. When Erica greeted me at the door, she was briefly perplexed by my parcel — the previous evening I’d brought a more traditional dinner-guest gift, a bottle of Burgundy — then remembered the sample. “Oh, I know what that is!” she said and, gamely pulling the chilled cup from the bag, tossed it in the freezer next to a quart of Häagen-Dazs.

In the living room, Claire, 9, and Camille, 6, conducted a pillow fight on the sofa (GO WITH YOUR GUT, read one pillow). Justin, who is wiry, with a friendly intensity, and Erica, who is quieter but equally exuberant when talk turns to microbes, busied themselves preparing tonight’s high-fiber meal. Justin treats the kitchen like an extension of his lab. He’s an avid baker and favors sourdoughs, which leaven with bacteria as well as yeast. Tonight, he rolled his sourdough out thin for use in a flatbread pizza piled high with veggies. Erica worked on a kale salad made from our morning haul. We’d be washing down the meal with his home-brewed beer, an unfiltered ale still shot through with the live cultures that fermented it.

When dinner was ready, we sat down at the dining-room table, next to a large photograph of wormlike bacteria. I asked Erica if it was any bacteria in particular. “It’s E. coli,” she said.

Eating with Justin and Erica requires some intestinal fortitude. The previous day, I’d visited them at the Sonnenburg Lab, which Justin runs and where Erica is a senior researcher. Around noon, we headed to the cafeteria for lunch. “The American salad is actually pretty pathetic,” Justin remarked on our way. “There’s like a few leaves of lettuce and maybe a cucumber. There’s not that much dietary fiber.” Eager to eat something more satisfying for my “bugs,” as the Sonnenburgs fondly call their microbes, I followed Justin and Erica’s lead as they heaped their plates high with spinach, beets, beans, and, inevitably, quinoa. At Justin’s suggestion, we took our lunches back to the lab, where a graduate student was giving a detailed PowerPoint presentation on the devastating effects of diarrhea on the microbiota. The Sonnenburgs ate their salads with undiminished appetites.

At Saturday dinner, the conversation turned to the family dog, a Havanese named Louis, a seemingly safe topic. Louis is named for Louis Pasteur, the father of germ theory, and while he’s a beloved member of the family, he also plays a role in their efforts to maintain maximal gut health. Dogs are apparently excellent vectors for microbes, spreading bacteria on their fur and tongues to their human co-habitants; dog owners have been shown to have greater microbial diversity than the dogless.

“I wonder what Louis’s microbiota looks like,” I wondered aloud.

“We know,” Justin said.

“You sequenced his stool?” I asked.

“We did,” he said.

Justin explained that while human Americans tend to have minimal fiber intake, canine Americans are doing better. “They’ve totally optimized this fiber issue,” he said of dog-food companies. “It’s not for the health of the dog; it’s for the convenience of the owner. Nothing will switch a dog owner’s choice of food quicker than seeing digestive issues that you have to deal with on the sidewalk. It’s like, We’re buying a different food.”

“So are our dogs eating better than us?” I asked.

“You could argue that it’s too solid, too cohesive,” Justin said of Louis’s stool.

“It’s borderline constipated,” Erica agreed. “If it was my bowel movement, I’d be like, This is not the best.”

“But it can hit the sidewalk and you can pick it up without it leaving a big smudge,” Justin said.

The family’s fecal samples stored in their freezer. Photo: Cody Pickens

The Sonnenburgs’ advice on how to eat is rooted in their scientific work, which explores the effect of changes in diet on the microbiota. At their lab, Erica showed me the results of her current experiment, in which she successfully decreased the diversity of microbial communities in the guts of mice by feeding them a low-fiber diet. But The Good Gut is as inspired by the ongoing experiment at the Sonnenburg home as it is by the work of the Sonnenburg Lab. Shortly after they arrived at Stanford, Claire, then 3 years old, experienced persistent, painful constipation. “The issue became so bad that most trips to the bathroom ended in tears,” they write. “We felt that we, of all people, should not have a child with gastrointestinal issues.”

