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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 71, Issue 1

sp. nov., p. nov. and sp. nov., isolated from faeces of Free

Abstract

Six aerobic, non-motile, non-haemolytic, Gram-stain-negative, oxidase-negative strains (185, 187, 323-1, 194, dk386 and dk771) were recovered from different faecal samples of on the Qinghai–Tibet Plateau. In the 16S rRNA gene sequences, one strain pair, 185/187, shared highest similarity to 114 (97.9 %), and the other two (323-1/194 and dk771/dk386) to CGMCC 1.12528 (98.6 and 97.0 %, respectively). Phylogenomic tree analysis showed that these six strains formed three separate clades in the genus . Digital DNA–DNA hybridization values of each pair of the isolates with all members of the genus were far below 70 %. The main cellular fatty acids of all six strains were C 9, C and summed feature 3 (C 7/C 6). Q-9 was the predominant respiratory quinone for strains 185, 323-1 and dk386. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the genotypic, phenotypic and biochemical analyses, these six strains represent three novel species of the genus , for which the names sp. nov., sp. nov. and sp. nov. are proposed. The type strains are 185 (=CGMCC 1.13636=JCM 33607), 323-1 (=CGMCC 1.13940=JCM 33608) and dk386 (=CGMCC 1.16589=JCM 33592), respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Acinetobacter lanii , Acinetobacter shaoyimingii , Acinetobacter wanghuae , Equus kiang and Qinghai–Tibet Plateau
Funding
This study was supported by the:
  • Research Units of Discovery of Unknown Bacteria and Function, Chines Academy of Medical Sciences (Award 2018RU010)
    • Principle Award Recipient: Jianguo Xu
  • Sanming Project of Medicine in Shenzhen (Award SZSM201811071)
    • Principle Award Recipient: Jianguo Xu
  • National Science and Technology Major Project of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: Shan Lu
  • National Science and Technology Major Project of China (Award 2018ZX10712001-017)
    • Principle Award Recipient: Not Applicable
  • National Science and Technology Major Project of China (Award 2018ZX10712001-007)
    • Principle Award Recipient: Jing Yang
  • National Key R&D Program of China (Award 2019YFC1200505)
    • Principle Award Recipient: Jing Yang
  • National Key R&D Program of China (Award 2019YFC1200500)
    • Principle Award Recipient: Jing Yang
© 2021 The Authors
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2020-11-16
2025-04-27
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References

  1. Brisou J, Prévot AR. [Studies on bacterial taxonomy. X. The revision of species under Acromobacter group]. Ann Inst Pasteur 1954; 86:722–728[PubMed]
     [Google Scholar]
  2. Touchon M, Cury J, Yoon EJ, Krizova L, Cerqueira GC et al. The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Genome Biol Evol 2014; 6:2866–2882 [View Article][PubMed]
     [Google Scholar]
  3. Kim D, Baik KS, Kim MS, Park SC, Kim SS et al. Acinetobacter soli sp. nov., isolated from forest soil. J Microbiol 2008; 46:396–401 [View Article][PubMed]
     [Google Scholar]
  4. Hu Y, Feng Y, Qin J, Radolfova-Krizova L, Maixnerova M et al. Acinetobacter wuhouensis sp. nov., isolated from hospital sewage. Int J Syst Evol Microbiol 2018; 68:3212–3216 [View Article][PubMed]
     [Google Scholar]
  5. Dijkshoorn L, Nemec A, Seifert H. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii . Nat Rev Microbiol 2007; 5:939–951 [View Article][PubMed]
     [Google Scholar]
  6. Joly-Guillou ML. Clinical impact and pathogenicity of Acinetobacter . Clin Microbiol Infect 2005; 11:868–873 [View Article][PubMed]
     [Google Scholar]
