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Whole-Genome Sequencing Redefines Shewanella Taxonomy

Journal article
Authors Kaisa Thorell
J. P. Meier-Kolthoff
A. Sjoling
A. J. Martin-Rodriguez
Published in Frontiers in Microbiology
Volume 10
ISSN 1664-302X
Publication year 2019
Published at Institute of Biomedicine, Department of Infectious Medicine
Language en
Links dx.doi.org/10.3389/fmicb.2019.01861
Keywords phylogenomics, GBDP, digital DDH, species delineation, taxonomic revision, comparative genomics, DNA-DNA hybridization, ad-hoc-committee, sp-nov., genus shewanella, marine fish, sp. nov., bacterium, sea, deep, reclassification, Microbiology, x ge, 1992, international journal of systematic bacteriology, v42, p166
Subject categories Microbiology in the medical area

Abstract

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 2000 s has prompted questions on the real taxonomic position of some isolates and species. Recent work by us and others identified inconsistencies in the existing species classification. In this study we 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 64 of the 131 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.

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