title: A genome-based identification approach for members of the genus Bifidobacterium.
abstract: During recent years, the significant and increasing interest in novel bifidobacterial strains with health-promoting characteristics has catalyzed the development of methods for efficient and reliable identification of Bifidobacterium strains at (sub) species level. We developed an assay based on recently acquired bifidobacterial genomic data and involving 98 primer pairs, called the Bifidobacterium-ampliseq panel. This panel includes multiplex PCR primers that target both core and variable genes of the pangenome of this genus. Our results demonstrate that the employment of the Bifidobacterium-ampliseq panel allows rapid and specific identification of the so far recognized 48 (sub)species harboring the Bifidobacterium genus, and thus represents a cost- and time-effective bifidobacterial screening methodology.
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Ferrario
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mancabelli
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy.
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.affiliation: Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland.
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Duranti
authors.affiliation: GenProbio srl, 43124, Parma, Italy.
authors.forename: Marta
authors.initials: M
authors.lastname: Mangifesta
authors.affiliation: GenProbio srl, 43124, Parma, Italy.
authors.forename: Alice
authors.initials: A
authors.lastname: Viappiani
authors.affiliation: Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland.
authors.forename: Douwe van
authors.initials: Dv
authors.lastname: Sinderen
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy marco.ventura@unipr.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
mesh_terms: D001483:Base Sequence; D001644:Bifidobacterium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Bifidobacterium; Ion Torrent; ampliseq; core genes; multiplex PCR; truly unique genes