New Insight into Antimicrobial Compounds from Food and Marine-sourced <i>Carnobacterium</i> Species through Phenotype and Genome Analyses

• Main Authors: Simon Begrem, Flora Ivaniuk, Frédérique Gigout-Chevalier, Laetitia Kolypczuk, Sandrine Bonnetot, Françoise Leroi, Olivier Grovel, Christine Delbarre-Ladrat, Delphine Passerini
• Format: Article
• Language: English
• Published: MDPI AG 2020-07-01
• Series: Microorganisms
• Subjects: lactic acid bacteria; antimicrobial activity; <i>Carnobacterium </i>spp.; hydrogen peroxide; bacteriocin; RiPP
• Online Access: https://www.mdpi.com/2076-2607/8/7/1093

<i>Carnobacterium</i> <i>maltaromaticum</i> and <i>Carnobacterium</i> <i>divergens</i>, isolated from food products, are lactic acid bacteria known to produce active and efficient bacteriocins. Other species, particularly those originating from marine sources, are less studied. The aim of the study is to select promising strains with antimicrobial potential by combining genomic and phenotypic approaches on large datasets comprising 12 <i>Carnobacterium</i> species. The biosynthetic gene cluster (BGCs) diversity of 39 publicly available <i>Carnobacterium</i> spp. genomes revealed 67 BGCs, distributed according to the species and ecological niches. From zero to six BGCs were predicted per strain and classified into four classes: terpene, NRPS (non-ribosomal peptide synthetase), NRPS-PKS (hybrid non-ribosomal peptide synthetase-polyketide synthase), RiPP (ribosomally synthesized and post-translationally modified peptide). In parallel, the antimicrobial activity of 260 strains from seafood products was evaluated. Among the 60% of active strains, three genomes were sequenced and submitted to a dereplication process. <i>C. inhibens</i> MIP2551 produced a high amountof H₂O₂, probably thanks to the presence of four oxidase-encoding genes. <i>C. maltaromaticum</i> EBP3019 and SF668 strains were highly efficient against <i>Listeria monocytogenes</i>. A new extracellular 16 kDa unmodified bacteriocin in the EBP3019 strain and five different bacteriocins in SF668 were highlighted. In this study, the overview of antimicrobial BGC and inhibitory activities of <i>Carnobacterium</i> spp. allowed the prediction of potential innovative natural products that could be relevant for biotechnological applications.