Written by: Lauren Milligan Newmark, Ph.D. | Issue # 124 | 2025
- Kefir cheese found buried with 3,500-year-old mummies in Western China was so well preserved that researchers were able to recover ancient DNA from the milk and kefir grains.
- Goat’s milk mitochondrial DNA indicated ancestral ties to goats used by Neolithic pastoralists from Eastern Europe and Western Asia, and DNA analysis of lactic acid bacteria from kefir grains showed connections to cultures in Tibet.
- Genetic evidence suggests humans may have selected for functions of particular lactic acid bacteria strains in kefir grains, such as adaptations to the human intestinal environment, thereby contributing to the bacteria’s evolution.
When it comes to aged cheese, you might think of a tangy two-year aged Spanish Manchego, a nutty three-year aged Italian Parmesan, or even a ten-year-old sharp Wisconsin cheddar. But these cheeses are infants compared with the world’s oldest cheese, aged nearly 4,000 years in a coffin buried in Western China.
Excavated in the early 2000s from the Xiaohe Cemetery in the Tarim Basin, this ancient cheese was found with some of the most well-preserved mummified humans ever discovered [1]. Unlike Egyptian mummies that were intentionally preserved at their time of death, the 3,500-year-old Xiaohe mummies were naturally mummified by the arid desert environment where they were buried. This environment was so ideal for preservation that it even mummified the cheese that was spread across many of the mummies’ necks.
Over 20 years later, the reason why the Xiaohe mummies were interred with cheese necklaces remains a mystery. But DNA analyses from three different cheese samples—the oldest cheese DNA in the world—has helped researchers answer long-held questions about the Xiaohe people and the prehistoric production of fermented dairy in East Asia [2].
Using DNA recovered from mummified cheese is a novel (and completely ingenious) approach for reconstructing prehistoric human behavior. Much like modern day personal genetics companies use cheek swab samples to help customers understand where their ancestors came from, the team of Chinese anthropologists and paleogeneticists [2] used DNA extracted from the cheese samples to trace its origins. And because the mammals milked for cheese-making and the bacterial strains used to ferment that milk into cheese are linked to human activities, the DNA extracted from the cheese could also be used to trace the movements and cultural practices of the Xiaohe people during the early Bronze Age [2].
Previous research [3] had already determined that the mummified cheese was Kefir. Kefir cheese is made by adding kefir grains—a symbiotic community of bacteria and yeasts embedded in proteins and complex sugars—to ruminant milk. Kefir grains vary in types of microbial species but usually include lactic acid bacteria, such as Lactobacillus. These bacteria eat lactose (milk’s primary sugar); in doing so, they increase their numbers while reducing the cheese’s lactose content. This makes kefir cheese easier to digest than milk (important for the genetically lactose intolerant Xiaohe populations) and a good source of probiotics [2].
To identify the specific type of milk used to make the ancient kefir cheese, the research team [2] analyzed mitochondrial DNA (mtDNA) extracted from three cheese samples. They found that two of the kefir samples were made from bovine milk while the third was from goat milk [2]. The researchers then took a deeper dive into this goat’s family tree by comparing its mtDNA sample to 185 mitochondrial genomes of ancient and modern goats across Eurasia [2]. The mtDNA from the Bronze Age Xiaohe goat clustered with Bronze Age and modern goat mtDNA from Europe and Central Asia and away from mtDNA samples from East Asian goats. This suggests the Xiaohe goat, and therefore the Xiaohe people who milked that goat, can trace their ancestry (and dairying culture) to Neolithic pastoralists from the Steppe regions of Eastern Europe and Central Asia [2].
Goats were not the only organisms to leave traces of their DNA in the mummified cheese. Kefir grains are composed of a multitude of bacterial and fungal species. And because kefir cheese can only be produced by adding existing kefir grains to milk, the bacteria present in the mummified kefir grains also have a family tree. From one of the bovine kefir samples, the research team could only identify two bacteria species, Lactobacillus kefiranofaciens and Lactobacillus helleticus (L. kefiranofaciens was also identified in the other bovine kefir cheese) [2]. Amazingly, these same species are commonly found in kefir grains used today.
