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Volume 70, Issue 2

sp. nov., an actinobacterium isolated from sand of the Taklamakan desert, and emended description of the genus Free

Abstract

A novel actinobacterium, designated strain 16Sb5-5, was isolated from a sand sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, China. The strain was examined by a polyphasic approach to clarify its taxonomic position. Cells of the isolate were Gram-staining-positive, aerobic, non-motile and short-rod shaped. Strain 16Sb5-5 grew optimally at 37 °C, pH 7.0 and with 0‒2 % (w/v) NaCl. The cell-wall peptidoglycan was of the A3 type and contained alanine, glycine, glutamic acid and -diaminopimelic acid (-DAP). Ribose, arabinose and glucose were detected in the whole-cell hydrolysates. The predominant menaquinone was MK-9(H). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, three unidentified glycolipids and three unidentified lipids. The major whole-cell fatty acids were anteiso-C and iso-C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 16Sb5-5 was closely related to CPCC 204711 (99.8 % similarity) and formed a robust clade with in the phylogenetic trees. genomic comparisons showed that strain 16Sb5-5 exhibited ANI values of 94.8–94.9 % and GGDC value of 59.5 % to CPCC 204711. The genomic G+C content was 73.3 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, strain 16Sb5-5 could be distinguishable from its closest phylogenetic relative and represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 16Sb5-5 (=KCTC 49116=CGMCC 1.16553). The description of the genus has also been emended.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): actinobacteria , Desertihabitans brevis , Propionibacteriaceae , strain 16Sb5-5T and taxonomy
Funding
This study was supported by the:
  • National Natural Sciences Foundation of China (Award 81621064)
    • Principle Award Recipient: Cheng-Hang Sun
  • National Natural Sciences Foundation of China (Award 81321004)
    • Principle Award Recipient: Cheng-Hang Sun
  • National Natural Sciences Foundation of China (Award 81803411)
    • Principle Award Recipient: Shao-Wei Liu
  • CAMS innovation Fund for Medical Sciences (Award 2017-I2M-B and R-08)
  • the Drug Innovation Major Project of China (Award 2018ZX09711001-007-001)
    • Principle Award Recipient: Li-Yan Yu
© 2020 The Authors
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2019-11-26
2024-04-20
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References

  1. Delwiche EA. Family XI. Propionibacteriaceae fam. nov. Bergey’s Manual of Determinative Bacteriology 7 1957 p 569
     [Google Scholar]
  2. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new Hierarchic classification system, actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
     [Google Scholar]
  3. Zhi X-Y, Li W-J, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589–608 [View Article]
     [Google Scholar]
  4. Scholz CFP, Kilian M. The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov. Int J Syst Evol Microbiol 2016; 66:4422–4432 [View Article]
     [Google Scholar]
  5. Sun Y, Wang H, Zhang T, Liu WH, Liu HY et al. Desertihabitans aurantiacus gen. nov., sp. nov., a novel member of the family Propionibacteriaceae . Int J Syst Evol Microbiol 2019
     [Google Scholar]
  6. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. Journal of Fermentation Technology 1987; 65:501–509 [View Article]
     [Google Scholar]
  7. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  8. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article]
     [Google Scholar]
  9. 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 [View Article]
     [Google Scholar]
  10. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
     [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  12. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  14. 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]
     [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  16. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1 [View Article]
     [Google Scholar]
  17. Chen Y, Chen Y, Shi C, Huang Z, Zhang Y et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 2018; 7:1–6 [View Article]
     [Google Scholar]
  18. 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]
     [Google Scholar]
  19. 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]
     [Google Scholar]
  20. 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]
     [Google Scholar]
  21. 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]
     [Google Scholar]
  22. 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 [View Article]
     [Google Scholar]
  23. Magee CM, Rodeheaver G, Edgerton MT, Edlich RF. A more reliable gram staining technic for diagnosis of surgical infections. Am J Surg 1975; 130:341–346 [View Article]
     [Google Scholar]
  24. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  25. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article]
     [Google Scholar]
  26. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 6th edn. San Francisco: Benjamin Cummings Pearson Education; 2002
     [Google Scholar]
  27. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article]
     [Google Scholar]
  28. Kim SJ, Cho H, Joa JH, Hamada M, Ahn JH et al. Nakamurella intestinalis sp. nov., isolated from the faeces of Pseudorhynchus japonicus . Int J Syst Evol Microbiol 2017; 67:2970–2974 [View Article]
     [Google Scholar]
  29. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  30. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
     [Google Scholar]
  31. Guo L, Tuo L, Habden X, Zhang Y, Liu J et al. Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 2015; 65:206–213 [View Article]
     [Google Scholar]
  32. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231
     [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI inc; 1990
     [Google Scholar]
  34. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477
     [Google Scholar]
  35. Fujii K, Ikai Y, Oka H, Suzuki M, Harada K-ichi. A nonempirical method using LC/MS for determination of the absolute configuration of constituent amino acids in a peptide: combination of marfey's method with mass spectrometry and its practical application. Anal Chem 1997; 69:5146–5151 [View Article]
     [Google Scholar]
  36. Liu SW, Li FN, Zheng HY, Qi X, Huang DL et al. Planctomonas deserti gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from soil of the Taklamakan desert. Int J Syst Evol Microbiol 2019; 69:616–624 [View Article]
     [Google Scholar]
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Desertihabitans brevis sp. nov., an actinobacterium isolated from sand of the Taklamakan desert, and emended description of the genus Desertihabitans
Int J Syst Evol Microbiol 70, 1166 (2020); https://doi.org/10.1099/ijsem.0.003896
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