Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Abstract

Background: Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat.

Results: Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages.

Conclusions: Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.

Figure 1

Overview of the V. cholerae strains analyzed in this study. Approximate geographical origin, isolation source and date of 274 V. cholerae strains. See Additional file 1 for details.

Figure 2

V. cholerae genome plot. Circos plots [14] of the two major V. cholerae R-18308 scaffolds representing chromosome 1 (top) and chromosome 2 (bottom). From the outer circle inwards: scale; ORFs per strand (colored by functional category, see legend); prophages (orange: small defective prophage; red: CTX; green: PP1; blue: superintegron, SI); and read mappings of the 38 other sequenced genomes (blue, from the middle circle outwards: R-18246, R-18273, R-18303, R-18304, R-18316, R-18317, R-18327, R-18338, R-18348, VC08, VC1005, VC102, VC111, VC120, VC14, VC150, VC172, VC179, VC200, VC201, VC21, VC214, VC22, VC307, VC311, VC33, VC341, VC434, VC46, VC500, VC504, VC75, VC77, VC83, VC833, VC91, VC95, VC998).

Figure 3

Phylogenomic tree of V. cholerae genomes. A phylogenomic tree based on genome-wide marker SNPs illustrates the breadth of 274 V. cholerae genomes included in this study. Four complete V. mimicus genomes were included as an outgroup. Branch lengths indicate the number of substitutions per SNP site. Several clusters mentioned in the text are shown. Branches are colored by the continent where the strains were isolated. The isolation source (habitat) of the strains is indicated. All strains belong to the O1 serogroup unless mentioned otherwise. Note that the transcontinental transmission event from South America to Southeast Asia (labeled “D” in reference [3], see Figure one and Supplementary Figure S3 therein) was not confirmed, and we suspect this is due to switching of the labels between strain A390 (Bangladesh 1987) and strain A316 (Argentina 1993) in that article as the positions of those strains are switched in our phylogeny.

Figure 4

The important subsystems for each niche dimension. Presence of level-1 subsystem categories in the top 5% most important functionally annotated genotypic variables for RFs in three niche dimensions. See Additional file 5 for details, the percentage can be changed in that file to dynamically update the bar chart.