Focusing on just L. kefiranofaciens, the researchers compared the DNA from the Xiaohe sample with 15 L. kefiranofaciens strains from modern-day kefir grains using a method called average nucleotide identity. Reconstructing the entire genome of this bacterium was a tedious process, but the time and hard work paid off. Analytical techniques that enrich DNA brought the completeness of the L. kefiranofaciens genome to 92%. When they calculated the number of shared nucleotides (the Cs, Ts, Gs, and As that make up the DNA code) within a selected section of the genome, they found the ancient and modern L. kefiranofaciens to have between 95% to 97% similarity [2].
Sequence data were then used to build a phylogeny for the ancient and modern L. kefiranofaciens strains. Like a family tree, a phylogeny is a branching diagram that shows the evolutionary relationships between species. The research team identified two major branches of the phylogenetic tree; the Xiaohe L. kefiranofaciens sample is found at the base of branch one that also included L. kefiranofaciens strains from inland East Asia, whereas branch two included L. kefiranofaciens strains from Europe and East Asian coastal and island regions.
Kefir grains are hypothesized to have originated in the Caucasus region, spreading west to Europe and then spreading East to coastal and island Asia [2]. The phylogenetic reconstructions from the ancient Xiaohe kefir strains uncovered a second spreading route starting in the Tarim Basin (where the Xiaohe cheese was found) and spreading to inland East Asia, including Tibet [2]. These genetic findings are bolstered by archaeological evidence for Bronze age interactions and cultural exchanges between the Xiaohe population and Tibetan populations [2].
As if using molecular data from mummified cheese to reconstruct ancient human population movements weren’t astounding enough, the study authors were also able to use molecular evidence to investigate human-microbial interactions—how might human selection for preferred kefir cheese traits have influenced the evolution of L. kefiranofaciens? Rather than combing through the entire genome to look for evidence of human selection, the researchers decided to focus on areas of modern day genomes with tell-tale evidence of a past horizontal gene transfer (HGT) event. Bacteria like Lactobacillus commonly acquire new genetic traits through HGT with other bacteria in their environment, including different bacteria species. By chance, some of these random transfers of genetic code from one bacterium to another could have provided ancient L. kefiranofaciens strains with genes whose functions made them more attractive to humans to use in kefir production and were thus passed on (through continued use) across generations.
The researchers identified several HGT regions among genomes of modern L. kefiranofaciens strains and the function of the genes in three of these regions were highlighted as potential targets for human selection. These genes were associated with adaptation to environmental stress, such as antibiotic exposure, improved bacterial genome defense mechanisms, and adaptations related to the human intestinal environment [2].
Human domestication, whether of plants or animals, influences the evolution of the domesticated species through targeted selection of preferred traits. Kefir grains are yet another product of human domestication; past human populations, including the Xiaohe, influenced the evolution of L. kefiranofaciens (and presumably other lactic acid bacteria) by propagating kefir grains with preferred attributes. It took the Chinese research team over a decade to determine how these bacteria changed over that last three millennia, but their findings pave the way for future studies to use ancient DNA from organisms other than humans to reconstruct past human behaviors.
References
- Kang IU, Han J, Hong JH, Kim J, Shin DH, Mair VH. Archaeological findings of the Tarim Basin graves and mummies. In: The Handbook of Mummy Studies: New Frontiers in Scientific and Cultural Perspectives 2021; Nov 19: (1033-1048).
- Liu Y, Miao B, Li W, Hu X, Bai F, Abuduresule Y, Liu Y, Zheng Z, Wang W, Chen Z, Zhu S. Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history. Cell. 2024 Oct 17;187(21):5891-900.
- Yang Y, Shevchenko A, Knaust A, Abuduresule I, Li W, Hu X, Wang C, Shevchenko A. Proteomics evidence for kefir dairy in Early Bronze Age China. Journal of Archaeological Science. 2014 May 1; (45):178-86.