We finally know how the world’s oldest cheese was made

For millennia, the Taklamakan Desert environment preserved more than the bodies of those buried in China’s Tarim Basin. Scattered around the necks of some laid to rest in Xiaohe, a Bronze Age cemetery, archaeologists found pebble-sized hunks of a yellowish substance: the world’s oldest cheese. A new analysis of the ancient dairy’s DNA hints at how it was made and how its production spread, researchers report today in Cell.

In a previous study, researchers took tiny samples of the 3,500-year-old cheese that bedecked the mummies’ necks. An analysis of proteins in those bits revealed the presence of Lactobacillus kefiranofaciens, a microbe used to produce a type of fermented cheese called kefir. That was “really amazing,” says Qiaomei Fu, a paleogeneticist at Chinese Academy of Sciences in Beijing. Having worked with ancient human DNA, she wanted to study the fermenting microbe’s DNA.

But “to extract genomes from these ancient samples is not trivial,” Fu says. The tiny amount of DNA left in the ancient cheese has degraded into tiny fragments over time and mixed with genetic information from the environment. In 2014, Fu began designing special molecules that could efficiently capture the microbe’s ancient DNA from the cheese. After years of work, the team has compiled a genome for the ancient organism that is 92 percent complete.

From this microbe’s DNA, the team could explore the history of the cheese’s production. Kefir begins with a culture, a slurry created by inoculating milk with an existing bit of kefir—just like how a lump of yogurt can be used to make new yogurt. As the cheese spread from place to place, so did the cultures used to make it.  To retrace the probiotic microbe’s journey, the researchers compared the DNA of the L. kefiranofaciens found in the mummies’ cheese with that of others in the family tree. Two separate branches emerged. One included strains from Europe and the Pacific Islands, while the cemetery kefir strains were related to those from Tibet and some from East Asia.

Researchers have previously proposed that kefir spread from the Northern Caucasus in modern Russia to other parts of Europe and beyond. But the microbe in the cemetery cheese evolved relatively early, suggesting another route from near Xiaohe, which is in Xinjiang, China, to East Asian locales, such as Tibet. During the Bronze Age, people from Xinjiang may have immigrated to Tibet, but more archaeological evidence is needed, says study coauthor Yimin Yang, a molecular archaeologist at the Chinese Academy of Sciences.

(Who were the Tarim Basin mummies?)

The milk also pointed to the mingling of ancient peoples. Two samples contained DNA from cows, while another had only had genetic material from goats. The goat DNA was similar to that of other ancient Central Asian samples, suggesting it may have been part of a group of domesticated goats that became widely distributed, Fu says. She and her colleagues previously found signs for the mixing of those in Xinjiang with other Bronze Age populations.

Along with people on the move, kefir may have spread in part because its fermentation decreases the dairy’s lactose, making it easier to consume for lactose-intolerant Bronze Age populations, including those of Xiaohe. L. kefiranofaciens isn’t the only microbe found in the Tarim mummy cheese, and the team may find further clues to past human activities from other bacteria and yeast in the mix. That, along with intel from other samples such as hardened dental plaque and fossilized poop, could reveal more about the interactions between Bronze Age populations.

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