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Volume 67, Issue 6

sp. nov., a novel member of the group isolated from wild bird faecal samples Free

Abstract

During a study on the prevalence and diversity of campylobacteria in wild birds faecal samples from the city of Valdivia (southern Chile) 17 Gram-stain-negative, curved-rod-shaped isolates, were initially identified as by PCR–RFLP. Further identification by 16S rRNA sequence analysis revealed that they formed a distinct group in the genus . This unique position was confirmed by the results of analysis of , and gene sequences. The average nucleotide identity between the representative strain WBE38 and the type strain of the most closely related taxon subsp. (LMG 11760) was 90.8 %. The oxidase and urease activity of the novel isolates enabled them to be phenotypically differentiated from species of the genus with validly published names. Therefore, on the basis of phenotypic, genetic and genomic characterizations, the results of this study clearly indicate that these strains represent a novel species within the genus , for which the name sp. nov. is proposed, with the type strain WBE38 (=CECT 9147=LMG 29815).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Campylobacter , Chile , Valdivia and wild bird
© 2017 IUMS
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2017-06-01
2024-04-16
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References

  1. Sebald M, Veron M. Base DNA content and classification of vibrios. Ann Inst Pasteur 1963; 105:897–910[PubMed]
     [Google Scholar]
  2. List of prokaryotic names with standing in nomenclature (LPSN); 2016 http://www.bacterio.cict.fr/c/campylobacter.html [accessed 17 September 2016]
  3. Piccirillo A, Niero G, Calleros L, Pérez R, Naya H et al. Campylobacter geochelonis sp. nov. isolated from the western Hermann's tortoise (Testudo hermanni hermanni). Int J Syst Evol Microbiol 2016; 66:3468–3476 [View Article][PubMed]
     [Google Scholar]
  4. Van TTH, Elshagmani E, Gor MC, Scott PC, Moore RJ. Campylobacter hepaticus sp. nov., isolated from chickens with spotty liver disease. Int J Syst Evol Microbiol 2016; 66:4518–4524 [View Article][PubMed]
     [Google Scholar]
  5. Man SM. The clinical importance of emerging Campylobacter species. Nat Rev Gastroenterol Hepatol 2011; 8:669–685 [View Article][PubMed]
     [Google Scholar]
  6. Iraola G, Pérez R, Naya H, Paolicchi F, Pastor E et al. Genomic evidence for the emergence and evolution of pathogenicity and niche preferences in the genus Campylobacter. Genome Biol Evol 2014; 6:2392–2405 [View Article][PubMed]
     [Google Scholar]
  7. Collado L, Jara R, González S. Description of Helicobacter valdiviensis sp. nov., an Epsilonproteobacteria isolated from wild bird faecal samples. Int J Syst Evol Microbiol 2014; 64:1913–1919 [View Article][PubMed]
     [Google Scholar]
  8. Marshall SM, Melito PL, Woodward DL, Johnson WM, Rodgers FG et al. Rapid identification of Campylobacter, Arcobacter, and Helicobacter isolates by PCR–restriction fragment length polymorphism analysis of the 16S rRNA gene. J Clin Microbiol 1999; 37:4158–4160[PubMed]
     [Google Scholar]
  9. Debruyne L, On SLW, de Brandt E, Vandamme P. Novel Campylobacter lari-like bacteria from humans and molluscs: description of Campylobacter peloridis sp. nov., Campylobacter lari subsp. concheus subsp. nov. and Campylobacter lari subsp. lari subsp. nov. Int J Syst Evol Microbiol 2009; 59:1126–1132 [View Article][PubMed]
     [Google Scholar]
  10. Foster G, Holmes B, Steigerwalt AG, Lawson PA, Thorne P et al. Campylobacter insulaenigrae sp. nov., isolated from marine mammals. Int J Syst Evol Microbiol 2004; 54:2369–2373 [View Article][PubMed]
     [Google Scholar]
  11. Debruyne L, Broman T, Bergström S, Olsen B, On SLW et al. Campylobacter subantarcticus sp. nov., isolated from birds in the sub-Antarctic region. Int J Syst Evol Microbiol 2010; 60:815–819 [View Article][PubMed]
     [Google Scholar]
  12. Debruyne L, Broman T, Bergström S, Olsen B, On SLW et al. Campylobacter volucris sp. nov., isolated from black-headed gulls (Larus ridibundus). Int J Syst Evol Microbiol 2010; 60:1870–1875 [View Article][PubMed]
