Research article

Genomic taxonomy of vibrios

Cristiane C Thompson¹ , Ana Carolina P Vicente¹ , Rangel C Souza² , Ana Tereza R Vasconcelos² , Tammi Vesth³ , Nelson Alves Jr⁴ , David W Ussery³ , Tetsuya Iida⁵ and Fabiano L Thompson⁴

¹Laboratory of Molecular Genetics of Microrganims, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil

²National Laboratory for Scientific Computing, Department of Applied and Computational Mathematics, Laboratory of Bioinformatics, Av. Getúlio Vargas 333, Quitandinha, 25651-070, Petropolis, RJ, Brazil

³Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark

⁴Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, UFRJ, Brazil

⁵Laboratory of Genomic Research on Pathogenic Bacteria, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan

author email corresponding author email

BMC Evolutionary Biology 2009, 9:258doi:10.1186/1471-2148-9-258

Published:	27 October 2009

Abstract

Background

Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios.

Results

We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree.

Conclusion

The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.