The answer to lactose intolerance might be in Mongolia

Lake Khövsgöl is about as far north of the Mongolian capital of Ulaanbaatar as you can get without leaving the country. If you’re too impatient for the 13-hour bus ride, you can take a prop plane to the town of Murun, then drive for three hours on dirt roads to Khatgal, a tiny village nestled against the lake’s southern shore. The felt yurts that dot the surrounding green plains are a throwback to the days—not so long ago—when most Mongolians lived as subsistence herders.

In July 2017, archaeogeneticist Christina Warinner headed there to learn about the population’s complex relationship with milk. In Khatgal, she found a cooperative called Blessed by Yak, where families within a few hours’ drive pooled the bounty from their cows, goats, sheep, and yaks to supply tourists with heirloom dairy products.

Warinner watched for hours as Blessed by Yak members transformed the liquid into a dizzying array of foods. Milk was everywhere in and around these homes: splashing from swollen udders into wooden buckets, simmering in steel woks atop fires fueled by cow dung, hanging in leather bags from riblike wooden rafters, bubbling in specially made stills, crusting as spatters on the wood-lattice inner walls. The women even washed their hands in whey. “Working with herders is a five-senses experience,” Warinner says. “The taste is really strong; the smell is really strong. It reminds me of when I was nursing my daughter, and everything smelled of milk.”

Each family she visited had a half-dozen dairy products or more in some stage of production around a central hearth. And horse herders who came to sell their goods brought barrels of airag, a slightly alcoholic fizzy beverage that set the yurts abuzz.

Airag, made only from horse milk, is not to be confused with aaruul, a sour cheese, created from curdled milk, that gets so hard after weeks drying in the sun that you’re better off sucking on it or softening it in tea than risking your teeth trying to chew it. Easier to consume is byaslag, rounds of white cheese pressed between wooden boards. Roasted curds called eezgi look a little like burnt popcorn; dry, they last for months stored in cloth bags. Carefully packed in a sheep-stomach wrapper, the buttery clotted cream known as urum—made from fat-rich yak or sheep milk—will warm bellies all through the winter, when temperatures regularly drop well below zero.

Warinner’s personal favorite? The “mash” left behind when turning cow or yak milk into an alcoholic drink called shimin arkhi. “At the bottom of the still, you have an oily yogurt that’s delicious,” she says.

Her long trip to Khatgal wasn’t about culinary curiosity, however. Warinner was there to solve a mystery: Despite the dairy diversity she saw, an estimated 95 percent of Mongolians are, genetically speaking, lactose intolerant. Yet, in the frost-free summer months, she believes they may be getting up to half their calories from milk products.

Scientists once thought dairying and the ability to drink milk went hand in hand. What she found in Mongolia has pushed Warinner to posit a new explanation. On her visit to Khatgal, she says, the answer was all around her, even if she couldn’t see it.

Sitting, transfixed, in homes made from wool, leather, and wood, she was struck by the contrast with the plastic and steel kitchens she was familiar with in the US and Europe. Mongolians are surrounded by microscopic organisms: the bacteria that ferment the milk into their assorted foodstuffs, the microbes in their guts and on the dairy-soaked felt of their yurts. The way these invisible creatures interact with each other, with the environment, and with our bodies creates a dynamic ecosystem.

That’s not unique. Everyone lives with a billions-strong universe of microbes in, on, and around them. Several pounds’ worth thrive in our guts alone. Researchers have dubbed this wee world the microbiome and are just beginning to understand the role it plays in our health.

Some of these colonies, though, are more diverse than others: Warinner is still working on sampling the Khatgal herders’ microbiomes, but another team has already gathered evidence that the Mongolian bacterial makeup differs from those found in more-industrial areas of the world. Charting the ecosystem they are a part of might someday help explain why the population is able to eat so much dairy—​and offer clues to help people everywhere who are lactose intolerant.

Warinner argues that a better understanding of the complex microbial universe inhabiting every Mongolian yurt could also provide insight into a problem that goes far beyond helping folks eat more brie. As communities around the world abandon traditional lifestyles, so-called diseases of civilization, like dementia, diabetes, and food intolerances, are on the rise.

