Gruyère cheese, or a history of the domestication of bacteria

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

The domestication of livestock and plants marked an important stage in the settlement of human populations in the Neolithic period, as they moved from a hunter-gatherer lifestyle to a subsistence model based on animal husbandry and agriculture. Because of the microscopic size and virtual absence of fossils of micro-organisms, their domestication is more difficult to prove than that of flora and fauna. Although several studies have already demonstrated this in the case of yeasts (microscopic, single-celled fungi with nuclei), the case of bacteria (micro-organisms that are mainly single-celled and have no nuclei) has yet to be elucidated. This was the objective of Vincent Somerville, a former doctoral student in Philipp Engel's team at the Department of Fundamental Microbiology (DFM) in 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, have been published in the journal Nature Communications.

An old 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. As human population has grown throughout history, and food demand has increased, long-term storage solutions were needed. ‘This is the case with fermentation, which converts sugars into acids, protects against the proliferation of undesirable microbes and therefore enables food to be preserved for longer,’ explains Philipp Engel, co-director of the study. This technique, which dates back several thousand years, uses micro-organisms such as yeast to make beer or wine, or bacteria to make cheese. The first indirect archaeological evidence of milk fermentation dates back around 10,000 years, to the Neolithic period.

Swiss cheeses as study subjects

Thanks to collaboration with Agroscope, the Swiss centre of competence for agronomic and food research, the Lausanne group had access to a collection of bacterial strains used in 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 some sort of laboratory mini cheeses’, explains Vincent Somerville, first author of the article. ‘We then analysed the evolution of the genetic and phenotypic characteristics of this collection over time in order to identify markers indicative of domestication. By observing more than 100 bacterial isolates and almost 1,000 samples, the scientists found, respectively, low genetic diversity and high stability of traits specific to the food preservation process (for example, acidification) over this half-century period. Those are indicators of an ancient, or even very ancient, adaptation, which by extrapolation corresponds to the appearance of the first fermented dairy products. ‘The temporal concordance between the dating of the micro-organisms and the archaeological history of this fermented food was quite unexpected’, enthuses researcher Florent Mazel. In other words, it is possible to trace the past of the domestication of bacteria from Swiss cheeses.

Guaranteeing food safety

In the future, cheeses from different parts of the world could be compared in order to generalize the study. In addition, research into the domestication of bacterial communities used to initiate the fermentation of other products, such as kefir, looks promising. ‘A better understanding of bacterial domestication will enable us to optimize the characteristics of these microbiota, improve the use of this process and make it a more sustainable method of food storage’, hopes Florent Mazel.

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More info on the Swiss National Centre of Competence in Research (NCCR) Microbiomes