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

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.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-654) contains supplementary material, which is available to authorized users.     

Distribution of cytokeratin polypeptides in epithelia of the adult human urinary tract

Summary Cytokeratin expression was studied in the epitheha lining the normal human urine conducting system using immunohistochemistry on frozen sections employing a panel of 14 monoclonal antibodies. Eleven of these anti-cytokeratin antibodies reacted specifically with one of the 19 human cytokeratin polypeptides. Profound differences were found in the cytokeratin expression patterns between the different types of epithelium in the male and female urinary tract. In the areas showing morphological transitions of transitional epithelium to columnar epithelium and of nonkeratinizing sqamous epithelium to keratinizing squamous epithelium gradual shifts of cytokeratin expression patterns were observed, often anticipating the morphological changes. However, also within one type of epithelium, i.e. the transitional epithelium, two different patterns of cytokeratin expression were found. Expression of cytokeratin 7 was homogeneous in the transitional epithelium of renal pelvis and ureter but heterogeneous in the transitional epithelium of the bladder. Furthermore, intraepithelial differences in cytokeratin expression could be shown to be differentiation related. Using a panel of chain-specific monoclonal antibodies to cytokeratin 8 and 18 conformational and/or biochemical changes in the organization of these intermediate filaments were demonstrated upon differentiation in columnar and transitional epithelium.This study was supported in part by the Netherlands Cancer Foundation