Warinner is convinced that the Mongolian affinity for dairy is made possible by a mastery of bacteria 3,000 years or more in the making. By scraping gunk off the teeth of steppe dwellers who died thousands of years ago, she’s been able to prove that milk has held a prominent place in the Mongolian diet for millennia. Understanding the differences between traditional microbiomes like theirs and those prevalent in the industrialized world could help explain the illnesses that accompany modern lifestyles—and perhaps be the beginning of a different, more beneficial approach to diet and health.

Nowadays, Warinner does her detective work at the Max Planck Institute for the Science of Human History’s ancient DNA lab, situated on the second floor of a high-rise bioscience facility overlooking the historic center of the medieval town of Jena, Germany. To prevent any errant DNA from contaminating its samples, entering the lab involves a half-hour protocol, including disinfection of foreign objects, and putting on head-to-toe Tyvek jumpsuits, surgical face masks, and eye shields. Inside, postdocs and technicians wielding drills and picks harvest fragments of dental plaque from the teeth of people who died long ago. It’s here that many of Warinner’s Mongolian specimens get cataloged, analyzed, and archived.

Her path to the lab began in 2010, when she was a postdoctoral researcher in Switzerland. Warinner was looking for ways to find evidence of infectious disease on centuries-old skeletons. She started with dental caries, or cavities—spots where bacteria had burrowed into the tooth enamel. To get a good look, she spent a lot of time clearing away plaque:​ mineral deposits scientists call “calculus,” and that, in the absence of modern dentistry, accumulate on teeth in an unsightly brown mass.

Around the same time, Amanda Henry, now a researcher at the University of Leiden in the Netherlands, put calculus scraped from Neanderthal teeth under the microscope and spotted starch grains trapped in the mineral layers. The results provided evidence that the population ate a diverse diet that included plants as well as meat.

Hearing about the work, Warinner wondered if looking at specimens from a medieval German cemetery might yield similar insights. But when she checked for food remains under the microscope, masses of perfectly preserved bacteria blocked her from doing so. “They were literally in your way, obscuring your view,” she recalls. The samples were teeming with microbial and human genes, preserved and protected by a hard mineral matrix.

Warinner had discovered a way to see the tiny organisms in the archaeological record, and with them, a means to study diet. “I realized this was a really rich source of bacterial DNA no one had thought of before,” Warinner says. “It’s a time capsule that gives us access to information about an individual’s life that is very hard to get from other places.”

The dental calculus research dovetailed with rising interest in the microbiome, rocketing Warinner to a coveted position at Max Planck. (In 2019, Harvard hired her as an anthropology professor, and she now splits her time between Cambridge, Massachusetts, and Jena, overseeing labs on two continents.) Her TED talks have racked up more than 2 million views. “I never expected to have an entire career based on something people spend lots of time and money trying to get rid of,” she quips.

That grimy dental buildup, Warinner has learned, preserves more than just DNA. In 2014, she published a study in which she and her colleagues looked at the teeth of Norse Greenlanders, seeking insight into why Vikings abandoned their settlements there after just a few hundred years. She found milk proteins suspended in the plaque of the area’s earliest settlers—and almost none in that of people buried five centuries later. “We had a marker to trace dairy consumption,” Warinner says.

This discovery led Warinner to turn to one of the biggest puzzles in recent human evolution: Why milk? Most people in the world aren’t genetically equipped to digest dairy as adults. A minority of them—including most northern Europeans—​have one of several mutations that allows their bodies to break down the key sugar in milk, lactose, beyond early childhood. That ability is called lactase persistence, after the protein that processes lactose.

Until recently, geneticists thought that dairying and the ability to drink milk must have evolved together, but that didn’t prove out when investigators went looking for evidence. Ancient DNA samples from all across Europe suggest that even in places where lactase persistence is common today, it didn’t appear until 3000 BCE—long after people domesticated cattle and sheep and started consuming dairy products. For 4,000 years prior to the mutation, Europeans were making cheese and eating dairy despite their lactose intolerance. Warinner guessed that microbes may have been doing the job of dairy digestion for them.

