Abstract
Carnobacteriummaltaromaticum and Carnobacterium divergens, 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 Carnobacterium species. The biosynthetic gene cluster (BGCs) diversity of 39 publicly available Carnobacterium 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. C. inhibens MIP2551 produced a high amountof H2O2, probably thanks to the presence of four oxidase-encoding genes. C. maltaromaticum EBP3019 and SF668 strains were highly efficient against Listeria monocytogenes. 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 Carnobacterium spp. allowed the prediction of potential innovative natural products that could be relevant for biotechnological applications.
Highlights
Lactic acid bacteria (LAB) are microaerophilic Gram-positive bacteria capable of fermenting sugars into lactic acid
Eighty-nine Carnobacterium spp. genome sequences were retrieved from the NCBI database (Table S2)
The species affiliation was checked by 16S rDNA-based phylogeny (Figure S1) and by phylogenomics using the ANI (Average Nucleotide Identity) similarity values (Figure 1)
Summary
Lactic acid bacteria (LAB) are microaerophilic Gram-positive bacteria capable of fermenting sugars into lactic acid. Due to this feature, LAB are involved in various food fermentations such as dairy, meat, or vegetable products. The production of active secondary metabolites by LAB is well documented They include end or by-products such as organic acids, diacetyl, and hydrogen peroxide [3], and active peptides named bacteriocins [4,5,6]. These peptides exhibit antimicrobial activities against Gram-positive bacteria and rarely against Gram-negative bacteria and fungi [7]. One of them is involved in oxidative stress resistance [14], and the other inhibits Gram-positive bacteria growth [15]
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