title: Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food).
abstract: This work presents the first study on the bacterial communities in Pico cheese, a traditional cheese of the Azores (Portugal), made from raw cow's milk. Pyrosequencing of tagged amplicons of the V3-V4 regions of the 16S rDNA and Operational Taxonomic Unit-based (OTU-based) analysis were applied to obtain an overall idea of the microbiota in Pico cheese and to elucidate possible differences between cheese-makers (A, B and C) and maturation times. Pyrosequencing revealed a high bacterial diversity in Pico cheese. Four phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) and 54 genera were identified. The predominant genus was Lactococcus (77% of the sequences). Sequences belonging to major cheese-borne pathogens were not found. Staphylococcus accounted for 0.5% of the sequences. Significant differences in bacterial community composition were observed between cheese-maker B and the other two units that participated in the study. However, OTU analysis identified a set of taxa (Lactococcus, Streptococcus, Acinetobacter, Enterococcus, Lactobacillus, Staphylococcus, Rothia, Pantoea and unclassified genera belonging to the Enterobacteriaceae family) that would represent the core components of artisanal Pico cheese microbiota. A diverse bacterial community was present at early maturation, with an increase in the number of phylotypes up to 2 weeks, followed by a decrease at the end of ripening. The most remarkable trend in abundance patterns throughout ripening was an increase in the number of sequences belonging to the Lactobacillus genus, with a concomitant decrease in Acinetobacter, and Stenotrophomonas. Microbial rank abundance curves showed that Pico cheese's bacterial communities are characterized by a few dominant taxa and many low-abundance, highly diverse taxa that integrate the so-called "rare biosphere".
authors.affiliation: CITA-A, Centro de Investigação e Tecnologias Agrárias dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal.
authors.forename: Cristina
authors.initials: C
authors.lastname: Riquelme
authors.affiliation: CITA-A, Centro de Investigação e Tecnologias Agrárias dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal.
authors.forename: Sandra
authors.initials: S
authors.lastname: Câmara
authors.affiliation: CITA-A, Centro de Investigação e Tecnologias Agrárias dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal. Electronic address: mariaenes@uac.pt.
authors.forename: Maria de Lurdes N Enes
authors.initials: Mde L
authors.lastname: Dapkevicius
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors.forename: Pablo
authors.initials: P
authors.lastname: Vinuesa
authors.affiliation: CITA-A, Centro de Investigação e Tecnologias Agrárias dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal.
authors.forename: Célia Costa Gomes
authors.initials: CC
authors.lastname: da Silva
authors.affiliation: Department of Chemical Engineering, University of Oporto, Oporto, Portugal.
authors.forename: F Xavier
authors.initials: FX
authors.lastname: Malcata
authors.affiliation: CITA-A, Centro de Investigação e Tecnologias Agrárias dos Açores, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal.
authors.forename: Oldemiro A
authors.initials: OA
authors.lastname: Rego
mesh_terms: D000818:Animals; D001394:Azores; D001419:Bacteria / Q000145:classification / Q000235:genetics; D018407:Bacterial Physiological Phenomena; D044822:Biodiversity; D002417:Cattle; D002611:Cheese / Q000382:microbiology*; D005516:Food Microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Artisanal cheese; Bacterial diversity; Next-generation sequencing