In the late 1970s, a team of archaeologists became obsessed with a set of mummies so peculiar that some thought they were a hoax. They were found in the Tarim Basin in northeastern China. Hundreds of human remains had been naturally mummified there for centuries, thanks to the arid, cold desert climate. As research continued, scientists began to ask more questions about the origins and habits of the so-called “Tarim mummies.” But there was one question in particular that kept Qiaomei Fu’s team awake. She is a paleogeneticist and director of the Ancient DNA Laboratory at the Institute of Vertebrate Paleontology and Paleoanthropology at the Chinese Academy of Sciences. Some of the mummies had a mysterious white substance spread across their necks, and no one could explain what it was or why it was there. Twenty years later, thanks to advances in ancient DNA analysis techniques, she has found the answer: kefir cheese.
Qiaomei and her team have succeeded, for the first time, in extracting and analysing the genetic material preserved in samples of this cheese, which date back 3,600 years, making them the oldest ever recorded. The results of the research, published today, Wednesday, in the magazine Cellsuggest a new origin for this fermented food and provide evidence of how evolution and collaboration between humans and probiotic bacteria has always been very close. The author explains that foods such as cheese are extremely difficult to preserve for thousands of years, which is why it is “a unique and valuable opportunity”. The analysis of this food can help scientists better understand prehistoric diet and culture.
“The interaction between people and microbes has always been with us. Ancient humans used their wisdom to apply and domesticate microbes to preserve and produce fermented foods, which shaped specific lifestyles and promoted techno-cultural exchanges,” Qiaomei explains about her research. Using advanced ancient DNA recovery techniques, the researchers were able to reconstruct the genome of the bacteria involved in fermentation processes and explore how humans had a direct influence on the evolution of these microorganisms.
It was a matter of survival. Developing fermentation techniques in the Bronze Age made food more durable. In the case of dairy products, people could turn raw milk into products such as kefir cheese, which not only extended their shelf life but also made them more digestible, especially in populations genetically intolerant to lactose.
The kefir route
Not long ago, it was thought that kefir originated in the mountainous region of the Caucasus and then spread to the rest of Europe and Asia. In fact, the etymological origin of the word is Turkish and means “blessing”. However, the study published in Cell suggests other dispersal routes for this technique, raising the question of whether it actually originated independently in other parts of the world before spreading.
The key seems to be in the type of bacteria found in the samples. The researchers managed to extract mitochondrial DNA from the strain of cheese Lactobacillusthe main microbe in kefir fermentation, whose origins are located in Tibet. This showed a subtle difference, since the strains found in the mummy samples belong to the subspecies kefiranofacienswhile the strains found in Europe and other eastern coastal regions belong to the subspecies kefir granum. Both are commonly found in modern kefir grains. This reinforces the idea of multiple routes of cultural and food spread. But not only that.
During that long journey, the microbes did not stay still. The study helped determine how the Lactobacillus kefiranofaciens exchanged genetic material with related strains and improved, over time, its genetic stability and milk fermentation capabilities. Compared to the old Lactobacillusmodern bacteria are less likely to trigger an immune response and be rejected by the human gut. This suggests that genetic exchanges also helped the Lactobacillus to better adapt to human hosts over thousands of years of interaction. That is, at the same time that humans adapted to bacteria in order to stay fed, bacteria, on an invisible scale, also adapted to humans in order to survive inside them.
“People in the past already used microbes to preserve and produce fermented foods early on, and these production techniques were widely disseminated across populations,” Qiaomei said. “Our new insights into microbial genomes are valuable as they allow us to explore more details about changes in human lifestyle, cultural exchanges, and especially interactions with the environment on an evolutionary scale.”
Thanks to this discovery, scientists will be able to better understand the coevolution between humans and microbes over more than three thousand years. These symbiotic relationships, often ignored but still perpetuated, helped humans adapt to new environmental conditions and improve their diet. The fascination of scientists – and of the general public – with the longest-lived samples is not an academic whim. It is explained, believes Qiaomei, because “perhaps, through older things, people feel closer to their origins.”
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