     [Google Scholar]
  13. Miller WG, Yee E, Chapman MH, Smith TP, Bono JL et al. Comparative genomics of the Campylobacter lari group. Genome Biol Evol 2014; 6:3252–3266 [View Article][PubMed]
     [Google Scholar]
  14. Houf K, de Zutter L, van Hoof J, Vandamme P. Assessment of the genetic diversity among arcobacters isolated from poultry products by using two PCR-based typing methods. Appl Environ Microbiol 2002; 68:2172–2178 [View Article][PubMed]
     [Google Scholar]
  15. Vandamme P, Holmes B, Bercovier H, Coenye T. Classification of centers for disease control group eugonic fermenter (EF)-4a and EF-4b as Neisseria animaloris sp. nov. and Neisseria zoodegmatis sp. nov., respectively. Int J Syst Evol Microbiol 2006; 56:1801–1805 [View Article][PubMed]
     [Google Scholar]
  16. Korczak BM, Stieber R, Emler S, Burnens AP, Frey J et al. Genetic relatedness within the genus Campylobacter inferred from rpoB sequences. Int J Syst Evol Microbiol 2006; 56:937–945 [View Article][PubMed]
     [Google Scholar]
  17. Miller WG, Yee E, Jolley KA, Chapman MH. Use of an improved atpA amplification and sequencing method to identify members of the Campylobacteraceae and Helicobacteraceae. Lett Appl Microbiol 2014; 58:582–590 [View Article][PubMed]
     [Google Scholar]
  18. Hill JE, Paccagnella A, Law K, Melito PL, Woodward DL et al. Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database. J Med Microbiol 2006; 55:393–399 [View Article][PubMed]
     [Google Scholar]
  19. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  20. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article][PubMed]
     [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
     [Google Scholar]
  22. 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]
  23. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  28. Debruyne L, Gevers D, Vandamme P. Taxonomy of the family Campylobacteraceae. In Nachamkin I, Szymanski CM, Blaser MJ. (editors) Campylobacter Washington, DC: American Society for Microbiology; 2008 pp. 3–26
     [Google Scholar]
  29. On SL, Holmes B. Effect of inoculum size on the phenotypic characterization of Campylobacter species. J Clin Microbiol 1991; 29:923–926[PubMed]
     [Google Scholar]
  30. On SL, Holmes B. Reproducibility of tolerance tests that are useful in the identification of campylobacteria. J Clin Microbiol 1991; 29:1785–1788[PubMed]
     [Google Scholar]
  31. On SL, Holmes B. Assessment of enzyme detection tests useful in identification of campylobacteria. J Clin Microbiol 1992; 30:746–749[PubMed]
     [Google Scholar]
  32. Ursing JB, Lior H, Owen RJ. Proposal of minimal standards for describing new species of the family Campylobacteraceae. Int J Syst Bacteriol 1994; 44:842–845 [View Article][PubMed]
     [Google Scholar]
  33. Mills CK, Gherna RL. Hydrolysis of indoxyl acetate by Campylobacter species. J Clin Microbiol 1987; 25:1560–1561[PubMed]
     [Google Scholar]
  34. Vandamme P, Dewhirst FE, Paster BJ, On SLW. Genus I. Campylobacter Sebald and Véron 1963, 907,AL emend. Vandamme, Falsen, Rossau, Hoste, Segers, Tytgat and De Ley 1991a, 98. In Brenner DJ, Kreig NP, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 2 New York: Springer; 2005 pp. 1147–1160 [CrossRef]
     [Google Scholar]
  35. Kawamura Y, Kuwabara S, Kania SA, Kato H, Hamagishi M et al. Porphyromonas pogonae sp. nov., an anaerobic but low concentration oxygen adapted coccobacillus isolated from lizards (Pogona vitticeps) or human clinical specimens, and emended description of the genus Porphyromonas Shah and Collins 1988. Syst Appl Microbiol 2015; 38:104–109 [View Article][PubMed]
     [Google Scholar]
  36. Matsuda M, Moore JE. Urease-positive thermophilic Campylobacter species. Appl Environ Microbiol 2004; 70:4415–4418 [View Article][PubMed]
     [Google Scholar]
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Campylobacter ornithocola sp. nov., a novel member of the Campylobacter lari group isolated from wild bird faecal samples
Int J Syst Evol Microbiol 67, 1643 (2017); https://doi.org/10.1099/ijsem.0.001822
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