Scientists Sequence DNA of 3,600-Year-Old Cheese

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The bodies of Bronze Age desert dwellers who were exhumed from their graves in what is now northwestern China were found buried with cheese scattered on their heads and necks – perhaps as a snack for the afterlife.

After a decade Discovering dairy On remarkably intact remains mummified by the arid conditions of the Taklamakan Desert, scientists have extracted and sequenced DNA from 3,600-year-old cheese, the oldest in the archaeological record.

The analysis revealed how the Xiaohe people made cheese, showed how humans exploited microbes to improve their food and how microbes can be used to trace cultural influences through the ages.

Results, Published Wednesday in the journal Cell“This discovery opens up ‘new frontiers in ancient DNA studies,’ a type of research that would have been ‘unthinkable even a decade ago,’” said Christina Wariner, an assistant professor of social sciences and anthropology at Harvard University. Wariner was not involved in the research.

“Fermented foods are now widely produced using a few strains of commercial bacteria and yeast grown in the lab,” she said.

“Little is known about the diverse array of heritage microbes that people in the past used to produce today’s most popular foods – from bread to cheese and from beer to wine.”

A team led by Chinese paleontologist Qiaomei Fu was able to identify goat and cow DNA in the cheese samples. The researchers were also able to sequence the DNA of microbes in the cheese, confirming that it was kefir, a type of cheese that is still widely made and eaten today. Fu is director of the Ancient DNA Laboratory at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing.

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. The bodies were naturally preserved by the dry desert air, and their facial features and hair color are clearly distinguishable despite being up to 4,000 years old.

The Tarim Basin mummies, buried in unusual boat graves in felt and woven clothing, have long puzzled archaeologists. Despite being a genetically isolated group, the individuals adopted new ideas and techniques, according to a report from Harvard University. October 2021 Study.

New research suggests 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, although it’s not clear why.

“The Xiaohe people made cheese in much the same way that traditional producers make kefir cheese today, using pre-made kefir grains (similar to a kombucha mother drink 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 research.

“That’s what makes the study so important — we can see how these microbial commodities moved and spread throughout Asia,” Hermes said.

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

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

Today, there are two main groups of Lactobacillus bacteria — one originating in Russia and the other from Tibet, an autonomous region of China, according to the study. The Russian variety is widely used worldwide, including in the United States, Japan and European countries, to make yogurt and cheese.

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

The origins of the bacteria challenge the long-held belief that kefir only began in Caucasus Mountains Region“Fu said.”

“This is an unprecedented study that allows us to observe how bacteria have evolved over the past 3,000 years. Furthermore, by examining dairy products, we have gained a clearer picture of ancient human life and its interactions with the world,” Fu said in a statement. “This is just the beginning.”

Surprisingly, Hermes said, not only did the cheese survive, but it was also possible to sequence DNA from the food item. “Analyzing ancient DNA, especially on microbes, is fraught with technical problems, which often stem from contamination with modern bacteria,” he said.

It’s no surprise that the Xiaohe people fermented cheese, Wariner said. The process made the milk more digestible, with microbes producing lactic acid that caused the milk to curdle and form the basis for cheese.

“In the absence of refrigeration, it is impossible to store milk for more than a few hours with spontaneous fermentation occurring, so there may never have been a time when milk and dairy products were used without fermentation,” she said.

“Over time, people have gotten better and better at controlling fermentation and selecting the specific microbes that produce 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 suggests that cheesemaking originated much earlier, perhaps more than 9,000 years ago in Anatolia or LevantWariner pointed out that.

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

“It’s amazing to see how complex the products people were making were, which are not usually preserved in the archaeological record,” said Taylor, who was not involved in the research.

“These amazing results show us that cheese and other dairy products were in fact the foundation of an entire way of life that would continue to be important for thousands of years and are still a major part of life today.”