1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 3

sp. nov., a glutamate producing bacterium isolated from soil and its complete genome-based analysis Free

Abstract

Strain N24 was isolated from soil contaminated with starling’s feces collected from Roi-Et province, Thailand. Cells of N24 were Gram-stain-positive rods, aerobic and non-spore-forming. N24 was positive for catalase, urease, citrate utilization, nitrate reduction and Methyl Red (MR) test but negative for oxidase, casein, gelatin liquefaction, tyrosine, Voges–Proskauer (VP) reaction and starch hydrolysis. -diaminopimelic acid, rhamnose, ribose, arabinose and galactose were detected in its whole-cell hydrolysates. The results of the 16S rRNA gene sequence analysis indicated that N24 represented a member of the genus . N24 was closely related to ATCC 13032, with 99.0 % 16S rRNA gene sequence similarity. According to results obtained using DNA–DNA hybridization approaches, N24 showed highest DNA–DNA relatedness (27.6 %) and average nucleotide identity (84.1 %) to ATCC 13032. The DNA G+C content of N24 was 51.8 mol% (genome based). The major cellular fatty acids of N24 were C, and Cω9. N24 had the nine isoprenes unit, MK-9(H) as the predominant menaquinone. The predominant polar lipids were phosphatidylglycerol, phosphatidylinositol and diphosphatidylglycerol. Mycolic acids were also present. According to the complete genome sequence data, strain N24 and ATCC 13032 are close phylogenetic neighbours, but have different genome characteristics. On the basis of the results of the genotypic and genomic studies and phenotypic characteristics including chemotaxonomy, strain N24 should be classified as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is N24 (TBRC 5845=NBRC 113465).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): Corynebacterium , glutamate producing bacteria , polyphasic taxonomy and soil
Funding
This study was supported by the:
  • Ratchadaphiseksomphot Endowment Fund (Award GCURP_58_01_33_01)
    • Principle Award Recipient: Somboon Tanasupawat
  • Japan Science and Technology Agency (Award JPMJAL1106)
    • Principle Award Recipient: Kazunobu Matsushita
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003993
2020-01-23
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/3/1903.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003993&mimeType=html&fmt=ahah

