Genomes of Vibrio metoecus co-isolated with Vibrio cholerae extend our understanding of differences between these closely related species

Abstract

Background: Vibrio cholerae, the causative agent of cholera, is a well-studied species, whereas Vibrio metoecus is a recently described close relative that is also associated with human infections. The availability of V. metoecus genomes provides further insight into its genetic differences from V. cholerae. Additionally, both species have been co-isolated from a cholera-free brackish coastal pond and have been suggested to interact with each other by horizontal gene transfer (HGT).

Results: The genomes of 17 strains from each species were sequenced. All strains share a large core genome (2675 gene families) and very few genes are unique to each species (< 3% of the pan-genome of both species). This led to the identification of potential molecular markers-for nitrite reduction, as well as peptidase and rhodanese activities-to further distinguish V. metoecus from V. cholerae. Interspecies HGT events were inferred in 21% of the core genes and 45% of the accessory genes. A directional bias in gene transfer events was found in the core genome, where V. metoecus was a recipient of three times (75%) more genes from V. cholerae than it was a donor (25%).

Conclusion: V. metoecus was misclassified as an atypical variant of V. cholerae due to their resemblance in a majority of biochemical characteristics. More distinguishing phenotypic assays can be developed based on the discovery of potential gene markers to avoid any future misclassifications. Furthermore, differences in relative abundance or seasonality were observed between the species and could contribute to the bias in directionality of HGT.

Keywords: Comparative genomics; Evolution; Horizontal gene transfer; Vibrio cholerae; Vibrio metoecus.

Fig. 1

The phylogenetic relationship of V. cholerae and V. metoecus. The phylogeny was reconstructed from a core-genome alignment of ~ 2.8 Mb in length. Bootstrap values are indicated on the nodes. The scale bar represents 0.02 nucleotide substitutions per site. Parallel lines indicate shortened branch lengths, approximately 5× the scale bar. Dots after the strain names indicate genomes sequenced in this study

Fig. 2

Distribution of core genes and species-specific genes between V. cholerae and V. metoecus. The Venn diagram shows the number of genes shared between V. cholerae and V. metoecus or present within each species. Top numbers indicate total gene families in the pan-genome of both species. Bottom numbers (in bold and parentheses) indicate gene families exclusively present in all strains of V. cholerae, V. metoecus, or both

Fig. 3

Presence/absence map of selected virulence factors in V. cholerae and V. metoecus. The table of virulence factors for the genus Vibrio was obtained and modified from the VFDB [47, 48]. Colored squares represent BSRs of at least 0.3 against reference genes (i.e., homologues of genes are present); white squares represent absence of genes. The genes involved in iron uptake are further categorized into (A) periplasmic binding protein-dependent ABC transport systems, (B) vibriobactin biosynthesis, and (C) vibriobactin utilization. Locus tags of the genes in the V. cholerae N16961 reference genome are indicated after the gene names

Fig. 4

Inferred HGT events in the core and accessory genomes. The pie charts show the number of (A) core and (B) accessory gene families with and without HGT. The bars show the number of HGT events within the gene families, showing the frequency of V. cholerae or V. metoecus as recipients