Neither Sonnenburg thought they had poor eating habits. But in the wake of Claire’s distress, they started carefully cataloguing their diet, and were dismayed at what they found. “I mean, we weren’t eating Twinkies and McDonald’s,” Justin said. “But you know, flour-tortilla cheese quesadillas, white pasta, white rice.”

The family embarked on a radical dietary rethink, making a commitment to fiber consumption that today borders on the comical. The Sonnenburgs believe that the best fuel for your bugs comes from polysaccharides, the complex carbohydrates found in plant matter. And because different microbes feast on different types, they seek out a wide range of sources, including whole grains, beans, and seeds. Erica makes jam in which she substitutes polysaccharide-rich chia seeds for sugar. (I also sampled a surprisingly tasty chia-seed chocolate pudding.) Most brewers dispose of their spent grains, turning them into compost or animal feed. Justin pours the high-fiber brewing by-product — imagine a sodden Grape-Nut, depleted of all flavor — over his morning yogurt.

When Justin bakes, he does so with his own hand-ground flour. As we prepped two sourdough loaves one afternoon, he showed me why he goes to the trouble, pouring out a dusting of store-bought wheat flour beside a pinch of store-bought white. The wheat was darker in color, but appeared just as refined as the white. He then invited me to take a turn on his hand-cranked wheat-berry mill. The result of several minutes of tricep-taxing effort was flour that was noticeably rougher and, as a result, Justin said, more likely to arrive in the colon undigested, where our microbes could have at it.

This hardly seems like a kid-friendly approach to eating, but Claire and Camille by now have been indoctrinated. I watched them devour jicama, mashed sardines on an English cracker that had the appearance of 60-grit sandpaper, forests of kale. “You have to view what your kids are eating just like you view bedtime, going to school, buckling their seat belt,” Justin said. “They may not want it, but it’s what’s best for them. You just tell them there’s no option.”

One night, at dinner, the girls recounted a recent trip to Colorado during which Justin spoke at a conference on the microbiota. The kids’ meal at the ski lodge came with what was advertised as a miniature cookie for dessert. But when the meal arrived, the cookie was not mini. Claire and Camille were scandalized. “It was this big,” Camille noted, making a circle with her fingers that suggested, to me, a normal-size cookie. “I couldn’t finish it,” she said. I asked Claire if she finished hers.

“I powered through,” she said.

The couple’s decision to take their gut theories to the masses came two years ago at a nutrition conference in Seattle hosted by Andrew Weil, the bald, bearded guru of integrative medicine. Justin had been asked to give a plenary talk on the microbiota that Weil would later write was “the highlight of the event for me.” Weil believes the ongoing degradation of our microbial communities Justin described might explain a series of health developments that had confounded him, like the rising rates of peanut allergies and gluten sensitivity, both of which might be traced to malfunctioning immune responses in the gut. At a dinner that night for conference speakers, Weil offered to connect Justin with the literary agent who engineered his first megahit, 1995’s Spontaneous Healing, and to send him one of his own book proposals to use as a model.

The timing was propitious: Michael Pollan had just written a lengthy article on the gut in The New York Times Magazine, in which Justin had figured prominently. Marketers were touting the gut-nourishing qualities of everything from sauerkraut to buttermilk, and news outlets were running stories on the lifesaving treatment known as fecal transplant, in which a donor’s healthy microbiota is used to fight off the antibiotic-resistant bacteria C. difficile.

In admirably plain language, the Sonnenburgs’ book describes the latest science, how our microbiota functions and how it protects us from disease. They explain that if our immune system is the body’s Department of Defense, fighting off infection, gut microbes are the diplomats, determining what’s harmful and what’s harmless. The more robust the microbiota, the more sophisticated the diplomacy and the less likely the immune system will overreact and launch harmful autoimmune responses or fail to defend against invaders.

