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The Scientists Who Want to Fix America’s Guts

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Mmmm, fecal samples stored in the fridge with the high-fiber food!!!

I'm not sure that's an Mmmm, but it IS an interesting course of inquiry.

Beware the overselling of the microbiome!

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. 

They sequenced their stool?!

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 lengthyarticle 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.

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