Bioinformatic genome comparisons for taxonomic and phylogenic assignments using Aeromonas as a test case

Authors: COLSTON, SOPHIE - University Of Connecticut; FULLMER, MATTHEW - University Of Connecticut; BEKA, LIDIA - University Of Connecticut; LAMY, BRIGITTE - University Of Montpellier; GOGARTEN, JOHANN - University Of Connecticut; GRAF, JOERG - University Of Connecticut

Submitted to: mBio
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/17/2014
Publication Date: 11/18/2014
Citation: Colston, S., Fullmer, M., Beka, L., Lamy, B., Gogarten, J.P., Graf, J. 2014. Bioinformatic genome comparisons for taxonomic and phylogenic assignments using Aeromonas as a test case. mBio. 5(6):e02136-14. DOI:10.1128/mBio.02136-14.

Interpretive Summary: The genus Aeromonas contains important fish pathogens, human pathogens and benign species associated with aquatic environments. It is of critical importance to accurately differentiate between disease-causing and benign species and when novel pathogenic strains are discovered it is also important to be able to identify and classify these strains reliably. In this study, we used two bioinformatics approaches, in combination with phylogenetic approaches, to determine the evolutionary relationships of these bacteria. Using these approaches we were able to accurately recapitulate expected relationships and demonstrate that our bioinformatics approach is a suitable alternative. One advantage of this approach is that data can be readily exchanged between laboratories. In addition, we determined that two strains are likely members of new species of Aeromonas and that a large number of genomes in GenBank were misidentified. This study lays foundation for further studies that may reveal the evolutionary relationships of fish pathogenic Aeromonads.

Technical Abstract: Prokaryotic taxonomy is the underpinning of microbiology, providing a framework for the proper identification and naming of organisms. The 'gold standard' of bacterial species delineation is the overall genome similarity as determined by DNA-DNA hybridization (DDH), a technically rigorous yet sometimes variable method that may produce inconsistent results. Improvements in next-generation sequencing have resulted in an upsurge of bacterial genome sequences and bioinformatic tools that compare genomic data, such as average nucleotide identity (ANI), correlation of tetranucleotide frequencies, and the genome-to-genome distance calculator or in silico DDH (isDDH). Here, we evaluate ANI and isDDH in combination with phylogenetic studies using Aeromonas, a taxonomically challenging genus with many described species and several strains that were reassigned to different species as a test case. We generated improved, high-quality draft genome sequences for 33 Aeromonas strains and combined them with 23 publically available genomes. ANI and isDDH distances were determined and compared to phylogenies from multilocus sequence analysis of housekeeping genes, ribosomal proteins, and an expanded gene core. The expanded core phylogenetic analysis suggested relationships between distant Aeromonas clades that were inconsistent with studies using fewer genes. ANI values of greater than or equal to 96% and isDDH of greater than or equal to 70% consistently grouped genomes originating from strains of the same species together. Our study confirmed known misidentifications, validated the recent revisions in nomenclature, and revealed that a number of genomes deposited in GenBank are misnamed. In addition, two strains were included that may represent novel Aeromonas species.