  7. Nemec A, Krizova L, Maixnerova M, van der Reijden TJ, Deschaght P et al. Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU). Res Microbiol 2011; 162:393–404 [View Article][PubMed]
     [Google Scholar]
  8. Li W, Zhang D, Huang X, Qin W. Acinetobacter harbinensis sp. nov., isolated from river water. Int J Syst Evol Microbiol 2014; 64:1507–1513 [View Article][PubMed]
     [Google Scholar]
  9. Qin J, Maixnerová M, Nemec M, Feng Y, Zhang X et al. Acinetobacter cumulans sp. nov., isolated from hospital sewage and capable of acquisition of multiple antibiotic resistance genes. Syst Appl Microbiol 2019; 42:319–325 [View Article][PubMed]
     [Google Scholar]
  10. Huang Y, Wang X, Yang J, Lu S, Lai XH et al. Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces. Int J Syst Evol Microbiol 2019; 69:3629–3635 [View Article][PubMed]
     [Google Scholar]
  11. ZS W, GX Y. Status of wild ass in China 8 Chinese Biodiversity; 2000 pp 81–87
     [Google Scholar]
  12. Moehlman PDR. Equids: Zebras, Asses, and Horses: Status Survey and Conservation Action Plan Gland, Switzerland: IUCN; 2002
     [Google Scholar]
  13. Shah N. Status and action plan for the kiang (Equus kiang). In Moehlman PD. editor Status Survey and Conservation Action Plan Equids: Zebras, Asses and Horses International Union for Conservation of Nature; 2002 pp 72–81
     [Google Scholar]
  14. Wang X, Yang J, Lu S, Lai XH, Jin D et al. Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces. Int J Syst Evol Microbiol 2018; 68:3874–3880 [View Article][PubMed]
     [Google Scholar]
  15. Lane DJ. 16s/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp 125–175
     [Google Scholar]
  16. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, Chun J 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 [View Article][PubMed]
     [Google Scholar]
  17. La Scola B, Gundi VA, Khamis A, Raoult D. Sequencing of the rpoB gene and flanking spacers for molecular identification of Acinetobacter species. J Clin Microbiol 2006; 44:827–832 [View Article][PubMed]
     [Google Scholar]
  18. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article][PubMed]
     [Google Scholar]
  19. McCarthy A. Third generation DNA sequencing: pacific biosciences' single molecule real time technology. Chem Biol 2010; 17:675–676 [View Article][PubMed]
     [Google Scholar]
  20. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article][PubMed]
     [Google Scholar]
  21. Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 2019; 47:D687–D692 [View Article][PubMed]
     [Google Scholar]
  22. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P et al. Card 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017; 45:D566–D573 [View Article][PubMed]
     [Google Scholar]
  23. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
     [Google Scholar]
  24. 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 [View Article][PubMed]
     [Google Scholar]
  25. Lee I, Ouk Kim Y, Park S-C, 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. Nemec A, Krizova L, Maixnerova M, Sedo O, Brisse S et al. Acinetobacter seifertii sp. nov., a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex isolated from human clinical specimens. Int J Syst Evol Microbiol 2015; 65:934–942 [View Article][PubMed]
     [Google Scholar]
  27. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
     [Google Scholar]
  28. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012; 28:3150–3152 [View Article][PubMed]
     [Google Scholar]
  29. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article][PubMed]
     [Google Scholar]
  30. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012; 61:1061–1067 [View Article][PubMed]
     [Google Scholar]
