The Tarim mummies of northwestern China have been hiding a culinary secret for millennia. Now, for the first time, scientists have uncovered that secret: ancient kefir cheese. A team of researchers successfully extracted DNA from cheese found alongside these mummies, dating back 3,600 years.

The Oldest Cheese Ever Found

In 2003, archaeologists discovered white substances on the heads and necks of the Tarim mummies. These mummies were unearthed in the Xiaohe cemetery of China’s Tarim Basin, dating from the Bronze Age. For years, scientists could only speculate on what these mysterious substances were. That is, until Qiaomei Fu, a scientist at the Chinese Academy of Sciences, and her team cracked the code.

Using advanced DNA analysis, the researchers confirmed the presence of cow and goat DNA in the samples. Even more strikingly, they identified bacterial and fungal DNA, including Lactobacillus kefiranofaciens and Pichia kudriavzevii species, both commonly found in present-day kefir grains. Fu calls it the “oldest known cheese sample ever discovered.”

 “Food items like cheese are extremely difficult to preserve over thousands of years, making this a rare and valuable opportunity. Studying the ancient cheese in great detail can help us better understand our ancestors’ diet and culture,” the researchers added.

Interestingly, the ancient Xiaohe people used different types of animal milk in separate batches. The approach is unlike the mixing of milk types common in Middle Eastern and Greek cheesemaking.

But why was cheese found with the mummies? Some theories suggest it might have held ritualistic or symbolic importance in death. Others think the cheese might have been left as offerings for the afterlife.

Challenging Kefir’s History

Kefir, a fermented dairy product known for its probiotic benefits, is most commonly associated with the Caucasus mountain region of Russia. But this study challenges that idea. DNA from the cheese’s Lactobacillus kefiranofaciens bacteria revealed a closer connection to Tibetan strains, suggesting that kefir culture was alive and well in Xinjiang over 3,000 years ago.

The researchers also examined how these ancient strains evolved. By comparing the genetic makeup of ancient and modern Lactobacillus, they saw how the bacteria changed to better adapt to human hosts over time. The probiotic bacteria in today’s kefir are less likely to provoke immune reactions in our intestines.

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

The Desert Mummies

The Tarim Basin mummies, dating back as far as 4,000 years, were first discovered in the early 20th century. Their well-preserved bodies, with fair hair and European facial features, stood out amid the predominantly East Asian populations of the region.

For years, scholars debated the origins of these people. Some hypothesized they were migrants from Europe or Central Asia, part of the westward movement of Indo-European speakers. Others suggested they were indigenous to the area, developing distinct features over time due to genetic isolation.

In 2021, scientists from Seoul National University and Harvard University finally shed light on the origins of these Bronze Age people. Unlike neighboring groups, the Tarim people were genetically isolated, descended from a once-widespread group known as Ancient North Eurasians (ANE).

An Isolated People

“These people have been so enigmatic,” said Christina Warinner, an anthropologist at Harvard University and co-author of the study. “Ever since they were found almost by accident, they have raised so many questions because so many aspects of them are either unique, puzzling, or contradictory.”

10,000 years ago, the ANE population largely vanished following the end of the last Ice Age, leaving only traces of their genes in modern populations in Siberia and the Americas. The Tarim mummies, however, show no signs of genetic mixing with other groups in the region, such as the Dzungarian people, who lived just 500 miles to the north. The Dzungarians, in contrast, mixed with pastoralist herders from southern Siberia known as the Afanasievo, who were genetically linked to the Indo-European Yamnaya people of southern Russia.

Researchers speculate that the harsh desert environment might have acted as a natural barrier to migration and gene flow. The Tarim Basin, surrounded by towering mountain ranges, was an inhospitable region where rivers — fed by seasonal snowmelt — were the only reliable sources of water.

But the region’s unforgiving environment could also have contributed to the eventual collapse of the Tarim civilization. When the rivers shifted due to seasonal changes, villages were stranded far from water sources, leading to their abandonment. Today, the once-lush riverbanks of the Tarim Basin are now part of a vast desert.

What Does This Mean?

The implications of this discovery go beyond cheese. It gives scientists a rare look into how ancient people interacted with their environment — and their food. The study also highlights the role of fermentation in human history, a practice that likely served multiple purposes, from nutrition to food preservation.

Understanding the evolution of probiotic bacteria can have modern implications. Probiotics play a significant role in gut health, and tracing their development could inform future research in nutrition and medicine.

“This is just the beginning, and with this technology, we hope to explore other previously unknown artifacts,” Fu said.

The findings appeared in the journal Cell.