A study of ancient kefir cheese reveals the complex history and evolution of milk fermentation in Eurasia and highlights how Lactobacillus kefiranofaciens has adapted over centuries of human interaction. Food fermentation is the oldest production method using microorganisms in human history. For example, milk fermentation in India dates back to B.C. We can trace it back to 6,000-4,000 years ago, and people in the Mediterranean were producing and consuming cheese as far back as 7,000 years ago.

Despite the long history of human consumption of fermented foods, little is known about the history of the use of fermentative microorganisms and the history of related cultural transmission. In particular, due to the long-term interaction of these fermenting microorganisms with humans, their evolutionary trajectories, especially their functional adaptation, remain unclear.

A group of Chinese scientists recently completed the world’s first metagenomic study on Bronze Age kefir cheese found in the Xiaohe Cemetery, the oldest known milk remains to date, adding to our knowledge of the spread of early milk fermentation techniques. Molecular evidence from the remains of ancient fermented dairy products is a powerful tool for understanding past interactions between humans and fermentation microbes.

Groundbreaking development in fermentation research

In this study, scientists extracted high-quality genomes Lactobacillus kefiranofaciens (L. kefiranofaciens)) Data from three ancient cheese samples found in the Xiaohe Cemetery in Xinjiang, dated to approximately 3,500 years ago. The group’s findings were published online at: Cell In the article “Bronze Age Cheese Reveals Human Interaction” on September 25 and lactobacilli throughout evolutionary history.” Presented as a document highlighting cells.

“We have been working on this project for more than 11 years,” FU said. Qiaomei is the last corresponding author and director of the Laboratory of Molecular Paleontology at the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences. Importantly, he developed probes for DNA enrichment. lactobacilluswhich increases target DNA from <1% to 64-80% and allows reconstruction of the entire genome lactobacillus.

“This is an unprecedented study that allowed us to observe how bacteria evolved over the last 3000 years. We also obtained a clearer picture of the life of ancient man and his interaction with the world by studying dairy products,” says FU. “This is just the beginning, and we hope to discover other previously unknown artifacts with this technology.”

Ancient milk technologies unearthed

A cheese sample excavated from the Xiaohe Cemetery in Xinjiang is the oldest cheese product ever found. It was previously identified using paleoproteomics as kefir cheese, a fermented dairy product made from kefir grains containing fermentation microbes.

By reconstructing the fermentation microbial community, the study confirms that cheese is made using lactic acid bacteria and yeast. The researchers also found that the milk used to make the cheese came from goats that were common in post-Neolithic Eurasia, as opposed to modern domesticated goats in Inner East Asia. This finding suggests that the ancient people of Tarim-Basim likely learned kefir-making technology from populations in the Eurasian steppes.

Genetic ideas of ancient fermentation

The spread of milk fermentation technology accompanied human migration and interaction, a process that largely accelerated the evolution of lactic acid bacteria. But this study also reveals a new way of spread L. kefiranofaciens By analyzing the phylogenetic relationships of ancient times L. kefiranofaciens in Xinjiang.

Researchers found that L. kefiranofaciens, It consists of two branches used for fermentation. The former consisted mainly of species from Europe (such as the area occupied by modern Germany) and coastal areas and islands in Asia (such as the areas occupied by modern Guangdong, the island of Taiwan, Japan, and Singapore). This distribution coincided with the path of spread from the Caucasus to Europe, on the one hand, and to the coastal regions of Asia and Southeast Asia, on the other hand. The other clade consisted mainly of species distributed in the interior of East Asia (including Tibet).

The reconstructed ancient strains lie at the base of the clade, indicating an additional way that kefir production technology spread from Xinjiang to Inner East Asia through techno-cultural exchange.

Difference of two classes L. kefiranofaciensIt probably results from the spread of common ancestors originally domesticated in different populations and represents migration and interactions that occurred during the use and domestication of fermentative microorganisms by different ancient populations.

“It is very interesting to see how much information can be obtained from these cheeses,” said YANG Yimin, a professor at the University of the Chinese Academy of Sciences. “Organic remains provide a window into past human behavior and culture lost in history and record.”

ideas about evolution lactobacillus

This study also revealed that human use and domestication played an important role in evolution. L. kefiranofaciens. Comparative analysis of genomes L. kefiranofaciens The period from the Bronze Age to modern times allows us to characterize adaptive evolution lactobacillus kefiranofaciens in the last few thousand years.

Extensive horizontal gene transfer is one of the main mechanisms of adaptive evolution of lactic acid bacteria. Comparison of functional profiles of ancient and modern L. kefiranofaciensStudy reveals three main evolutionary trajectories L. kefiranofaciens : 1) adaptation to environmental stress through the emergence of drug resistance-associated genes in modern species; 2) strengthening the protective mechanisms of the bacterial genome and modern ones L. kefiranofaciens It indicates gene clusters, such as the RM system and the related toxin-antitoxin system, that can prevent the entry of exogenous DNA and thus reduce the associated fitness costs; and 3) adaptations to the human intestinal environment; for example, modern species have acquired sets of genes that could potentially interact with the host’s gut, probably due to their long-term interactions with humans.

This study also examines long-term human use and domestication. L. kefiranofaciens, It probably also affected its evolution. compared L. kefiranofaciens Modern strains from Bronze Age Tibet display two horizontally transferred gene clusters associated with facilitating the inflammatory response in the gut. This not only promotes survival L. kefiranofaciens It is found in the human intestine and also contributes to the functioning of the intestine.

Considering that ancient populations were able to easily spread kefir production technology using kefir grains, the existence of these gene clusters is likely due to the predominance of kefir grains containing different classes among the populations of that time. L.kefiranofaciens.

Cultural impact of fermentation

“The interaction between a human and a microbe is always fascinating,” said LIU Yichen, one of the first authors and an associate professor in IVPP’s Laboratory of Molecular Paleontology. “Fermenting microbes played a very important role in the daily lives of these ancient people, and they proliferated these microbes for thousands of years, often without knowing they existed.”

Using ancient DNA information about fermentative microorganisms closely associated with past human activities and culture, this study provides a new framework for using ancient DNA to study the cultural interactions of ancient people.