But if The Good Gut is a success, it will likely be because, like the best-selling gluten-free and Paleo diet guides before it, it taps into our interest in how best to optimize the functioning of our bodies and our fears that our modern lifestyles are harming us. For the Sonnenburgs, optimization entails making peace with our bacterial bedfellows, rather than trying to Clorox-wipe them to oblivion. The Good Gut describes the devastating toll that antibiotics take on the microbiota as well as other forms of anti-bacterial practice, like the growing frequency of C-sections, which rob newborns of a bacteria-rich trip through the vaginal canal, and the use of formula, which deprives them of both good bacteria from Mom and special carbohydrates in breast milk that help infant gut flora bloom.

Most of the book, though, is given over to eating. Like the Paleo diet, the gut diet looks suspiciously on processed foods and fondly on the habits of our preindustrial ancestors. Erica likes to wear a T-shirt silk-screened with an image of a hominid holding a tray of fast food. She told me the shirt captures how our diet has evolved far more rapidly than our bodies. When scientists study the microbiota of a traditional hunter-gatherer society like that of the Hadza in Tanzania, who eat ten times the fiber of the average American, they find far greater microbial diversity. (The Hadza also slaughter animals with their hands and clean off the blood using the animal’s digesta — a boost to microbial exposure.) The Hadza have avoided Western afflictions such as obesity and diabetes, which the Sonnenburgs see as evidence that their guts are in better shape than our own.

Most diet guides pander to our narcissism — do this and you’ll feel, and look, great. The Good Gut more often makes the altruistic pitch that we should all do our part to fend off the decline in Western bacterial diversity. Their appeal to Save the Bugs is one Justin and Erica honed on their daughters. When Claire and Camille do occasionally resist their parents’ healthy-eating habits, their parents remind the girls that they’re not just eating for themselves but for their microbes too.

I’ve used a version of this logic on myself. Since starting the gut diet, I’ve come to think of myself as akin to Lord Grantham from Downton Abbey. I am the lord of a manor over which I have ostensibly unlimited power. Yet if I am a cruel and ungenerous master to my tenant farmers and downstairs servants, they might revolt or simply decamp, especially at this precarious historical moment, when the forces of modernity have beset our ancient social arrangement. I wouldn’t have thought that noblesse oblige would make for a powerful dieting aid, but it has. When I’ve been tempted to cheat, an image has flashed before me of my embattled microbes, those blameless tillers of my intestinal soil, and I’ve stayed my hand.

Not all scientists believe the gut is in decline, however. Jonathan Eisen, who studies the microbiome at UC Davis, made the case to me that just because the Hadza have more strains of bacteria in their colons doesn’t mean we all once had those bugs: They could be a feature of the Hadza’s Tanzanian environment, not a relic passed down from some common ancestor. The science writer Ed Yong, who is also writing a book on microbes, has argued that it’s a mistake to think of any set of bacteria as “ideal” — the Western microbiota may be as well evolved for the modern diet as the Hadza’s is for the premodern one. As for our eating habits, Eisen is not convinced, based on the studies he’s read, that the health benefits of a high-fiber diet are necessarily the result of nourishing our gut bacteria.

Eisen keeps a blog in which he periodically bestows an “Overselling the Microbiome Award” to scientists (and journalists) who hype the potential power of the gut. While he shares the Sonnenburgs’ bullishness about gut science, he’s skeptical that it will be the key that will unlock all of Western disease. And he fears that overselling the still-nascent science can have negative effects. After a recent talk at South by Southwest, two parents came up to him and told him that they were giving their kids fecal transplants, at home, in the hopes of curing their autism: a potentially dangerous measure based on a very preliminary study of mice.

