title: Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study.
abstract: Probiotics are microorganisms that confer beneficial effects on the host; nevertheless, before being allowed for human consumption, their safety must be verified with accurate protocols. In the genomic era, such procedures should take into account the genomic-based approaches. This study aims at assessing the safety traits of Bacillus coagulans GBI-30, 6086 integrating the most updated genomics-based procedures and conventional phenotypic assays. Special attention was paid to putative virulence factors (VF), antibiotic resistance (AR) genes and genes encoding enzymes responsible for harmful metabolites (i.e. biogenic amines, BAs). This probiotic strain was phenotypically resistant to streptomycin and kanamycin, although the genome analysis suggested that the AR-related genes were not easily transferrable to other bacteria, and no other genes with potential safety risks, such as those related to VF or BA production, were retrieved. Furthermore, no unstable elements that could potentially lead to genomic rearrangements were detected. Moreover, a workflow is proposed to allow the proper taxonomic identification of a microbial strain and the accurate evaluation of risk-related gene traits, combining whole genome sequencing analysis with updated bioinformatics tools and standard phenotypic assays. The workflow presented can be generalized as a guideline for the safety investigation of novel probiotic strains to help stakeholders (from scientists to manufacturers and consumers) to meet regulatory requirements and avoid misleading information.
authors.affiliation: Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.|APC Microbiome Institute, University College Cork, Western Road, Cork, T12 Y337, Ireland.
authors.forename: Elisa
authors.initials: E
authors.lastname: Salvetti
authors.affiliation: Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria, Genomics Research Centre, Via S. Protaso 302 Fiorenzuola d'Arda, 29017, Piacenza, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Orrù
authors.affiliation: Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122, Foggia, Italy.
authors.forename: Vittorio
authors.initials: V
authors.lastname: Capozzi
authors.affiliation: Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
authors.forename: Alessia
authors.initials: A
authors.lastname: Martina
authors.affiliation: Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria, Genomics Research Centre, Via S. Protaso 302 Fiorenzuola d'Arda, 29017, Piacenza, Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Lamontanara
authors.affiliation: Ganeden Biotech Inc., 5800 Landerbrook Drive Suite 300, Mayfield Heights, OH, 44124, USA.
authors.forename: David
authors.initials: D
authors.lastname: Keller
authors.affiliation: Ganeden Biotech Inc., 5800 Landerbrook Drive Suite 300, Mayfield Heights, OH, 44124, USA.
authors.forename: Howard
authors.initials: H
authors.lastname: Cash
authors.affiliation: Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
authors.forename: Giovanna E
authors.initials: GE
authors.lastname: Felis
authors.affiliation: Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria, Genomics Research Centre, Via S. Protaso 302 Fiorenzuola d'Arda, 29017, Piacenza, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Cattivelli
authors.affiliation: Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. sandra.torriani@univr.it.
authors.forename: Sandra
authors.initials: S
authors.lastname: Torriani
authors.affiliation: Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122, Foggia, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Spano
mesh_terms: D000070000:Bacillus coagulans / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D001679:Biogenic Amines / Q000378:metabolism; D003257:Consumer Product Safety; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D007612:Kanamycin / Q000494:pharmacology; D010641:Phenotype; D019936:Probiotics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013307:Streptomycin / Q000494:pharmacology
chemical_list: D001679:Biogenic Amines; D012336:RNA, Ribosomal, 16S; D007612:Kanamycin; D013307:Streptomycin
keywords: Antibiotic resistance; Bacillus coagulans; Genomics; Probiotics; Safety; Virulence factors