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.
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The authors would like to thank Fausto Gardini (University of Bologna) for the help with HPLC analysis.
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This work was funded by the Italian Ministry for Development in the framework of the project “Pass-World–pasta e salute nel mondo—Industria 2015” (MI01_00138). GS is supported by Ministry of Education, University and Research (PON02_00186_2937475) in the framework of the project named “Protocolli innovativi per lo sviluppo di alimenti funzionali” (Pro. Ali. Fun.). Vittorio Capozzi was supported by a grant of the Apulian Region in the framework of ‘FutureInResearch’ programme (practice code 9OJ4W81).
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The authors declare that they have no conflict of interest, with the exception of HC and DK who are paid employees of Ganeden Biotech Inc.
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Elisa Salvetti and Luigi Orrù made equal contributions to this article.
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Salvetti, E., Orrù, L., Capozzi, V. et al. Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study. Appl Microbiol Biotechnol 100, 4595–4605 (2016). https://doi.org/10.1007/s00253-016-7416-9
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DOI: https://doi.org/10.1007/s00253-016-7416-9