Comparative Analyses of Pediococcus pentosaceus Strains Isolated from Milk Cattle Reveal New Insights for Screening Food-Protective Cultures

<i>Pediococcus pentosaceus</i> is a lactic acid bacterium used inter alia for the fermentation of milk, meat, vegetables, fruits, and even for brewing beer. Several health-promoting effects, such as antibacterial and antifungal activities or microphage and immune system stimulation, have been attributed. Apart from refining foods during the fermentation process, <i>P. pentosaceus</i> strains are added to meat and meat products as protective cultures to improve food safety, while leaving the organoleptic properties untouched. Since knowledge on the latter issue is still limited, we investigated 32 isolates from milk samples and teat canal biofilms regarding their antibacterial efficacy as a prerequisite for possible application as protective cultures. <i>P. pentosaceus</i> strains were unequivocally identified by DNA sequencing of the <i>rrnA</i> gene encoding 16S rRNA. Binary matrices obtained from random amplification of polymorphic DNA experiments showed that all isolates differed by more than 5% and thus represented subspecies. The antibacterial profiles against eight food-borne pathogens and food spoilage bacteria were determined. They efficiently combatted, although to various extents, Gram-negative bacteria such as <i>Pseudomonas aeruginosa</i> or <i>Salmonella enterica</i>, and Gram-positive bacteria such as <i>Staphylococcus aureus</i> and <i>Listeria monocytogenes</i>. Interestingly, acid production was dependent on the presence of the challenged pathogen and did not correlate with the extent of inhibition. Bioinformatic analyses of the genomes of the three top-ranked isolates revealed a pronounced genomic plasticity with a core genome of 1460 genes and additional 91, 130, and 161 unique genes, respectively. Each strain included a set of three, five, or six plasmids and was equipped with different genes encoding bacteriocins. The data suggest that multiple strains of <i>P. pentosaceus</i> should be included in order to optimize the selection of a culture for food preservation. The approach could also be applicable to other bacterial species.