Despite the protracted history of consuming fermented dairy products, a comprehensive understanding of how these microbial communities were harnessed and evolved throughout human civilization remains elusive. Through the molecular analysis of ancient DNA extracted from 3,500-year-old kefir cheese originating from Xinjiang, China, Dr. Qiaomei Fu, affiliated with the Institute of Vertebrate Paleontology and Paleoanthropology at the Chinese Academy of Sciences, and her research associates embarked on an investigation into historical human-microbial interdependencies. While prior hypotheses posited the dissemination of kefir from the Northern Caucasus to Europe and beyond, this new research uncovers an additional migratory pathway for kefir, extending from Xinjiang into the interior regions of East Asia.
These 3,500-year-old kefir cheese samples represent some of the most ancient dairy remnants discovered, predating 3,000 years. They were crafted by the Bronze Age Xiaohe populace, known for their diverse subsistence strategies, encompassing agriculture, dairy husbandry, and hunting. Although early members of the Xiaohe population exhibited minimal genetic exchange with neighboring groups, mitochondrial DNA analysis indicates matrilineal links to both East and West Eurasian populations. By extracting genetic data from these archeological dairy artifacts, Liu et al. have illuminated the daily practices associated with fermented dairy consumption by the Xiaohe people and examined the symbiotic evolution of these microorganisms and their human hosts. Photography attribution: Liu et al., doi: 10.1016/j.cell.2024.08.008.
“This constitutes the most venerable cheese specimen ever unearthed globally,” stated Dr. Fu, the senior author of a publication featured today in the esteemed journal Cell.
“Perishable consumables like cheese are exceptionally challenging to preserve across millennia, rendering this discovery a singular and significant opportunity.”
“In-depth analysis of this ancient cheese can substantially enhance our comprehension of our ancestors’ dietary habits and cultural practices.”
The scientific team successfully identified bovine and caprine mitochondrial DNA within the cheese specimens recovered from Xinjiang.
Notably, the ancient Xiaohe inhabitants utilized distinct types of animal milk in separate production batches, a departure from the common practice of blending milk varieties observed in contemporaneous cheesemaking traditions of the Middle East and Greece.
Crucially, the researchers were able to isolate and sequence microbial DNA from the dairy composites, thereby confirming their identification as genuine kefir cheese.
Their analyses revealed the presence of bacterial and fungal species, including Lactobacillus kefiranofaciens and Pichia kudriavzevii, both of which are ubiquitously found in contemporary kefir grain cultures.
Kefir grains function as symbiotic microbial matrices, integrating a diverse array of probiotic bacteria and yeasts instrumental in the fermentation of milk into kefir cheese, analogous to the role of a sourdough starter.
The capacity to sequence the genetic material of bacteria within this ancient kefir cheese provided researchers with an invaluable avenue to trace the evolutionary trajectory of probiotic bacteria over the preceding 3,600 years.
Specifically, a comparative analysis was conducted between the Lactobacillus kefiranofaciens strains preserved in the ancient cheese and their modern-day counterparts.
Currently, two principal lineages of the Lactobacillus bacteria are recognized: one with origins in Eastern Europe and another from the Tibetan region.
The European variant is predominantly employed worldwide, including in nations such as the United States, Japan, and across Europe, for the production of yogurt and cheese.
The research cohort determined that the Lactobacillus kefiranofaciens detected in the archeological samples exhibited closer genetic affiliation with the Tibetan lineage. This finding directly challenges the long-standing paradigm that ascribed the sole origin of kefir to the North Caucasus mountain range in present-day Europe.
“Our findings strongly indicate that the kefir culture has been sustained within the Xinjiang region of Northwestern China since the Bronze Age,” Dr. Fu commented.
Furthermore, the investigation elucidated the mechanisms by which Lactobacillus kefiranofaciens engaged in the exchange of genetic material with related bacterial strains. This inter-strain genetic transfer is posited to have fortified its genomic stability and enhanced its efficacy in milk fermentation over time.
In contrast to their ancient progenitors, contemporary Lactobacillus strains are less prone to eliciting an immune response within the human intestinal tract.
This observation suggests that the genetic interplays facilitated Lactobacillus‘s adaptation to human hosts through millennia of cohabitation and interaction.
“This research represents an unparalleled endeavor, affording us a direct glimpse into the evolutionary processes of a bacterium spanning over three millennia,” Dr. Fu emphasized.
“Moreover, by scrutinizing ancient dairy products, we have gained a more refined perspective on the lives of early humans and their intricate relationships with their environment.”
“This study marks merely the commencement of our exploration. Leveraging this advanced technological framework, we aspire to investigate other presently enigmatic archeological findings.”
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Yichen Liu et al. Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history. Cell, published online September 25, 2024; doi: 10.1016/j.cell.2024.08.008
