New Insight into Antimicrobial Compounds from Food and Marine-Sourced Carnobacterium Species through Phenotype and Genome Analyses

Abstract

Carnobacterium maltaromaticum 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.

Distribution and ecology of the generalist lactic acid bacterium Carnobacterium maltaromaticum in different freshwater habitats: Metabolic and antagonistic abilities

“…Kinetics of C. maltaromaticum 3 Ba‐2‐II H 2 O 2 production was compared to a Lactococcus garvieae freshwater isolate (this study), a species known to produce inhibitory amounts of H 2 O 2 (Delpech et al, 2017). Cultures were grown in Erlenmeyer flasks with 20 mL ATP medium, at 25°C with 150‐rpm shaking and OD600 nm for 24 h. H 2 O 2 concentration was measured at 2‐h intervals using Dosatest® Peroxide test strips (VWR, Fontenay‐sous‐Bois, France) (Begrem et al, 2020).…”

“…Genome annotation was performed using Prokka v. 1.13 (Seemann, 2014) and RAST (Aziz et al, 2008;Brettin et al, 2015;Overbeek et al, 2014). The presence of genes encoding the production of antimicrobial compounds was probed with query sequences from Begrem et al (2020) and UniProt (https://www.uniprot. org/), as well as by AntiSMASH 6.0 (Blin et al, 2021) andBAGEL 4 (van Heel et al, 2018).…”

Impact of Putative Probiotics on Growth, Behavior, and the Gut Microbiome of Farmed Arctic Char (Salvelinus alpinus)

“…Antimicrobial activities of probiotic strains were assessed using a miniaturized spot-on-lawn method as previously described ( Begrem et al, 2020 ). Briefly, 10 μl of 24 h-probiotic strain cultures were spotted onto soft agar plates inoculated with one of 24 target strains involved in fish diseases, human infections or seafood spoilage ( Supplementary Table S1 ).…”

Contribution of omics to biopreservation: Toward food microbiome engineering

“…Comparative genomics of Carnobacterium highlighted potential new candidate strains for biopreservation, efficient against L. monocytogenes and harbouring original bacteriocin gene equipment. For example, five different bacteriocins and a 16 kDa new one were predicted in the C. maltaromaticum SF668 and C. maltaromaticum EBP3019 genomes, respectively ( Begrem et al, 2020 ). Combining genome analysis and peptidomics of a Companilactobacillus crustorum strain enabled, from the peptides produced during the growth of this strain, the discovery of eight novel bacteriocins and two other antimicrobials with a broad spectrum of action against Gram-positive and Gram-negative pathogens ( Yi et al, 2018 ).…”

“…Such molecules may have antimicrobial functions or be associated with oxidative stress resistance, and immunomodulatory or cytotoxicity activities. Comparative genomic analysis of Carnobacterium strains showed that this PKS/NRPS gene cluster is unique in C. divergens V41 ( Begrem et al, 2020 ). Other PKs/NRPs antimicrobial compounds, such as milkisin produced by a Pseudomonas sp.…”