DNA from 3,600-year-old cheese sequenced by scientists

(CNN) — Bronze Age desert dwellers unearthed from graves in what’s now northwest China were buried with cheese scattered on their heads and necks — perhaps as a snack packed for the afterlife.

A decade after the dairy discovery on strikingly intact remains mummified by the Taklamakan Desert’s arid conditions, scientists have extracted and sequenced DNA from the 3,600-year-old cheese, the oldest in the archaeological record.

The analysis revealed how the Xiaohe people made cheese, showing the way humans harnessed microbes to improve their food and how microbes can be used to track cultural influences through the ages.

The findings, published Wednesday in the journal Cell, open a “new frontier in ancient DNA studies,” with this “type of research unthinkable even a decade ago,” said Christina Warinner, John L. Loeb Associate Professor of the Social Sciences and Anthropology at Harvard University. Warinner wasn’t involved in the research.

“Fermented foods today are overwhelmingly produced using only a handful of mostly lab-grown commercial strains of bacteria and yeasts,” she said.

“Little is known about the once diverse range of heirloom microbes that people used in the past to produce today’s most iconic foods — ranging from bread to cheese and from beer to wine.”

A team led by Chinese paleogeneticist Qiaomei Fu identified goat and cattle DNA in samples of the cheese. The researchers were was also able to sequence DNA of microbes contained in the cheese, confirming it was kefir, a type of cheese that’s still widely made and eaten today. Fu is director of the ancient DNA laboratory at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing.

How an enigmatic desert people made kefir

Hundreds of mummified individuals were found in the 1990s in what’s known as the Xiaohe cemetery in the Tarim Basin, an inhospitable desert area in China’s Xinjiang region. Naturally preserved by the dry desert air, their facial features and hair color are clearly discernible despite being up to 4,000 years old.

Buried with felted and woven clothing in unusual boat graves, the so-called Tarim Basin mummies and their assortment of cultural influences have long puzzled archaeologists. Despite belonging to a genetically isolated group, the individuals nevertheless embraced new ideas and technologies, according to an October 2021 study.

The new research suggested that the Xiaohe people did not mix different types of animal milk when making kefir, a practice common in traditional Middle Eastern and Greek cheesemaking, although it’s not clear why.

“The Xiaohe people would have made cheese in the same manner that traditional producers make kefir cheese today, by using previously made kefir grains (similar to kombucha mother or bread starter) that was passed on through family, friends and other social contact,” said Taylor Hermes, an assistant professor in the department of anthropology at the University of Arkansas, who was not involved in the research.

“This is what makes the study so important — we can see how these microbial commodities were handed down and spread throughout Asia,” Hermes said.

Evolution of probiotic bacteria

Fu’s team discovered that the three cheese samples from the graves contained bacterial and fungal species, including Lactobacillus kefiranofaciens and Pichia kudriavzevii, respectively, both commonly found in present-day kefir grains. The grains are a mix of probiotic bacteria and yeast that ferment milk into kefir cheese.

Fu and her colleagues also sequenced the bacterial genes in the ancient kefir cheese, revealing insights into how probiotic bacteria evolved over the past 3,600 years.

Today, there are two major groups of Lactobacillus bacteria — one that originated in Russia and another from Tibet, an autonomous region of China, according to the study. The Russian type is widely used globally, including in the United States, Japan and European countries, for making yogurt and cheese.

When Fu and her colleagues compared Lactobacillus kefiranofaciens from the ancient kefir cheese with the modern-day species, they found that it was closely related to a less common group of Lactobacillus that originated in Tibet.

The bacterium’s origins challenge a long-held belief that kefir began solely in the Caucasus Mountains region, Fu said.

“This is an unprecedented study, allowing us to observe how a bacterium evolved over the past 3,000 years. Moreover, by examining dairy products, we’ve gained a clearer picture of ancient human life and their interactions with the world,” Fu said in a statement. “This is just the beginning.”

It was remarkable that not only had the cheese survived but that it was possible to sequence DNA from the foodstuff, Hermes said. “Ancient DNA analysis, especially on microbes, is fraught with technical problems, mostly stemming from contamination by modern bacteria,” he added.

When did cheesemaking really start?

It wasn’t surprising that the Xiaohe people fermented cheese, Warinner said. The process made milk more easily digestible, with microbes producing lactic acid that causes milk to curdle and form the basis of cheese.

“In the absence of refrigeration, it is essentially impossible to store milk for more than a few hours with spontaneous fermentation setting in so there was probably never a time when milk and dairy were used without fermentation,” she said.

“However, over time people became better and better at controlling fermentation and selecting for specific microbes that produced the most desirable effects in dairy production,” she added.

While the dairy product found with the mummies is the oldest intact cheese in the archaeological record, other evidence such as animal proteins in human dental calculus and milk residues on pottery suggest that cheesemaking originated much earlier, likely more than 9,000 years ago in Anatolia or the Levant, Warinner noted.

The genomic analysis that the team performed was truly groundbreaking, said William Taylor, an assistant professor of anthropology at the University of Colorado Boulder and curator of archaeology at the school’s Museum of Natural History.

“It’s amazing to see the complexity of the products that folks were making, which normally isn’t preserved in the archaeological record,” said Taylor, who wasn’t involved in the research.

“These incredible findings show us that cheese and other dairy products were really the foundation of a whole way of life that would continue to be important for millennia and is still a huge part of life today.”

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