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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Microbiol. | doi: 10.3389/fmicb.2019.01861

Whole-genome sequencing redefines Shewanella taxonomy

  • 1Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
  • 2German Collection of Microorganisms and Cell Cultures GmbH (DSMZ), Germany
  • 3Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden

The genus Shewanella encompasses a diverse group of Gram negative, primarily aquatic bacteria with a remarkable ecological relevance, an outstanding set of metabolic features and an emergent clinical importance. The rapid expansion of the genus over the 2000s has prompted questions on the real taxonomic position of some isolates and species. Recent work by us and others have identified inconsistencies in the existing species classification. In this study we have aimed to clarify such issues across the entire genus, making use of the genomic information publicly available worldwide. Phylogenomic analyses, including comparisons based on genome-wide identity indexes (digital DNA-DNA hybridization and Average Nucleotide Identity) combined with core and accessory genome content evaluation suggested that the taxonomic position of 56 of the 112 analyzed strains should be revisited. Based on the genomic information currently available, emended descriptions for some Shewanella species are proposed. Our study establishes for the first time a whole-genome based phylogeny for Shewanella spp. including a classification at the subspecific level.

Keywords: phylogenomics, GBDP, digital DDH, Species delineation, Taxonomic revision, Comparative genomics

Received: 30 May 2019; Accepted: 29 Jul 2019.

Copyright: © 2019 Thorell, Meier-Kolthoff, Sjöling and Martín-Rodríguez. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Alberto J. Martín-Rodríguez, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-171 77, Stockholm, Sweden, jonatan.martin.rodriguez@ki.se