To prove it, she began looking for places where the situation was similar. Mongolia made sense: There’s evidence that herding and domestication there dates back 5,000 years or more. But, Warinner says, direct evidence of long-ago dairy consumption was absent—until ancient calculus let her harvest it straight from the mouths of the dead.

Starting in 2016, in her Jena lab, Warinner and her team scraped the teeth of skeletons buried on the steppes thousands of years ago and excavated by archaeologists in the 1990s. Samples about the size of a lentil were enough to reveal proteins from cow, goat, and sheep milk. By tapping the same remains for ancient DNA, Warinner could go one step further and show that they belonged to people who lacked the gene to digest lactose—​just like modern Mongolians do.

Samples of the microbiome from in and around today’s herders, Warinner realized, might offer a way to understand how this was possible. Though it’s estimated that just 1 in 20 Mongolians has the mutation allowing them to digest milk, few places in the world put as much emphasis on dairy. They include it in festivities and offer it to spirits before any big trip to ensure safety and success. Even their metaphors are dairy-based: “The smell from a wooden vessel filled with milk never goes away” is the rough equivalent of “old habits die hard.”

Down the hall from the ancient DNA lab, thousands of microbiome samples the team has collected over the past two summers pack tall industrial freezers. Chilled to minus 40 degrees F—colder, even, than the Mongolian winter—the collection includes everything from eezgi and byaslag to goat turds and yak-udder swabs. Hundreds of the playing-card-size plastic baggies new mothers use to freeze breast milk contain raw, freshly squeezed camel, cow, goat, reindeer, sheep, and yak milk.

Warinner’s initial hypothesis was that the Mongolian herders—​past and present—​were using lactose-​eating microbes to break down their many varieties of dairy, making it digestible. Commonly known as fermentation, it’s the same bacteria-assisted process that turns malt into beer, grapes into wine, and flour into bubbly sourdough.

Fermentation is integral to just about every dairy product in the Mongolian repertoire. While Western cheeses also utilize the process, makers of Parmesan, brie and Camembert all rely on fungi and rennet—​an enzyme from the stomachs of calves—to get the right texture and taste. Mongolians, on the other hand, maintain microbial cultures called starters, saving a little from each batch to inoculate the next.

Ethnographic evidence suggests that these preparations have been around a very, very long time. In Mongolian, they’re called khöröngö, a word that’s derived from the term for wealth or inheritance. They are living heirlooms, typically passed from mother to daughter. And they require regular care and feeding. “Starter cultures get constant attention over weeks, months, years, generations,” says Björn Reichhardt, a Mongolian-​speaking ethnographer at Max Planck and member of Warinner’s team responsible for collecting most of the samples in the Jena freezers. “Mongolians tend to dairy products the way they would an infant.” As with a child, the environment in which they’re nurtured is deeply influential. The microbial makeup of each family’s starters seems to be subtly different.

After returning from Khatgal in 2017, Warinner launched the Heirloom Microbe project to identify and catalog the bacteria the herders were using to make their dairy products. The name reflected her hope that the yurts harbored strains or species ignored by industrial labs and corporate starter-​culture manufacturers. Perhaps, Warinner imagined, there would be a novel strain or some combination of microbes Mongolians were using to process milk in a way that Western science had missed.

So far, she’s found Enterococcus, a bacterium common in the human gut that excels at digesting lactose but was eliminated from US and European dairy commodities decades ago. And they’ve spotted some new strains of familiar bacteria like Lactobacillus. But they haven’t identified any radically different species or starters—no magic microbes ready to package in pill form. “It doesn’t seem like there is a range of superbugs in there,” says Max Planck anthropologist Matthäus Rest, who works with Warinner on dairy research.

The reality might be more daunting. Rather than a previously undiscovered strain of microbes, it might be a complex web of organisms and practices—the lovingly maintained starters, the milk-soaked felt of the yurts, the gut flora of individual herders, the way they stir their barrels of airag—that makes the Mongolian love affair with so many dairy products possible.

