Strain-specific Molecular Diagnostics for Pediococcus acidilactici: Functional Genomics in Food Safety

Abstract

Commercial strains of Pediococcus acidilactici are incorporated into food safety cultures that are used to inhibit the proliferation of foodborne pathogens. We employed comparative genomics and molecular biology to characterize Pediococcus acidilactici D3, an industrial food safety strain provided by the company Guardian Food Technologies. The objective of this research was to develop strain-specific molecular probes at unique genomic targets to uniquely identify P. acidilactici D3. The antimicrobial activity of P. acidilactici D3 was examined in this study. In addition, a carbohydrate utilization profile was prepared for this strain, from which it was observed that sucrose was readily metabolized by P. acidilactici D3. In order to identify the genes responsible for the observed antimicrobial activity and sucrose utilization, a draft sequence of the P. acidilactici D3 genome was generated. The genes putatively responsible for the expression of an antimicrobial peptide (pediocin) and the sucrose utilization loci were annotated. Using a combination of the two operons as genomic targets, strain-specific probes were successfully developed and validated with quantitative-PCR.