  31. Zhu W, Yang J, Lu S, Lai XH, Jin D et al. Fudania jinshanensis gen. nov., sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii) in China. Int J Syst Evol Microbiol 2019; 69:2942–2947 [View Article][PubMed]
     [Google Scholar]
  32. Nemec A, Musílek M, Maixnerová M, De Baere T, van der Reijden TJ et al. Acinetobacter beijerinckii sp. nov. and Acinetobacter gyllenbergii sp. nov., haemolytic organisms isolated from humans. Int J Syst Evol Microbiol 2009; 59:118–124 [View Article][PubMed]
     [Google Scholar]
  33. Krizova L, Maixnerova M, Sedo O, Nemec A. Acinetobacter bohemicus sp. nov. widespread in natural soil and water ecosystems in the Czech Republic. Syst Appl Microbiol 2014; 37:467–473 [View Article][PubMed]
     [Google Scholar]
  34. Krizova L, McGinnis J, Maixnerova M, Nemec M, Poirel L et al. Acinetobacter variabilis sp. nov. (formerly DNA group 15 sensu Tjernberg & Ursing), isolated from humans and animals. Int J Syst Evol Microbiol 2015; 65:857–863 [View Article][PubMed]
     [Google Scholar]
  35. Nemec A, Musílek M, De Baere T, Maixnerová M et al. Acinetobacter bereziniae sp. nov. and Acinetobacter guillouiae sp. nov., to accommodate Acinetobacter genomic species 10 and 11, respectively. Int J Syst Evol Microbiol 2010; 60:896–903 [View Article][PubMed]
     [Google Scholar]
  36. Hu Y, Feng Y, Zhang X, Zong Z. Acinetobacter defluvii sp. nov., recovered from hospital sewage. Int J Syst Evol Microbiol 2017; 67:1709–1713 [View Article][PubMed]
     [Google Scholar]
  37. Carr EL, Kämpfer P, Patel BKC, Gürtler V, Seviour RJ. Seven novel species of Acinetobacter isolated from activated sludge. Int J Syst Evol Microbiol 2003; 53:953–963 [View Article][PubMed]
     [Google Scholar]
  38. Nemec A, Radolfová-Křížová L, Maixnerová M, Nemec M, Clermont D et al. Revising the taxonomy of the Acinetobacter lwoffii group: The description of Acinetobacter pseudolwoffii sp. nov. and emended description of Acinetobacter lwoffii . Syst Appl Microbiol 2019; 42:159–167 [View Article][PubMed]
     [Google Scholar]
  39. Liu Y, Rao Q, Tu J, Zhang J, Huang M et al. Acinetobacter piscicola sp. nov., isolated from diseased farmed Murray cod (Maccullochella peelii peelii). Int J Syst Evol Microbiol 2018; 68:905–910 [View Article][PubMed]
     [Google Scholar]
  40. Nemec A, De Baere T, Tjernberg I, Vaneechoutte M, van der Reijden TJ et al. Acinetobacter ursingii sp. nov. and Acinetobacter schindleri sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol 2001; 51:1891–1899 [View Article][PubMed]
     [Google Scholar]
  41. Qin J, Hu Y, Feng Y, Lv X, Zong Z. Acinetobacter sichuanensis sp. nov., recovered from hospital sewage in China. Int J Syst Evol Microbiol 2018; 68:3897–3901 [View Article][PubMed]
     [Google Scholar]
  42. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  43. Ventosa A, Marquez MC, Kocur M, Tindall BJ. Comparative study of "Micrococcus sp." strains CCM 168 and CCM 1405 and members of the genus Salinicoccus . Int J Syst Bacteriol 1993; 43:245–248 [View Article][PubMed]
     [Google Scholar]
  44. Watanabe M, Aoyagi Y, Ohta A, Minnikin DE. Structures of phenolic glycolipids from Mycobacterium kansasii . Eur J Biochem 1997; 248:93–98 [View Article][PubMed]
     [Google Scholar]
  45. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article][PubMed]
     [Google Scholar]
  46. 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]
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Acinetobacter lanii sp. nov., Acinetobacter shaoyimingii sp. nov. and Acinetobacter wanghuae sp. nov., isolated from faeces of Equus kiang
Int J Syst Evol Microbiol 71, 004567 (2020); https://doi.org/10.1099/ijsem.0.004567
/content/journal/ijsem/10.1099/ijsem.0.004567
/content/journal/ijsem/10.1099/ijsem.0.004567
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