Warinner’s project now has a new name, Dairy Cultures, reflecting her growing realization that Mongolia’s microbial toolkit might not come down to a few specific bacteria. “Science is often very reductive,” she says. “People tend to look at just one aspect of things. But if we want to understand dairying, we can’t just look at the animals, or the microbiome, or the products. We have to look at the entire system.”

The results could help explain another phenomenon, one that affects people far from the Mongolian steppes. The billions of bacteria that make up our microbiomes aren’t passive passengers. They play an active—if little understood—role in our health, helping regulate our immune systems and digest our food.

Over the past two centuries, industrialization, sterilization, and antibiotics have dramatically changed these invisible ecosystems. Underneath a superficial diversity of flavors—​mall staples like sushi, pad thai, and pizza—​food is becoming more and more the same. Large-scale dairies even ferment items like yogurt and cheese using lab-grown starter cultures, a $1.2 billion industry dominated by a handful of industrial producers. People eating commoditized cuisine lack an estimated 30 percent of the gut microbe species that are found in remote groups still eating “traditional” diets. In 2015, Warinner was part of a team that found bacteria in the digestive tracts of hunter-gatherers living in the Amazon jungle that have all but vanished in people consuming a selection of typical Western fare.

“People have the feeling that they eat a much more diverse and global diet than their parents, and that might be true,” Rest says, “but when you look at these foods on a microbial level, they’re increasingly empty.”

A review paper in Science in October 2019 gathered data from labs around the world beginning to probe if this dwindling variety might be making us sick. Dementia, diabetes, heart disease, stroke, and certain cancers are sometimes termed diseases of civilization. They’re all associated with the spread of urban lifestyles and diets, processed meals, and antibiotics. Meanwhile, food intolerances and intestinal illnesses like Crohn’s disease and irritable bowel disease are on the rise.

Comparing the microbiome of Mongolian herders to samples from people consuming a more industrialized diet elsewhere in the world could translate into valuable insights into what we’ve lost—and how to get it back. Identifying the missing species could refine human microbiome therapies and add a needed dose of science to probiotics.

There might not be much time left for this quest. Over the past 50 years, hundreds of thousands of Mongolian herders have abandoned the steppes, their herds, and their traditional lifestyle, flocking to Ulaanbaatar. Around 50 percent of the country’s population, an estimated 1.5 million people, now crowds into the capital.

In summer 2020, Warinner’s team will return to Khatgal and other rural regions to collect mouth swabs and fecal specimens from herders, the last phase in cataloging the traditional Mongolian micro-biome. She recently decided she’ll sample residents of Ulaanbaatar too, to see how urban dwelling is altering their bacterial balances as they adopt new foods, new ways of life, and, in all likelihood, newly simplified communities of microbes.

Something important, if invisible, is being lost, Warinner believes. On a recent fall morning, she was sitting in her sunlit office in the Peabody Museum of Archaeology and Ethnography on Harvard’s campus. Mostly unpacked from her latest trans-Atlantic move, she was contemplating a creeping, yurt-by-yurt extinction event.

It’s a conundrum vastly different in size, but not in scale, from those facing wildlife conservationists the world over. “How do you restore an entire ecology?” she wondered. “I’m not sure you can. We’re doing our best to record, catalog, and document as much as we can, and try to figure it out at the same time.”

Preserving Mongolia’s microbes, in other words, won’t be enough. We also need the traditional knowledge and everyday practices that have sustained them for centuries. Downstairs, display cases hold the artifacts of other peoples—​from the Massachusett tribe that once lived on the land where Harvard now stands to the Aztec and Inca civilizations that used to rule vast stretches of Central and South America—whose traditions are gone forever, along with the microbial networks they nurtured. “Dairy systems are alive,” Warinner says. “They’ve been alive, and continuously cultivated, for 5,000 years. You have to grow them every single day. How much change can the system tolerate before it begins to break?”

This story appears in the Spring 2020, Origins issue of Popular Science.