References

  1. Lehmann KB, Neumann RO. Atlas Und Grundriss Der Bakteriologie Und Lehrbuch Der Speziellen Bakteriologischen Diagnostik, 1st ed. Germany: JF Lehmann; 1896
     [Google Scholar]
  2. Bernard KA, Funke G, Genus I. Corynebacterium . In Whitman W, Goodfellow M, Kämpfer P, Busse H-J, Trujillo M et al. (editors) Bergey's Manual of Systematic Bacteriology: the Actinobacteria New York: Springer; 2012 pp 245–289
     [Google Scholar]
  3. Collins MD, Goodfellow M, Minnikin DE. A survey of the structures of mycolic acids in Corynebacterium and related taxa. J Gen Microbiol 1982; 128:129–149 [View Article]
     [Google Scholar]
  4. Butler WR, Ahearn DG, Kilburn JO. High-performance liquid chromatography of mycolic acids as a tool in the identification of Corynebacterium, Nocardia, Rhodococcus, and Mycobacterium species. J Clin Microbiol 1986; 23:182–185 [View Article]
     [Google Scholar]
  5. Collins MD, Burton RA, Jones D. Corynebacterium amycolatum sp. nov. a new mycolic acid-less Corynebacterium species from human skin. FEMS Microbiol Lett 1988; 49:349–352 [View Article]
     [Google Scholar]
  6. Collins MD, Hoyles L, Foster G, Falsen E. Corynebacterium caspium sp. nov., from a Caspian seal (Phoca caspica). Int J Syst Evol Microbiol 2004; 54:925–928 [View Article]
     [Google Scholar]
  7. Collins MD, Goodfellow M, Minnikin DE. Fatty acid composition of some mycolic acid-containing coryneform bacteria. J Gen Microbiol 1982; 128:2503–2509 [View Article]
     [Google Scholar]
  8. Bernard KA, Bellefeuille M, Ewan EP. Cellular fatty acid composition as an adjunct to the identification of asporogenous, aerobic Gram-positive rods. J Clin Microbiol 1991; 29:83–89 [View Article]
     [Google Scholar]
  9. 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]
  10. Zimmermann O, Spröer C, Kroppenstedt RM, Fuchs E, Köchel HG et al. Corynebacterium thomssenii sp. nov., a Corynebacterium with N-acetyl-β-glucosaminidase activity from human clinical specimens. Int J Syst Bacteriol 1998; 48:489–494 [View Article]
     [Google Scholar]
  11. Kämpfer P, Lodders N, Warfolomeow I, Falsen E, Busse H-J. Corynebacterium lubricantis sp. nov., isolated from a coolant lubricant. Int J Syst Evol Microbiol 2009; 59:1112–1115 [View Article]
     [Google Scholar]
  12. Funke G, von Graevenitz A, Clarridge JE, Bernard KA. Clinical microbiology of coryneform bacteria. Clin Microbiol Rev 1997; 10:125–159 [View Article]
     [Google Scholar]
  13. Rückert C, Albersmeier A, Winkler A, Tauch A. Complete genome sequence of Corynebacterium kutscheri DSM 20755, a corynebacterial type strain with remarkably low G+C content of chromosomal DNA. Genome Announc 2015; 3:e00571–00515 [View Article]
     [Google Scholar]
  14. Liebl W. Corynebacterium taxonomy. In Eggeling L, Bott M. (editors) Handbook of Corynebacterium glutamicum Boca Raton: CRC press; 2005 pp 9–34
     [Google Scholar]
  15. Crumplin GC, Smith JT. Nalidixic acid: an antibacterial paradox. Antimicrob Agents Chemother 1975; 8:251–261 [View Article]
     [Google Scholar]
  16. Matsushita K, Yamamoto T, Toyama H, Adachi O. NADPH oxidase system as a superoxide-generating cyanide-resistant pathway in the respiratory chain of Corynebacterium glutamicum . Biosci Biotechnol Biochem 1998; 62:1968–1977 [View Article]
     [Google Scholar]
  17. 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]
  18. Steel KJ, Barrow G, Feltham R. Cowan and Steel's Manual for the Identification of Medical Bacteria, 3 ed. Cambridge: Cambridge University Press; 1993
     [Google Scholar]
  19. Tindall B, Sikorski J, Smibert R, Krieg N. Phenotypic characterization and the principles of comparative systematics. In Reddy C, Beveridge TJ, Breznak JA, Marzluf G, Schmidt T. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology Press; 2007 pp 330–393
     [Google Scholar]
  20. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article]
     [Google Scholar]
  21. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article]
     [Google Scholar]
  22. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
     [Google Scholar]
  23. 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 Meth 1984; 2:233–241 [View Article]
     [Google Scholar]
  24. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides . J Bacteriol 1982; 151:828–837 [View Article]
     [Google Scholar]
  25. Saito H, Miura K-I. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [View Article]
     [Google Scholar]
  26. 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]
     [Google Scholar]
  27. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article]
     [Google Scholar]
  28. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article]
     [Google Scholar]
  29. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
     [Google Scholar]
  30. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid–deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
     [Google Scholar]
  31. Wayne L, Brenner D, Colwell R, Grimont P, Kandler O et al. International Committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463464
     [Google Scholar]
  32. 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]
     [Google Scholar]
  33. Matsutani M, Nantapong N, Murata R, Paisrisan P, Hirakawa H et al. Complete genome sequencing of newly isolated thermotolerant Corynebacterium glutamicum N24 provides a new insights into its thermotolerant phenotype. J Biotechnol 2017; 247:29–33 [View Article]
     [Google Scholar]
  34. Hyatt D, LoCascio PF, Hauser LJ, Uberbacher EC. Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics 2012; 28:2223–2230 [View Article]
     [Google Scholar]
  35. Tatusova T, Ciufo S, Fedorov B, O'Neill K, Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res 2014; 42:D553–D559 [View Article]
     [Google Scholar]
  36. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580 [View Article]
     [Google Scholar]
  37. Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform 2009; 23:205–211
     [Google Scholar]
  38. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785–786 [View Article]
     [Google Scholar]
  39. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2016; 44:D279–D285 [View Article]
     [Google Scholar]
  40. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article]
     [Google Scholar]
  41. Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 2005; 21:537–539 [View Article]
     [Google Scholar]
  42. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article]
     [Google Scholar]
  43. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–D269 [View Article]
     [Google Scholar]
  44. Teeling H, Meyerdierks A, Bauer M, Amann R, Glöckner FO. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 2004; 6:938–947 [View Article]
     [Google Scholar]
  45. 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]
  46. 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]
     [Google Scholar]
  47. 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]
     [Google Scholar]
  48. Rokas A, Williams BL, King N, Carroll SB. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003; 425:798–804 [View Article]
     [Google Scholar]
  49. Gontcharov AA, Marin B, Melkonian M. Are combined analyses better than single gene phylogenies? A case study using SSU rDNA and rbcL sequence comparisons in the Zygnematophyceae (Streptophyta). Mol Biol Evol 2004; 21:612–624 [View Article]
     [Google Scholar]
  50. Liu Y, Schmidt B, Maskell DL. MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinformatics 2010; 26:1958–1964 [View Article]
     [Google Scholar]
  51. Liu Y, Schmidt B. Multiple protein sequence alignment with MSAProbs. Multiple Sequence Alignment Methods Springer; 2014 pp 211–218
     [Google Scholar]
  52. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article]
     [Google Scholar]
  53. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007; 56:564–577 [View Article]
     [Google Scholar]
  54. Matsutani M, Ito K, Azuma Y, Ogino H, Shirai M et al. Adaptive mutation related to cellulose producibility in Komagataeibacter medellinensis (Gluconacetobacter xylinus) NBRC 3288. Appl Microbiol Biotechnol 2015; 99:7229–7240 [View Article]
     [Google Scholar]
  55. 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]
     [Google Scholar]
  56. Suzuki H, Lefébure T, Bitar PP, Stanhope MJ. Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae . BMC Genomics 2012; 13:38 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003993
Loading
Corynebacterium suranareeae sp. nov., a glutamate producing bacterium isolated from soil and its complete genome-based analysis
Int J Syst Evol Microbiol 70, 1903 (2020); https://doi.org/10.1099/ijsem.0.003993
/content/journal/ijsem/10.1099/ijsem.0.003993
/content/journal/ijsem/10.1099/ijsem.0.003993
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error