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Abstract

Isolate 4NS15 was isolated from a neglected arid habitat in Kerman, Iran. The strain showed 16S rRNA gene sequence similarity values of 98.9 % to the type strains of subsp. , and and 98.6 % to the type strain subsp. , respectively. Genome-based phylogenetic analysis revealed that isolate 4NS15 is closely related to subsp. DSM 43828. The digital DNA–DNA hybridization value between the genome sequences of 4NS15 and strain DSM 43828 is 29.8 %. Strain 4NS15 produces long chains of spores without a sporangium-like structure which can be distinguished from other species. Isolate 4NS15 has a genome size of 10.35 Mbp with a G+C content of 68.1 mol%. Whole-cell hydrolysates of isolate 4NS15 are rich in -diaminopimelic acid and cell-wall sugars such as arabinose, galactose, glucose and ribose. Major fatty acids (>10 %) are C, iso-C and iso-C. The phospholipid profile contains diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylhydroxyethanolamine, aminolipid and glycoaminolipid. The predominant menaquinone is MK-9(H). Based on its phenotypic and genotypic characteristics, isolate 4NS15 (NCCB 100701=CIP 111705=DSM 110728) merits recognition as representing a novel species of the genus , for which the name sp. nov. is proposed.

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2021-01-11
2021-08-02
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References

