1887

Abstract

A Gram-stain-negative, facultatively anaerobic strain, designated NFH.MB010, was isolated from an epidermal lesion on the test (hard shell skeleton) of a green sea urchin () collected from northern Norway. Cells of strain NFH.MB010 were rod shaped and motile by means of a single, long polar flagellum. Growth was observed at 1–5% NaCl (w/v) and at 4 °C, but not above 28 °C. Phylogenetic analyses based on eight-gene multilocus sequence analysis (16S rRNA, , , , , , and ) suggested novelty at the species level. DNA–DNA hybridization and orthologous average nucleotide identity estimates showed percentage genomic resemblances to its closest relative, , that were well below the established same species threshold values. Phenotypically, utilization of glycogen and gentiobiose, inability of acetoin production, and undetectable valine arylamidase and trypsin activity discriminated strain NFH.MB010 from the closely related reference strains. Protein spectra generated by mass spectrometry further consolidated the species level uniqueness of strain NFH.MB010. Based on the described polyphasic approach, strain NFH.MB010 therefore appears as a novel species within the Splendidus clade of the genus , and the name sp. nov. is proposed, with NFH.MB010 (=DSM 107264=LMG 30656) as the type strain.

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2019-08-01
2024-03-29
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References

  1. Thompson FL, Iida T, Swings J. Biodiversity of vibrios. Microbiol Mol Biol Rev 2004; 68:403–431 [View Article][PubMed]
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  3. Sawabe T, Ogura Y, Matsumura Y, Feng G, Amin AR et al. Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Front Microbiol 2013; 4:414 [View Article][PubMed]
    [Google Scholar]
  4. Pérez-Cataluña A, Lucena T, Tarazona E, Arahal DR, Macián MC et al. An MLSA approach for the taxonomic update of the Splendidus clade, a lineage containing several fish and shellfish pathogenic Vibrio spp. Syst Appl Microbiol 2016; 39:361–369 [View Article][PubMed]
    [Google Scholar]
  5. Kim D, Baik KS, Hwang YS, Choi JS, Kwon J et al. Vibrio hemicentroti sp. nov., an alginate lyase-producing bacterium, isolated from the gut microflora of sea urchin (Hemicentrotus pulcherrimus). Int J Syst Evol Microbiol 2013; 63:3697–3703 [View Article][PubMed]
    [Google Scholar]
  6. Travers MA, Boettcher Miller K, Roque A, Friedman CS. Bacterial diseases in marine bivalves. J Invertebr Pathol 2015; 131:11–31 [View Article][PubMed]
    [Google Scholar]
  7. Andrews S. FastQC: a quality control tool for high throughput sequence data; 2010 http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  8. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  9. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  10. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed]
    [Google Scholar]
  11. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  12. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
    [Google Scholar]
  13. Thompson CC, Thompson FL, Vicente AC, Swings J. Phylogenetic analysis of vibrios and related species by means of atpA gene sequences. Int J Syst Evol Microbiol 2007; 57:2480–2484 [View Article][PubMed]
    [Google Scholar]
  14. Faury N, Saulnier D, Thompson FL, Gay M, Swings J et al. Vibrio crassostreae sp. nov., isolated from the haemolymph of oysters (Crassostrea gigas). Int J Syst Evol Microbiol 2004; 54:2137–2140 [View Article][PubMed]
    [Google Scholar]
  15. Le Roux F, Gay M, Lambert C, Nicolas JL, Gouy M et al. Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences. Dis Aquat Organ 2004; 58:143–150 [View Article][PubMed]
    [Google Scholar]
  16. Thompson CC, Thompson FL, Vandemeulebroecke K, Hoste B, Dawyndt P et al. Use of recA as an alternative phylogenetic marker in the family Vibrionaceae. Int J Syst Evol Microbiol 2004; 54:919–924 [View Article][PubMed]
    [Google Scholar]
  17. Thompson FL, Gevers D, Thompson CC, Dawyndt P, Naser S et al. Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol 2005; 71:5107–5115 [View Article][PubMed]
    [Google Scholar]
  18. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  19. Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. Version 3.51; 2018 http://www.mesquiteproject.org
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  23. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  24. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  25. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  26. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
    [Google Scholar]
  27. Freiwald A, Sauer S. Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc 2009; 4:732–742 [View Article][PubMed]
    [Google Scholar]
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