Comparative Genomics of Leuconostoc carnosum

Abstract

Leuconostoc carnosum is a known colonizer of meat-related food matrices. It reaches remarkably high loads during the shelf life in packaged meat products and plays a role in spoilage, although preservative effects have been proposed for some strains. In this study, the draft genomes of 17 strains of L. carnosum (i.e., all the strains that have been sequenced so far) were compared to decipher their metabolic and functional potential and to determine their role in food transformations. Genome comparison and pathway reconstruction indicated that L. carnosum is a compact group of closely related heterofermentative bacteria sharing most of the metabolic features. Adaptation to a nitrogen-rich environment, such as meat, is evidenced by 23 peptidase genes identified in the core genome and by the autotrophy for nitrogen compounds including several amino acids, vitamins, and cofactors. Genes encoding the decarboxylases yielding biogenic amines were not present. All the strains harbored 1-4 of 32 different plasmids, bearing functions associated to proteins hydrolysis, transport of amino acids and oligopeptides, exopolysaccharides, and various resistances (e.g., to environmental stresses, bacteriophages, and heavy metals). Functions associated to bacteriocin synthesis, secretion, and immunity were also found in plasmids. While genes for lactococcin were found in most plasmids, only three harbored the genes for leucocin B, a class IIa antilisterial bacteriocin. Determinants of antibiotic resistances were absent in both plasmids and chromosomes.

Keywords: Leuconostoc carnosum; bacteriocin; genomics; metabolism; pangenome analysis.

FIGURE 1

(A) Distributions of CDSs found in the pangenome of L. carnosum: core genes (blue), shell genes (orange), and cloud genes (green) in chromosome (plain colors) and plasmids (dotted colors). (B) Estimation of the pangenome (blue) and the core genome (green) by including genomes one by one.

FIGURE 2

(A) PCoA visualization of Jaccard distances among genomes, based on shared genes. Circles are the genomes published by Candeliere et al. (2020); triangles are the genomes already published. (B) Neighbor joining unrooted phylogenetic tree based on core genome alignment. In both panels, colors indicate the source of the strains: MAP cooked ham, green; MAP sausage, blue; packaged beef products, purple; and kimchi, red.

FIGURE 3

COG class abundances in core genome (A) and in the accessory genome (B). The number of CDSs predicted within each class is reported. The CDSs in plasmids are in brackets.

FIGURE 4

PCoA visualization of Jaccard distances among plasmids, based on shared genes.

FIGURE 5

Genetic potential for metabolism of carbohydrates based on the presence (green) or absence (white) of predicted transporters or enzymes.