  1. Mohammadipanah F, Wink J. Actinobacteria from arid and desert habitats: diversity and biological activity. Front Microbiol 2015; 6:1–10 [View Article][PubMed]
    [Google Scholar]
  2. Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and methods to access novel antibiotics from actinomycetes. Antibiotics 2018; 7:E4444 22 05 2018 [View Article][PubMed]
    [Google Scholar]
  3. Azman A-S, Othman I, Velu SS, Chan K-G, Lee L-H. Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity. Front Microbiol 2015; 6:1–15 [View Article]
    [Google Scholar]
  4. Shearer MC, Giovenella AJ, Grappel SF, Hedde RD, Mehta RJ et al. Kibdelins, novel glycopeptide antibiotics. I. discovery, production, and biological evaluation. J Antibiot 1986; 39:1386–1394 [View Article][PubMed]
    [Google Scholar]
  5. Jose PA, Jebakumar SRD, Jebakumar AJ, Solomon RD. Non-streptomycete actinomycetes nourish the current microbial antibiotic drug discovery. Front Microbiol 2013; 4:240 [View Article][PubMed]
    [Google Scholar]
  6. Cao Y, Yang W, Dao Y, Hu B, He Z et al. Kibdelosporangium metalli sp. nov.. isolated from a rare earth mine 2018101–107
    [Google Scholar]
  7. Goodfellow M, Kämpfer P, Trujillo M. Bergeuy’s Manual of Systematic Bacteriology 5 2012
    [Google Scholar]
  8. Wink J, Gandhi J, Kroppenstedt RM, Seibert G, Sträubler B et al. Amycolatopsis decaplanina sp. nov., a novel member of the genus with unusual morphology. Int J Syst Evol Microbiol 2004; 54:235–239 [View Article][PubMed]
    [Google Scholar]
  9. Shearer MC, Colman PM, Ferrin RM, Nisbet LJ, Nash CH. New genus of the Actinomycetales: Kibdelosporangium aridum gen. nov., sp. nov. Int J Syst Bacteriol 1986; 36:47–54 [View Article]
    [Google Scholar]
  10. Sitrin RD, Chan GW, Dingerdissen JJ, Holl W, Hoover JR et al. Aridicins, novel glycopeptide antibiotics. II. Isolation and characterization. J Antibiot 1985; 38:561–571 [View Article][PubMed]
    [Google Scholar]
  11. Folena-Wasserman G, Poehland BL, Yeung EW, Staiger D, Killmer LB et al. Kibdelins (AAD-609), novel glycopeptide antibiotics. II. Isolation, purification and structure. J Antibiot 1986; 39:1395–1406 [View Article][PubMed]
    [Google Scholar]
  12. Hayakawa M. Studies on the isolation and distribution of rare actinomycetes in soil. Actinomycetologica 2008; 22:12–19 [View Article]
    [Google Scholar]
  13. Williams ST, Davies FL. Use of antibiotics for selective isolation and enumeration of actinomycetes in soil. J Gen Microbiol 1965; 38:251–261 [View Article][PubMed]
    [Google Scholar]
  14. Yang H, Zou H, Chen M, Li S, Jin J et al. The green synthesis of ultrafine palladium–phosphorus alloyed nanoparticles anchored on polydopamine functionalized graphene used as an excellent electrocatalyst for ethanol oxidation. Inorganic Chemistry Frontiers 2017; 4:1881–1887 [View Article]
    [Google Scholar]
  15. Chun J, Lee J-H, Jung Y, Kim M, Kim S et al. Eztaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article][PubMed]
    [Google Scholar]
  16. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
    [Google Scholar]
  17. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  18. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  19. Arbo MM, Gonzalez AM, TNT SSM. A free program for phylogenetic analysis. Plant Syst Evol 2015; 301:774–786
    [Google Scholar]
  20. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article][PubMed]
    [Google Scholar]
  21. Rédei GP. PAUP (phylogenetic analysis using parsimony). Encycl Genet Genomics, Proteomics Informatics 20081455
    [Google Scholar]
  22. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article][PubMed]
    [Google Scholar]
  23. Jin J, Lee Y-K, Wickes BL. Simple Chemical Extraction Method for DNA Isolation from Aspergillus fumigatus and Other Aspergillus Species. J Clin Microbiol 2004; 42:4293–4296 [View Article]
    [Google Scholar]
  24. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article][PubMed]
    [Google Scholar]
  25. Castro JF, Razmilic V, Gomez-Escribano JP, Andrews B, Asenjo J et al. The ‘gifted’ actinomycete Streptomyces leeuwenhoekii. Antonie van Leeuwenhoek 2018; 111:1433–1448 [View Article]
    [Google Scholar]
  26. Charlop-Powers Z, Owen JG, Reddy BVB, Ternei MA, Brady SF. Chemical-biogeographic survey of secondary metabolism in soil. Proc Natl Acad Sci U S A 2014; 111:3757–3762 [View Article][PubMed]
    [Google Scholar]
  27. 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 [View Article][PubMed]
    [Google Scholar]
  28. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  29. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
    [Google Scholar]
  30. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. J Chem Inf Model 2018; 53:1689–1699
    [Google Scholar]
  31. Schumann P, Maier T. MALDI-TOF Mass Spectrometry Applied to Classification and Identification of Bacteria, 1st ed. Elsevier Ltd; Epub ahead of print 2014
    [Google Scholar]
  32. Collins MD, Goodfellow M, Minnikin DE. Polar lipid composition in the classification of Arthrobacter and Microbacterium. FEMS Microbiol Lett 1982; 15:299–302 [View Article]
    [Google Scholar]
  33. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  34. 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]
  35. Becker B, Wortzel EM, Nelson JH. Chemical composition of the cell wall of Caryophanon latum. Nature 1967; 213:300 [View Article][PubMed]
    [Google Scholar]
  36. Sasser M. Technical note # 101 identification of bacteria by gas chromatography of cellular fatty acids. Stat 20011–6
    [Google Scholar]
  37. Lechevalier MP, De Bievre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260 [View Article]
    [Google Scholar]
  38. Mertz FP, Yao RC. Kibdelosporangium philippinense sp. nov. isolated from soil. Int J Syst Bacteriol 2009; 38:282–286
    [Google Scholar]
  39. Xing K, Bian G-K, Qin S, Klenk H-P, Yuan B et al. Kibdelosporangium phytohabitans sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L. containing 1-aminocyclopropane-1-carboxylic acid deaminase. Antonie Van Leeuwenhoek 2012; 101:433–441 [View Article][PubMed]
    [Google Scholar]
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