title: A selected core microbiome drives the early stages of three popular italian cheese manufactures.
abstract: Mozzarella (M), Grana Padano (GP) and Parmigiano Reggiano (PR) are three of the most important traditional Italian cheeses. In the three cheese manufactures the initial fermentation is carried out by adding natural whey cultures (NWCs) according to a back-slopping procedure. In this study, NWCs and the corresponding curds from M, GP and PR manufactures were analyzed by culture-independent pyrosequencing of the amplified V1-V3 regions of the 16S rRNA gene, in order to provide insights into the microbiota involved in the curd acidification. Moreover, culture-independent high-throughput sequencing of lacS gene amplicons was carried out to evaluate the biodiversity occurring within the S. thermophilus species. Beta diversity analysis showed a species-based differentiation between GP-PR and M manufactures indicating differences between the preparations. Nevertheless, all the samples shared a naturally-selected core microbiome, that is involved in the curd acidification. Type-level variability within S. thermophilus species was also found and twenty-eight lacS gene sequence types were identified. Although lacS gene did not prove variable enough within S. thermophilus species to be used for quantitative biotype monitoring, the possibility of using non rRNA targets for quantitative biotype identification in food was highlighted.
authors.affiliation: Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: De Filippis
authors.affiliation: Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
authors.forename: Antonietta
authors.initials: A
authors.lastname: La Storia
authors.affiliation: Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
authors.forename: Giuseppina
authors.initials: G
authors.lastname: Stellato
authors.affiliation: Department of Food Science, University of Parma, Parma, Italy ; Multidisciplinary Interdepartmental Dairy Center - MILC, University of Parma, Parma, Italy.
authors.forename: Monica
authors.initials: M
authors.lastname: Gatti
authors.affiliation: Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
authors.forename: Danilo
authors.initials: D
authors.lastname: Ercolini
mesh_terms: D001483:Base Sequence; D044822:Biodiversity; D002611:Cheese / Q000382:microbiology*; D005285:Fermentation; D005516:Food Microbiology; D059014:High-Throughput Nucleotide Sequencing; D007558:Italy; D026901:Membrane Transport Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D026901:Membrane Transport Proteins; D012336:RNA, Ribosomal, 16S; C021499:lactose permease