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Abstract

Strain 7_F195 was previously isolated from chicken feather waste collected from an abattoir in Bloemfontein, South Africa. A polyphasic approach was followed to determine if strain 7_F195 belongs to the genus and if the organism can be classified as a new species. The nearest neighbours, based on 16S rRNA gene sequence similarity values (indicated in parentheses), were KCTC 12877 (98.42 %), LMG 8337 (98.24 %) and ATCC 35910 (97.71 %). Genome sequencing revealed a genome size of 4 796 535 bp and a DNA G+C content of 38.6 mol%. The ANI values of strain 7_F195 compared to and were 81.45, 81.86 and 82.38 %, respectively. The digital DNA–DNA hybridization values for strain 7_F195 with , and were 23.7, 23.7 and 24.9 %, respectively. Notable phenotypic differences include the presence of urease activity in LMG 8337 and NCTC 11432, but not in strain 7_F195 or KCTC 12877. The predominant fatty acids of strain 7_F195 were iso-C, iso-C 9c and iso-C 3-OH and the most abundant polar lipid was phosphatidylethanolamine. Menaquinone-6 was the only respiratory quinone. Based on the data generated from this polyphasic study, strain 7_F195 represents a novel species for which the name sp. nov. is proposed. The type strain is 7_F195 (=LMG 30781=KCTC 62760).

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2019-08-01
2019-08-22
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References

