1887

Abstract

A Gram-staining-negative non endospore-forming strain, T13(2019) was isolated from water samples from Atlantic salmon () fry culture in Chile and studied in detail for its taxonomic position. The isolate shared highest 16S rRNA gene sequence similarities with the type strains of (98.44 %) followed by and (both 98.22 %). Menaquinone MK-6 was the predominant respiratory quinone in T13(2019). Major polar lipids were phosphatidylethanolamine, an ornithine lipid and the unidentified polar lipids L1, L3 and L4 lacking a functional group. The major polyamine was -homospermidine. The fatty acid profile contained major amounts of iso-C, iso-C 3-OH, iso-C 3-OH, C, summed feature 3 (C c and/or iso-C 2-OH) and various hydroxylated fatty acids in smaller amounts, among them iso-C 3-OH, and C 3-OH, which supported the grouping of the isolate into the genus . Physiological/biochemical characterisation and ANI calculations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation. In addition it became obvious, that the type strains of and showed 100 % 16S rRNA gene sequence similarities and ANI values of 97.21%/ 97.59 % and DDH values of 80.40 % [77.5 and 83%]. These data indicate that and belong to the same species and it is proposed that is a later heterotypic synonym of . For strain T13(2019) (=CIP 111411=LMG 30298=CCM 8798) a new species with the name sp. nov. is proposed.

Keyword(s): Flavobacterium , salmonis and taxonomy
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004510
2020-10-14
2024-10-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/12/6147.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004510&mimeType=html&fmt=ahah

References

  1. Bernardet J-F, Bowman JP. Genus I. Flavobacterium . In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ et al. (editors) Bergey’s Manual of Systematic Bacteriology vol. 4, 2nd ed. New York: Springer-Verlag; 2011 pp 112–154
    [Google Scholar]
  2. Kämpfer P, Lodders N, Marti K, Avendaño-Herrera R. Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish. Int J Syst Evol Microbiol 2012; 62:1402–1408
    [Google Scholar]
  3. Zamora L, Vela AI, Sanchez-Porro C, Palacios MA, Moore ER et al. Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss). Int J Syst Evol Microbiol 2014; 64:392–399
    [Google Scholar]
  4. Loch TP, Faisal M. Flavobacterium spartansii sp. nov., a pathogen of fishes, and emended descriptions of Flavobacterium aquidurense and Flavobacterium araucananum . Int J Syst Evol Microbiol 2014; 64:406–412
    [Google Scholar]
  5. Chen WM, Guo YP, Kwon SW, Sheu SY. Flavobacterum piscinae sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 2019; 69:1775–1782
    [Google Scholar]
  6. Bernardet JF, Bowman JP. Genus Flavobacterium. Bergey´s Manual of Systematics of Archea and Bacteria 2015
    [Google Scholar]
  7. Holt RA, Rohovec JS, Fryer JL. Bacterial cold water. In Inglis V, Roberts RJ, Bromage NR. (editors) Bacterial Diseases of Fish Oxford: Blackwell Scientific Publication; 1993 pp 3–23
    [Google Scholar]
  8. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  9. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070
    [Google Scholar]
  10. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  11. Kämpfer P, Dreyer U, Neef A, Dott W, Busse H-J. Chryseobacterium defluvii sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 2003; 53:93–97
    [Google Scholar]
  12. Lane DJ. 16S/23S rRNA sequencing nucleic acid techniques in bacterial systematics. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: Wiley: Wiley; 1991 pp 115–175
    [Google Scholar]
  13. Brosius J, Dull T, Sleeter D, Noller H. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli . J Mol Biol 1978; 148:107–127
    [Google Scholar]
  14. Yoon SH, SM H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617
    [Google Scholar]
  15. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acid Res 2004; 32:1363–1371
    [Google Scholar]
  16. Yilmaz P, Parfrey Wegener L, Yarza P, Gerken J, Pruesse E et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res. 2014; 42:D643–D648
    [Google Scholar]
  17. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acid Res 2012; 35:7188–7196
    [Google Scholar]
  18. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. SINA: accurate high throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829
    [Google Scholar]
  19. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690
    [Google Scholar]
  20. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author Seattle: Department of Genome Sciences, University of Washington; 2005
    [Google Scholar]
  21. Jukes TH, Cantor CR. Evolution of the protein molecules. In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  22. Felsenstein J. Confidence limits of phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791
    [Google Scholar]
  23. Criscuolo A, Brisse S. AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. Genomics 2013; 102:500–506 [View Article][PubMed]
    [Google Scholar]
  24. Liu Y, Schöder J SB. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics 2013; 29:308–315
    [Google Scholar]
  25. 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
    [Google Scholar]
  26. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069
    [Google Scholar]
  27. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114
    [Google Scholar]
  28. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60
    [Google Scholar]
  29. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202
    [Google Scholar]
  30. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130
    [Google Scholar]
  31. Altenburger P, Kämpfer P, Makristathis A, Lubitz W, Busse H-J. Classification of bacteria isolated from a medieval wall painting. 1996. J Biotechnol 1996; 47:39–52
    [Google Scholar]
  32. Stolz A, Busse H-J, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576
    [Google Scholar]
  33. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a Giordian Knot: Emended classification and description of the genus Flavobacterium, emended description of the familiy Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Evol Microbiol 1996; 46:128–148
    [Google Scholar]
  34. Busse H-J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. 1988. Syst Appl Microbiol 1988; 11:1–8
    [Google Scholar]
  35. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 1997; 47:698–708
    [Google Scholar]
  36. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005
    [Google Scholar]
  37. Kämpfer P, Steiof M, Dott W. Microbiological characterisation of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 1991; 21:227–251
    [Google Scholar]
  38. Oren A, Garrity GM. IJSEM list Notification list. Notification that new names and new combinations have appeared in volume 64, part 2 of the IJSEM. Int J Syst Evol Microbiol 2014; 64:1459–1460
    [Google Scholar]
  39. Garcia-Lopez M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1000 type-strain genomes improves taxonomic classification of Bacteroidetes . Front Microbiol 2083; 2019:10
    [Google Scholar]
  40. Kim JH, Kim YK, Cha CJ. Flavobacterium chungangense sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2009; 59:1754–1758
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004510
Loading
/content/journal/ijsem/10.1099/ijsem.0.004510
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error