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Bronze Age desert dwellers excavated from tombs in what is now northwestern China were buried with cheese on their heads and necks, possibly as a snack for the afterlife.
Ten years after the discovery of remarkably intact dairy remains, mummified by the dry conditions of the Taklamakan Desert, scientists have extracted and sequenced DNA from the 3,600-year-old cheese. It is the oldest cheese ever found archaeologically.
The analysis revealed how the Xiaohe people made cheese, how people used microbes to improve their food, and how microbes can be used to trace cultural influences through the ages.
The findings, published Wednesday in the journal Cell, open up a "new frontier in ancient DNA studies," allowing "this type of research that would have been unthinkable even a decade ago," said Christina Warinner, John L. Loeb Associate Professor of the Social Sciences and Anthropology at Harvard University. Warinner was not involved in the study.
"The vast majority of fermented foods today are produced using just a handful of commercial strains of bacteria and yeast, usually grown in labs," she said.
"Little is known about the once diverse suite of heritage microbes that people in the past used to produce today's most iconic foods - from bread to cheese, beer to wine."
A team led by Chinese paleogeneticist Qiaomei Fu identified DNA from goats and cattle in samples of the cheese. The researchers were also able to sequence DNA from microbes in the cheese, confirming that it was kefir, a type of cheese still widely made and eaten today. Fu is director of the ancient DNA lab at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing.
How a mysterious desert people made kefir
Hundreds of mummified individuals were found in the 1990s in what is known as the Xiaohe Cemetery in the Tarim Basin, an inhospitable desert area in China's Xinjiang region. Their facial features and hair color have been naturally preserved by the dry desert air, but are clearly distinguishable despite being up to 4,000 years old.
Buried with felted and woven clothing in unusual boat burials, the so-called Tarim Basin mummies and their assortment of cultural influences have long puzzled archaeologists. Despite being genetically isolated, the individuals nevertheless embraced new ideas and technologies, according to an October 2021 study.
The new research shows that the Xiaohe people did not mix different types of animal milk when making kefir, a common practice in traditional cheesemaking in the Middle East and Greece. But it's not clear why.
"The Xiaohe people would have made cheese in the same way that traditional producers make kefir cheese today, using previously made kefir grains (similar to kombucha mother or bread starter) that were passed down through family, friends and other social contacts," said Taylor Hermes, an assistant professor in the department of anthropology at the University of Arkansas, who was not involved in the study.
"That's what makes the study so important: we can see how these microbial resources were passed on and spread throughout Asia," Hermes said.
Evolution of probiotic bacteria
Fu's team found that the three cheese samples from the graves contained bacterial and fungal species, including Lactobacillus kefiranofaciens and Pichia kudriavzevii , respectively, both of which are common in modern-day kefir grains. The grains are a mix of probiotic bacteria and yeast that ferment milk into kefir cheese.
Fu and her colleagues also mapped the bacterial genes in the ancient kefir cheese, providing insight into how probiotic bacteria have evolved over the past 3,600 years.
Today, there are two major groups of Lactobacillus bacteria: one native to Russia and another to Tibet, an autonomous region of China, the study said. The Russian type is widely used worldwide, 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 modern-day strains, they found that it was closely related to a less common group of Lactobacillus that originally came from Tibet.
Its origins contradict the long-held belief that kefir originated exclusively in the Caucasus region, Fu says.
"This is an unprecedented study, which allows us to observe how a bacterium has evolved over the past 3,000 years. In addition, by examining dairy products, we have 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 food, Hermes said. "Ancient DNA analysis, especially of microbes, is fraught with technical difficulties, most of which arise from contamination by modern bacteria," he added.
When did cheese making actually start?
It was no surprise that the Xiaohe people fermented cheese, Warinner said. The process made milk more easily digestible, with microbes producing lactic acid that curdled milk and became the basis for cheese.
"In the absence of refrigeration, it is essentially impossible to store milk for more than a few hours while spontaneous fermentation occurs. So there has probably never been a time when milk and dairy products were used without fermentation," she said.
"Over time, however, people became better at controlling fermentation and selecting 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 recorded in the archaeological record, other evidence, such as animal proteins in human tartar and milk residue on pottery, suggests cheesemaking began much earlier, likely more than 9,000 years ago in Anatolia or the Levant, Warinner noted.
The genomic analysis 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 people were making that aren't normally preserved in archaeological records," said Taylor, who was not involved in the study.
"These incredible findings show us that cheese and other dairy products really were the foundation of an entire way of life that would remain important for millennia and is still a huge part of life today."
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