1887

Abstract

A novel actinobacterium, designated strain NEAU-351, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, northeast PR China and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-351 belonged to the genus , with the highest similarity (98.96 %) to DSM 44801 and less than 98.0 % identity with other type strains of the genus . The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major menaquinone was observed to contain MK-8(H, ω-cycl) (78.2 %). The fatty acid profile mainly consisted of C, C 9 and 10-methyl C. Mycolic acids were present. The genomic DNA G+C content of strain NEAU-351 was 68.1 mol%. In addition, the average nucleotide identity values between strain NEAU-351 and its reference strains, DSM 44801 and NBRC 108935, were found to be 81.4 and 82.9 %, respectively, and the level of digital DNA–DNA hybridization between them were 24.8 % (22.5–27.3 %) and 26.3 % (24–28.8 %), respectively. Here we report on the taxonomic characterization and classification of the isolate and propose that strain NEAU-351 represents a new species of the genus , for which the name is proposed. The type strain is NEAU-351 (=CCTCC AA 2019090=DSM 110681).

Funding
This study was supported by the:
  • the National Natural Science Foundation of China (Award 31872037)
    • Principle Award Recipient: WenshengXiang
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2021-02-09
2022-01-25
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References

  1. Goodfellow M, Jones AL. Order V. Corynebacteriales ord. nov. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey’s Manual of Systematic Bacteriology 5, 2nd ed. New York: Springer; 2012 pp 235–243
    [Google Scholar]
  2. Trevisan V. I Generi E Le Specie Delle Bacteriaceae Milan: Zanaboni & Gabuzzi; 1889
    [Google Scholar]
  3. Goodfellow M, Maldonado LA et al. Genus I. Nocardia Trevisan 1889AL . In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey’s Manual of Systematic Bacteriology 5, 2nd ed. New York: Springer; 2012 pp 376–419
    [Google Scholar]
  4. Zhang J-X, Ming H, Zhao Z-L, Ji W-L, Chang X-L et al. Nocardia yunnanensis sp. nov., an actinomycete isolated from a soil sample. Int J Syst Evol Microbiol 2019; 69:3116–3120 [View Article][PubMed]
    [Google Scholar]
  5. Zhao J, Han X, Hu H, Ling L, Zhang X et al. Nocardia stercoris sp. nov., a novel actinomycete isolated from the cow dung. Int J Syst Evol Microbiol 2020; 70:493–498 [View Article][PubMed]
    [Google Scholar]
  6. Zhou T, Wang X-Y, Deng D-Q, Xu L-H, Li X-L et al. Nocardia colli sp. nov., a new pathogen isolated from a patient with primary cutaneous nocardiosis. Int J Syst Evol Microbiol 2020; 70:2981–2987 [View Article][PubMed]
    [Google Scholar]
  7. Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W et al. Nocardia aurantiaca sp. nov., isolated from soil in Thailand. Int J Syst Evol Microbiol 2020; 70:5432–5438 [View Article][PubMed]
    [Google Scholar]
  8. Piao C, Zheng W, Li Y, Liu C, Jin L et al. Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr. Arch Microbiol 2017; 199:963–970 [View Article][PubMed]
    [Google Scholar]
  9. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  10. Guan X, Liu C, Zhao J, Fang B, Zhang Y et al. Streptomyces maoxianensis sp. nov., a novel actinomycete isolated from soil in Maoxian, China. Antonie van Leeuwenhoek 2015; 107:1119–1126 [View Article][PubMed]
    [Google Scholar]
  11. Jin L, Zhao Y, Song W, Duan L, Jiang S et al. Streptomyces inhibens sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2019; 69:688–695 [View Article][PubMed]
    [Google Scholar]
  12. Waksman SA. The Actinomycetes. A summary of current knowledge New York: Ronald; 1967
    [Google Scholar]
  13. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article][PubMed]
    [Google Scholar]
  14. Waksman SA. The Actinomycetes, vol. 2, Classification, Identification and Descriptions of Genera and Species Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  15. Kelly KL. Inter-society color council-national Bureau of standards color-name charts illustrated with centroid colors published in US; 1964
  16. Zhao J, Han L, Yu M, Cao P, Li D et al. Characterization of Streptomyces sporangiiformans sp. nov., a novel soil actinomycete with antibacterial activity against Ralstonia solanacearum . Microorganisms 2019; 7:360 [View Article][PubMed]
    [Google Scholar]
  17. Cao P, Li C, Tan K, Liu C, Xu X et al. Characterization, phylogenetic analyses and pathogenicity of Enterobacter cloacae on rice seedlings in Heilongjiang Province, China. Plant Dis 2020; 104:1601–1609 [View Article][PubMed]
    [Google Scholar]
  18. Chapin KC, Murray PR. Stains. In Murray PR, Baron EJ, Pfaller MA, Tenover FC, Yolken RH. (editors) Manual of Clinical Microbiology Washington, DC: American Society for Microbiology; 1999 p 1678
    [Google Scholar]
  19. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  20. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  21. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicas gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales . Int J Syst Bacteriol 1993; 43:805–812 [View Article]
    [Google Scholar]
  22. CLSI Susceptibility Testing of Mycobacteria, Nocardiae, and Other Aerobic Actinomycetes, Approved Standard M24-A. Wayne, PA: Clinical and Laboratory Standards Institute; 2003
    [Google Scholar]
  23. McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM et al. A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 2000; 30:178–182 [View Article][PubMed]
    [Google Scholar]
  24. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy (Special publication vol 6) Arlington: Society of Industrial Microbiology; 1980 pp 227–291
    [Google Scholar]
  25. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [View Article]
    [Google Scholar]
  26. 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]
  27. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–284
    [Google Scholar]
  28. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing)] 1989; 16:176–178
    [Google Scholar]
  29. Zhuang X, Peng C, Wang Z, Zhao J, Shen Y et al. Actinomadura physcomitrii sp. nov., a novel actinomycete isolated from moss [Physcomitrium sphaericum (Ludw) Fuernr]. Antonie van Leeuwenhoek 2020; 113:677–685 [View Article][PubMed]
    [Google Scholar]
  30. Xiang W, Liu C, Wang X, Du J, Xi L et al. Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 2011; 61:1165–1169 [View Article][PubMed]
    [Google Scholar]
  31. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S et al. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000; 50 Pt 6:2031–2036 [View Article][PubMed]
    [Google Scholar]
  32. 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]
  33. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  34. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  35. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  36. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  37. 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]
  38. Yoon S-H, Ha S-M, 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][PubMed]
    [Google Scholar]
  39. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article][PubMed]
    [Google Scholar]
  40. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
    [Google Scholar]
  41. 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]
  42. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  43. 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]
  44. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 2006; 33:152–155
    [Google Scholar]
  45. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  46. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O. International Committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  47. 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]
  48. 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]
  49. Lasker BA, Bell M, Klenk H-P, Schumann P, Brown JM. Nocardia arizonensis sp. nov., obtained from human respiratory specimens. Antonie van Leeuwenhoek 2015; 108:1129–1137 [View Article][PubMed]
    [Google Scholar]
  50. Yamamura H, Hayakawa M, Nakagawa Y, Tamura T, Kohno T et al. Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge. Int J Syst Evol Microbiol 2005; 55:433–436 [View Article][PubMed]
    [Google Scholar]
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