title: Highlighting the microbial diversity of 12 French cheese varieties.
abstract: Surface-ripened cheeses host complex microbial communities responsible for the transformation of milk into cheese as well as the development of important properties in terms of texture, color and sensory perception. In this study, we used high-throughput amplicon sequencing to decipher the bacterial and fungal diversity of 60 cheeses belonging to 12 popular French cheese varieties. Using this approach, 76 bacterial and 44 fungal phylotypes were identified. 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. Finally, we observed patterns specific to the cheese production facility, supporting the importance of indigenous microorganisms for the microbial assemblage of cheese microbiota.
authors.affiliation: UMR Génie et Microbiologie des Procédés Alimentaires, GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France. Electronic address: eric.dugat-bony@grignon.inra.fr.
authors.forename: Eric
authors.initials: E
authors.lastname: Dugat-Bony
authors.affiliation: UMR Génie et Microbiologie des Procédés Alimentaires, GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France; Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France; INRA, UMR1253 Science et Technologie du Lait et de l'Œuf, F-35042 Rennes, France.
authors.forename: Lucille
authors.initials: L
authors.lastname: Garnier
authors.affiliation: Genoscreen, Campus de l'Institut Pasteur de Lille, 59000 Lille, France.
authors.forename: Jeremie
authors.initials: J
authors.lastname: Denonfoux
authors.affiliation: Genoscreen, Campus de l'Institut Pasteur de Lille, 59000 Lille, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Ferreira
authors.affiliation: UMR Génie et Microbiologie des Procédés Alimentaires, GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France.
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: Sarthou
authors.affiliation: UMR Génie et Microbiologie des Procédés Alimentaires, GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Bonnarme
authors.affiliation: UMR Génie et Microbiologie des Procédés Alimentaires, GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Irlinger
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D002611:Cheese / Q000382:microbiology*; D004269:DNA, Bacterial / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D005602:France; D005658:Fungi / Q000145:classification* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D064307:Microbiota / Q000235:genetics*; D008892:Milk / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004271:DNA, Fungal; D021901:DNA, Intergenic; D012336:RNA, Ribosomal, 16S
keywords: Amplicon sequencing; Cheese; Microbial diversity