The controversial nature of the Weissella genus: technological and functional aspects versus whole genome analysis-based pathogenic potential for their application in food and health

Abstract

Despite the use of several Weissella (W.) strains for biotechnological and probiotic purposes, certain species of this genus were found to act as opportunistic pathogens, while strains of W. ceti were recognized to be pathogenic for farmed rainbow trout. Herein, we investigated the pathogenic potential of weissellas based on in silico analyses of the 13 whole genome sequences available to date in the NCBI database. Our screening allowed us to find several virulence determinants such as collagen adhesins, aggregation substances, mucus-binding proteins, and hemolysins in some species. Moreover, we detected several antibiotic resistance-encoding genes, whose presence could increase the potential pathogenicity of some strains, but should not be regarded as an excluding trait for beneficial weissellas, as long as these genes are not present on mobile genetic elements. Thus, selection of weissellas intended to be used as starters or for biotechnological or probiotic purposes should be investigated regarding their safety aspects on a strain to strain basis, preferably also by genome sequencing, since nucleotide sequence heterogeneity in virulence and antibiotic resistance genes makes PCR-based screening unreliable for safety assessments. In this sense, the application of W. confusa and W. cibaria strains as starter cultures or as probiotics should be approached with caution, by carefully selecting strains that lack pathogenic potential.

Keywords: Weissella; antibiotic resistance; genome; in silico analysis; virulence.

FIGURE 1

Phylogenetic relationships of Weissella species and Leuconostoc Lactobacillus Enterococcus inferred from the alignment of collagen adhesin encoding genes. The sequences were aligned and the most parsimonious phylogenetic trees were constructed using the CLUSTAL W of Lasergene program, version 5.05 (MegAlign, Inc., Madison, WI, USA). The scale below indicates the number of nucleotide substitutions. Accession numbers are indicated in parentheses.

FIGURE 2

Phylogenetic relationships of Weissella species and Leuconostoc Enterococcus inferred from the alignment of aggregation substances (A) and aggregation substance Asa1/PrgB (B) encoding genes. The sequences were aligned and the most parsimonious phylogenetic trees were constructed using the CLUSTAL W of Lasergene program, version 5.05 (MegAlign, Inc., Madison, WI, USA). The scale below indicates the number of nucleotide substitutions. Accession numbers are indicated in parentheses.

FIGURE 3

Phylogenetic relationships of Weissella species and Leuconostoc Lactobacillus Enterococcus inferred from the alignment of mucus-binding protein encoding genes. The sequences were aligned and the most parsimonious phylogenetic trees were constructed using the CLUSTAL W of Lasergene program, version 5.05 (MegAlign, Inc., Madison, WI, USA). The scale below indicates the number of nucleotide substitutions. Accession numbers are indicated in parentheses.

FIGURE 4

Phylogenetic relationships of Weissella species and Leuconostoc Lactobacillus Enterococcus inferred from the alignment of multidrug transporter involved in fosfomycin resistance encoding genes. The sequences were aligned and the most parsimonious phylogenetic trees were constructed using the CLUSTAL W of Lasergene program, version 5.05 (MegAlign, Inc., Madison, WI, USA). The scale below indicates the number of nucleotide substitutions. Accession numbers are indicated in parentheses.

FIGURE 5

Phylogenetic relationships of Weissella species and Leuconostoc Lactobacillus Enterococcus inferred from the alignment of methicillin resistance protein encoding genes. The sequences were aligned and the most parsimonious phylogenetic trees were constructed using the CLUSTAL W of Lasergene program, version 5.05 (MegAlign, Inc., Madison, WI, USA). The scale below indicates the number of nucleotide substitutions. Accession numbers are indicated in parentheses.