Ancient Domestication of Bacteria Used in Cheese Production

The domestication of plants and animals has played a key role in the development of human societies. And microbes have also been tamed: a UNIL study, published in the journal "Nature Communications", shows that bacteria used to produce Gruyère, Emmental and Sbrinz show signs of ancient domestication.

The domestication of livestock and plants marked an important step in the sedentarization of human beings in the Neolithic period, moving from a hunter-gatherer lifestyle to a subsistence model based on livestock breeding and agriculture. Due to the microscopic size and the near absence of fossils of microorganisms, their domestication is more difficult to prove than that of fauna and flora. Even if a few studies have already confirmed it for yeasts (microscopic single-celled fungi with a nucleus), the case of bacteria (mostly single-celled germs without a nucleus) remained to be elucidated. This was the hobby horse of Vincent Somerville , a former doctoral student in Philipp Engel's team, at the Department of Fundamental Microbiology (DMF) of the Faculty of Biology and Medicine at UNIL. The results of his latest study, carried out under the co-direction of Florent Mazel and in collaboration with Agroscope, were published in the journal Nature Communications .

An ancestral process

Domestication consists of artificially selecting - generation after generation - variants of a wild species that have developed interesting characteristics for agriculture or livestock farming, such as the nutritional quality of plants or the size and docility of animals. With the increase in the human population throughout history and therefore the growing need for food, long-term storage solutions had to be found. "This is the case with fermentation, which converts sugars into acids, protects against the proliferation of unwanted microbes and therefore allows food to be preserved for longer," explains Philipp Engel, co-director of the study. This technique, which is several thousand years old, uses microorganisms, such as yeast for making beer or wine, or bacteria for making cheese. The first indirect archaeological traces of milk fermentation date back around 10,000 years ago, i.e. from the Neolithic period.

Swiss cheeses as subjects of study

Thanks to the collaboration with Agroscope, the Swiss center of expertise for agricultural and food research, the Lausanne group had access to a set of bacterial strains used for the production of three different Swiss cheeses: Gruyère, Emmental and Sbrinz, and stored for 50 years. "These cultures, also called "cheese starter cultures", were partially reactivated to create a kind of mini laboratory cheeses", explains Vincent Somerville, first author of the article. "We then carried out an analysis of the evolution of the genetic and phenotypic characteristics of this collection over time in order to identify markers revealing domestication." By observing more than 100 bacterial isolates and nearly 1000 samples, the scientists found, respectively, low genetic diversity and high stability of traits specific to the food preservation process (for example, acidification) during this half-century period. Indicators of an ancient, even very ancient, adaptation, which corresponds by extrapolation to the appearance of the first fermented dairy products. "The temporal concordance between the dating of the microorganisms and the archaeological history of these fermented foods was quite unexpected," rejoices the researcher, Florent Mazel. In other words, it is possible to trace the past of the domestication of bacteria from Swiss cheeses.

Ensuring food safety

In the future, cheeses from different regions of the world could be compared in order to generalize the study. In addition, research on the domestication of bacterial communities used to initiate the fermentation of other products, such as kefir, seems promising. "A better understanding of the domestication of bacteria will make it possible to optimize the characteristics of these microbiotas, improve the use of this process and make it a more sustainable way of storing food," ultimately hopes Florent Mazel.

Reference: Somerville V, Thierer N, Schmidt RS, et al. Genomic and phenotypic imprints of microbial domestication on cheese starter cultures. Nat Commun. 2024. doi: 10.1038/s41467-024-52687-7

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