# An high-throughput molecular tool for highlighting the eukaryotic food microbial communities: application on 12 french cheese varieties

Jeremie Denonfoux, Stéphanie Ferreira, Lucille Garnier, Anne-Sophie Sarthou, Pascal Bonnarme, Francoise Irlinger, Eric Dugat-Bony

<figure><img src="image_1.png" /></figure>

## ► To cite this version:

Jeremie Denonfoux, Stéphanie Ferreira, Lucille Garnier, Anne-Sophie Sarthou, Pascal Bonnarme, et al.. An high-throughput molecular tool for highlighting the eukaryotic food microbial communities: application on 12 french cheese varieties. 7. Congress of European Microbiologists (FEMS 2017), Jul 2017, Valencia, Spain. **hal-01567202**

HAL Id: hal-01567202

https://hal.science/hal-01567202

Submitted on 5 Jun 2020

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

<figure><img src="image_2.png" /></figure>
# AN HIGH-THROUGHPUT MOLECULAR TOOL FOR HIGHLIGHTING THE EUKARYOTIC FOOD MICROBIAL COMMUNITIES: APPLICATION ON 12 FRENCH CHEESE VARIETIES

Jérémie Denonfoux<fnref n="1" />*, Stéphanie Ferreira<fnref n="1" />, Lucille Garnier<fnref n="2" />, Anne-Sophie Sarthou<fnref n="2" />,<fnref n="3" />,<fnref n="4" />, Pascal Bonnarme<fnref n="2" />, Françoise Irlinger<fnref n="2" /> and Eric Dugat-Bony<fnref n="2" />

Cheese fermentation process is deeply related to culture and tradition. Indeed, the manufacturing processes shapes the chemistry and microbiology of cheeses, which contribute to express their organoleptic properties. France alone represents almost 1000 different cheese varieties harboring each a specific, dense microbiota (2−3 × 10⁹ cells/g cheese). Recently, the use of metagenomics combined with high-throughput sequencing (HTS) technologies offer the opportunity to profile cheese microbial populations on a large scale. Even if the knowledge associated with the bacterial communities of cheeses is well documented, it remains still missing for the eukaryotic fraction.

The GenoScreen company and the French National Institute for Agricultural Research (INRA) associated their expertise to develop a HTS tool for investigate the eukaryotic microbiota associated with 60 cheeses belonging to 12 traditional French cheese varieties. The high throughput ITS2 amplicon sequencing associated with bioinformatic processing was used to characterize the fungal community composition down to the species level.

The results showed that major differences were observed between rind and core samples and also according to cheese varieties and manufacturing processes. Occurrence analysis revealed the presence of widespread taxa as well as operational taxonomic units (OTUs) specific to one or several cheese varieties. We highlighted as well some cheese varieties such as Saint-Nectaire and Soumaintrain still hosted unknown species that may account for a large proportion of the total community.

Finally, this molecular tool could be employed as a large-scale microbial inventory in food-related habitats to identify microbial taxa without reference to food isolates.

Jérémie DENONFOUX

GENOSCREEN, Campus de l'Institut Pasteur de Lille
1 rue du Professeur Calmette, 59000 Lille - France
E-mail: jeremie.denonfoux@genoscreen.fr

Tel: +33(0)3.20.87.72.08

<footnote n="1">¹ Genoscreen, département Recherche, Développement et Innovation- Communautés microbiennes, Campus de l'Institut Pasteur de Lille, 59000 Lille, France</footnote>

<footnote n="2">² UMR Génie et Microbiologie des Procédés Alimentaires, GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France</footnote>

<footnote n="3">³ Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France</footnote>

<footnote n="4">⁴ INRA, UMR1253 Science et Technologie du Lait et de l'OEuf, F-35042 Rennes, France</footnote>

<footnote>*Corresponding author:</footnote>