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French cheeses, a microbial biodiversity that is both rich and specific

French cheeses represent more than 1000 varieties fashioned by humans and micro-organisms. Benefiting from the most modern techniques in massive DNA sequencing, INRA scientists and their colleagues have been able to demonstrate the wealth, diversity and specificity of the bacterial and fungal species that make up the microbial communities found in traditional French cheeses.

Assortiment de fromages français sélectionnés par la fromagerie Beaufils dans le cadre des travaux de l'UMR Génie et microbiologie des procédés alimentaires (Inra, AgroParisTech).
Eric Dugat-Bony et al. Highlighting the microbial diversity of 12 French cheese varieties. International Journal of Food Microbiology 238 (2016) 265.. © INRA, Eric Dugat-Bony et Françoise Irlinger
Updated on 11/17/2016
Published on 11/07/2016

Reblochon, Epoisses or Saint-Nectaire; these cow's milk cheeses that delight our palates are the result of both human know-how and the action of micro-organisms.

Benefiting from the most modern high-throughput sequencing techniques, INRA scientists at Versailles-Grignon and their colleagues from the company Genoscreen have chosen to revisit the biodiversity of the micro-organisms found in traditional French cheeses.

In practice, they explored the diversity of the microbial communities in sixty cheeses, carefully selected by Beaufils,  a renowned cheese shop in Paris.  These cheeses belong to 12 different varieties resulting from different technologies, which ranged from soft cheeses with a washed rind to hard cheeses with a natural rind.

A rich and diversified microbiota

The extraction and then sequencing of DNA fragments known to permit the identification of yeasts and moulds on the one hand, and bacteria on the other, enabled the scientists to detect 44 fungal taxonomic units and 76 bacterial taxonomic units. In the great majority of cases, the team was able to associate these taxonomic units with a known microbial species. It should be pointed out that Saint-Nectaire and Soumaintrain cheeses contained fungal taxonomic units whose sequences were very distant from those of the species described to date, proving once again that species as yet unknown may have taken up residence in these cheeses, although this needs to be confirmed by further studies.

The scientists were thus able to show that the composition of the fungal community was weakly diversified and varied little from one cheese to another. The Geotrichum candidum and Debaryomyces hansenii yeasts predominated in all the cheeses studied, and were sometimes associated withCandida sake.  On the other hand, the bacterial community was more varied and its composition depended markedly on the cheese variety. Eleven species were frequently detected, seven of which were mainly found on the surface of the cheeses, and two, Lactococcus lactis and Streptococcus thermophilus, inside them. The latter are well known because they are widely used to inoculate the milk used to manufacture cheese.

It should also be noted that numerous psychrophilic bacteria were identified in these cheeses. Epoisses thus contains bacteria from the Psychrobacter genus that is characteristic of cold and salty aqueous environments such as seawater.  The discovery of these bacteria in abundance in our cheeses, as in many other food products, suggests that they are particularly well suited to the storage conditions for these foods.

Specific micro-organisms

Rich and diversified, this microbiota also included micro-organisms characteristic of a single cheese variety (Desemzia incertawas thus characteristic of Mont d’Or,and Myroides sp. of Soumaintrain) or a production unit: for example, Arthrobacter alpinus and Lactococcus formosensis were only found in Saint-Nectaire produced by one of the three farms involved in our study. These findings underline the importance of indigenous micro-organisms and the ambience of each cheese-making facility to structuring the microbial communities of cheeses.


By using the most modern sequencing techniques, and for the first time in France, this work enabled a very detailed characterisation of the microbial biodiversity present in a wide selection of high-quality French cheeses. It has thus revealed the incredible richness and diversity of the micro-organisms which in recent decades have raised our cheeses to the rank of a gastronomic heritage.

Find out more

Highlighting the microbial diversity of 12 French cheese varieties.

Eric Dugat-Bony, Lucille Garnier, Jeremie Denonfoux, Stéphanie Ferreira, Anne-Sophie Sarthou, Pascal Bonnarme, Françoise Irlinger. International Journal of Food Microbiology 238 (2016) 265. http://dx.doi.org/10.1016/j.ijfoodmicro.2016.09.026