The Sonnenburgs admit that our knowledge of the microbiota is in its infancy and frequently remind their readers that scientists have a long way to go before we understand all the gut’s underlying mechanisms. And none of their lifestyle recommendations are nearly so radical as a do-it-yourself fecal transplant — few scientists or doctors would object to the idea that Americans should eat more vegetables, or pet more dogs. But unlike Eisen, they argue that it is imperative that we start caring for our long-overlooked bugs, even if we’ve yet to prove definitively that they are the lever by which the rest of our health can be regulated.

Five years of nurturing his microbiota and protecting it from antibacterial incursions has paid off for Justin, at least. Erica told me that when she compared a stool sample of his taken recently with an earlier one, the diversity of her husband’s gut bugs had nearly doubled.

The Sonnenburgs acknowledge that this is not a fact they could ever publish in a scientific journal. They don’t have any definitive proof that diet, or the other measures they’ve taken to make their home hospitable to their bugs, is the reason Justin’s gut has made so much progress. (Or the reason Erica professes to no longer suffer from the allergies that once plagued her.) Even in their own lab, there seems to be no consensus that a high-fiber diet is the essence of good health. Canvassing the staff, I found only a couple of researchers who had signed on to the gut diet and none at the grind-your-own-wheat-berries level. Drew Hryckowian, an affable postdoc from Pittsburgh, told me he was eating more beans since joining the lab in part because they’re high in fiber but also because they’re an inexpensive source of protein in wildly expensive Silicon Valley. “I’ve never paid so much money for rent in my whole life,” he said.

But as microbiota research continues, the Sonnenburgs are confident we’ll learn more about how our gut works and find better tools for repairing the damage done. I’m still awaiting the results of my stool sequencing, a process that remains slow given current technology. Still, I’d venture my bacteria are considerably happier than they were when I was all but starving them, though the first few weeks were rocky. The Sonnenburgs suggest a gradual ramping up of fiber consumption to avoid bloating or discomfort.

Justin recently recruited to the lab a graduate student who will be focusing on inventing a device that would allow you to collect a fecal sample at home, suspend it in solution, plug a meter into your iPhone, and check on the health of your gut bugs. “Wouldn’t it be wonderful, every time you go to the bathroom in the morning, to know if what you’ve done in the past week has had an impact on your microbiota?” he asked. His vision is of a nation of amateur micro­biologists working toward a better understanding of our intestinal inhabitants one bowel movement at a time.

On my last day out West, I climbed into the family’s Toyota 4Runner and we drove out to the Whole Foods in Redwood City. The supplements aisle is where the promise of the gut meets the predations of the market, and I was curious what Justin and Erica would make of the store’s cabinet of probiotic curiosities, which claim to foster a healthy gut without the need for massive kale intake. The bacteria on offer were mostly the same strains you’d find in yogurt and kefir, only in pill form. (Expensive pill form — many are a dollar-a-day habit.) Erica explained that there are few bacterial strains approved for sale in the U.S. Most companies hawk the same old strains to a public that can’t tell Bifidobacterium lactis from Lactobacillus acidophilus. Probiotics are good for us, she said, but they’re transient — they can’t repopulate a decimated gut — and we may never identify some magic combination of strains that will keep us healthy.

The Sonnenburgs prefer to dose themselves with probiotic foods, like fermented pickles (if they’re not refrigerated, they’re not fermented) and kimchee. They eat yogurt by the gallon, especially during cold season. Justin cultures his own kefir from mail-order grains. The kefir grain is a microbial community that, if fed a continuous diet of milk, will essentially live indefinitely. Justin told me that in certain Eastern European countries, kefir grains can be passed down from generation to generation. So far, he has no takers in his own household. “There’s a little bit of a vomit taste, in my opinion,” said Erica.

“Smell needs work, taste needs work,” said Claire.

“I’m the only one who didn’t get sick this winter,” replied Justin. “And I drank it every day.”

*This article appears in the April 20, 2015 issue of New York Magazine.