  1. Vandamme P, Bernardet J-F, Segers P, Kersters K, Holmes B. NOTES: New Perspectives in the Classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 1994;44:827–831 [CrossRef]
    [Google Scholar]
  2. Holmes B, Owen RJ, Steigerwalt AG, Brenner DJ. Flavobacterium gleum, a new species found in human clinical specimens. Int J Syst Bacteriol 1984;34:21–25 [CrossRef]
    [Google Scholar]
  3. Bernardet J-F, Hugo CJ, Bruun B, Genus X. et al. Chryseobacterium Vandamme, Bernardet, Segers, Kersters & Holmes 1994, 829VP. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. (editors) Bergey's Manual of Systematic Bacteriologyvol. 4 New York: Springer; 2011; pp.180–196
    [Google Scholar]
  4. Charimba G, Jooste P, Albertyn J, Hugo C. Chryseobacterium carnipullorum sp. nov., isolated from raw chicken. Int J Syst Evol Microbiol 2013;63:3243–3249 [CrossRef][PubMed]
    [Google Scholar]
  5. Euzéby JP. List of Prokaryotic Names with Standing in Nomenclature. http://www.bacterio.net/chryseobacterium.html Accessed 2018/10/15
  6. Gevers D, Dawyndt P, Vandamme P, Willems A, Vancanneyt M et al. Stepping stones towards a new prokaryotic taxonomy. Philos Trans R Soc Lond B Biol Sci 2006;361:1911–1916 [CrossRef][PubMed]
    [Google Scholar]
  7. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
  8. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef][PubMed]
    [Google Scholar]
  9. Bernardet JF, Nakagawa Y, Holmes B.. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes 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 [CrossRef][PubMed]
    [Google Scholar]
  10. Bekker A, Steyn L, Charimba G, Jooste P, Hugo C. Comparison of the growth kinetics and proteolytic activities of Chryseobacterium species and Pseudomonas fluorescens. Can J Microbiol 2015;61:977–982 [CrossRef][PubMed]
    [Google Scholar]
  11. Bekker A, Jooste P, Steyn L, Bothma C, Hugo A et al. Lipid breakdown and sensory analysis of milk inoculated with Chryseobacterium joostei or Pseudomonas fluorescens. Int Dairy J 2016;52:101–106 [CrossRef]
    [Google Scholar]
  12. Tsôeu I, Jooste PJ, Charimba G, Hugo CJ. Spoilage potential of a novel group of bacteria isolated from dairy products. South Afr J Sci 2016;112:140–147
    [Google Scholar]
  13. Charimba G. The Taxonomy and Significance of Chryseobacterium Isolates from Poultry, Ph.D. thesis. Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa. 2012
  14. Hugo CJ, Jooste PJ. Culture media for food-associated genera in the family Flavobacteriaceae. In Corry JEL, Curtis GDW, Baird RM. (editors) Handbook of Culture Media for Food and Water Microbiology Cambridge, UK: The Royal Society of Chemistry; 2012; pp.505–556
    [Google Scholar]
  15. de Beer H, Hugo CJ, Jooste PJ, Willems A, Vancanneyt M et al. Chryseobacterium vrystaatense sp. nov., isolated from raw chicken in a chicken-processing plant. Int J Syst Evol Microbiol 2005;55:2149–2153 [CrossRef][PubMed]
    [Google Scholar]
  16. de Beer H, Hugo CJ, Jooste PJ, Vancanneyt M, Coenye T et al. Chryseobacterium piscium sp. nov., isolated from fish of the South Atlantic Ocean off South Africa. Int J Syst Evol Microbiol 2006;56:1317–1322 [CrossRef][PubMed]
    [Google Scholar]
  17. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991; pp.115–175
    [Google Scholar]
  18. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  19. Tamura K, Stecher G, Kumar S. MEGA version 7.0.14. 2018;http://www.megasoftware.net/
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  22. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75–15 [CrossRef][PubMed]
    [Google Scholar]
  23. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014;64:316–324 [CrossRef][PubMed]
    [Google Scholar]
  24. Meier-Kolthoff JP, Auch AF, Klenk HP, Gӧker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef][PubMed]
    [Google Scholar]
  25. Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  26. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005;102:2567–2572 [CrossRef][PubMed]
    [Google Scholar]
  27. MacFaddin JF. Biochemical Tests for Identification of Medical Bacteria, 2nd ed. Baltimore: Williams and Wilkins; 1980
    [Google Scholar]
  28. Reichenbach H, Order I. Cytophagales Leadbetter. 1974. In Staley JT, Bryant MP, Pfennig JG. (editors) Bergey’s Manual of Systematic Bacteriologyvol. 3 Holt. Baltimore: Williams and Wilkins; 1989; pp.2011–2013
    [Google Scholar]
  29. Cowan ST. Cowan and Steel’s Manual for Identification of Medical Bacteria, 2nd ed. Cambridge, UK: University Press; 1974
    [Google Scholar]
  30. Yabuuchi E, Hashimoto Y, Ezaki T, Ido Y, Takeuchi N. Genotypic and phenotypic differentiation of Flavobacterium indologenes Yabuuchi et al 1983 from Flavobacterium gleum Holmes et al 1984. Microbiol Immunol 1990;34:73–76[PubMed]
    [Google Scholar]
  31. West PA, Colwell RR. Identification and classification of the Vibrionaceae – an overview. In Colwell RR. (editor) Vibrios in the Environment New York: John Wiley & Sons; 1984; pp.285–363
    [Google Scholar]
  32. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: University Press; 1993
    [Google Scholar]
  33. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13:128–130 [CrossRef]
    [Google Scholar]
  34. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  35. Tindall BJ, Sikorski J, Smibert RM, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marxluf G, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC, USA: ASM Press; 2007; pp.330–393
    [Google Scholar]
  36. Wu YF, Wu QL, Liu SJ, Yf W, Ql W. Chryseobacterium taihuense sp. nov., isolated from a eutrophic lake, and emended descriptions of the genus Chryseobacterium, Chryseobacterium taiwanense, Chryseobacterium jejuense and Chryseobacterium indoltheticum. Int J Syst Evol Microbiol 2013;63:913–919 [CrossRef][PubMed]
    [Google Scholar]
  37. Montero-Calasanz MC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense. Syst Appl Microbiol 2014;37:342–350 [CrossRef][PubMed]
    [Google Scholar]
  38. Matu A, Lum Nde A, Oosthuizen L, Hitzeroth A, Badenhorst M et al. Draft genome sequences of seven Chryseobacterium type strains. Microbiol Resour Announc 2019;8: Accepted for publication [CrossRef][PubMed]
    [Google Scholar]
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