1887

Abstract

The taxonomic position of an unknown bacterial strain designated CNM695-12, isolated from the blood of an immunocompromised subject, was investigated via phenotypic, chemotaxonomic, genotypic and genomic analyses. Bacterial cells were determined to be Gram-stain-negative bacilli, aerobic, non-motile and non-spore-forming. The strain showed catalase activity but no oxidase activity. Optimal growth occurred at 37 °C, pH 7 and with 0–1 % NaCl. C, summed feature 8 (comprising Cω7C ω6), and Cω9 were the most abundant fatty acids, and ubiquinone 8 was the major respiratory quinone. The polar lipids present included phosphatidylglycerol, phosphatidylethanolamine and other aminophospholipids. The 16S rRNA gene sequence showed approximately 93.5 % similarity to those of different species with validly published names within the order (e.g. Feox-1, B8 B4 and K14). Phylogenetic analyses based on 16S rRNA gene sequences and concatenated alignments including the sequences for 107 essential proteins, revealed the strain to form a novel lineage close to members of the family . The highest average nucleotide identity and average amino acid identity values were obtained with K14 (69.6 and 55.7 % respectively). The genome, with a size of 3.35 Mb, had a DNA G+C content of 52.4 mol% and encoded 3056 predicted genes, 3 rRNA, 1 transfer–messengerRNA and 51 tRNA. Strain CNM695-12 thus represents a novel species belonging to a novel genus within the order , for which the name gen. nov., sp. nov. is proposed. The type strain is CNM695-12 (=DSM 104959=CECT 9208).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004010
2020-01-31
2020-02-28
Loading full text...

Full text loading...

References

  1. Garrity GM, Bell JA, Lilburn T.Order I. Burkholderiales ord. nov In Garrity GM, Brenner DJ, Krieg NR, Staley JT. (editors) Bergey’s Manual of Systematic Bacteriology2, 2nd ed. New York: Springer Science & Business Media; 2006; pp575–759
    [Google Scholar]
  2. Hatayama K. Comamonas humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014;64:3976–3982 [CrossRef]
    [Google Scholar]
  3. Imai S, Yoshida R, Endo Y, Fukunaga Y, Yamazoe A et al. Rhizobacter gummiphilus sp. nov., a rubber-degrading bacterium isolated from the soil of a botanical garden in Japan. J Gen Appl Microbiol 2013;59:199–205 [CrossRef]
    [Google Scholar]
  4. Gomila M, Bowien B, Falsen E, Moore ERB, Lalucat J. Description of Roseateles aquatilis sp. nov. and Roseateles terrae sp. nov., in the class Betaproteobacteria, and emended description of the genus Roseateles. Int J Syst Evol Microbiol 2008;58:6–11 [CrossRef]
    [Google Scholar]
  5. Gilligan PH, Lum G, Vandamme AR, Whittier S.Burkholderia, Stenotrophomonas, Ralstonia, Brevundimonas, Comamonas, Delftia, Pandoraea, and Acidovorax In Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH. (editors) Manual of Clinical Microbiology1, 8th ed. Washington, DC: ASM Press; 2003; pp729–748
    [Google Scholar]
  6. Medina-Pascual MJ, Valdezate S, Villalón P, Garrido N, Rubio V et al. Identification, molecular characterisation and antimicrobial susceptibility of genomovars of the Burkholderia cepacia complex in Spain. Eur J Clin Microbiol Infect Dis 2012;31:3385–3396 [CrossRef]
    [Google Scholar]
  7. Tena D, Carranza R, Barberá JR, Valdezate S, Garrancho JM et al. Outbreak of long-term intravascular catheter-related bacteremia due to Achromobacter xylosoxidans subspecies xylosoxidans in a hemodialysis unit. Eur J Clin Microbiol Infect Dis 2005;24:727–732 [CrossRef]
    [Google Scholar]
  8. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173:697–703 [CrossRef]
    [Google Scholar]
  9. Baker GC, Smith JJ, Cowan DA. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 2003;55:541–555 [CrossRef]
    [Google Scholar]
  10. CLSIInterpretative criteria for identification of bacteria and fungi by DNA target sequencing approved guide CLSI document MM18-A Wayne, PA: Clinical and Laboratory Standards Institute; 2008
    [Google Scholar]
  11. Pittman GW, Brumbley SM, Allsopp PG, O'Neill SL. Assessment of gut bacteria for a paratransgenic approach to control Dermolepida albohirtum larvae. Appl Environ Microbiol 2008;74:4036–4043 [CrossRef]
    [Google Scholar]
  12. CLSIPerformance standards for antimicrobial susceptibility testing CLSI supplement M100, 29th ed. Wayne, PA: Clinical and Laboratory standard Institute; 2019
    [Google Scholar]
  13. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI technical note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  14. Sherlock Microbial Identification version 6.1 Mis System Operating Manual 2008; Newark, DE: MIDI Inc;
    [Google Scholar]
  15. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13:128–130 [CrossRef]
    [Google Scholar]
  16. Tindall BC, Sikorski J, Smibert R, Kreig N.Phenotypic characterization and the principles of comparative systematics In Reddy CA, Beveridge T, Brenak J, Marzluf G, Schmidt T. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007; pp330–393
    [Google Scholar]
  17. 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 [CrossRef]
    [Google Scholar]
  18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 1999;41:95–98
    [Google Scholar]
  19. Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 2017;1–7
    [Google Scholar]
  20. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition–transversion and G+C-content biases. Mol Biol Evol 1992;9:678–687
    [Google Scholar]
  21. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef]
    [Google Scholar]
  23. Kumar S, Stecher G, Tamura K. Mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef]
    [Google Scholar]
  24. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014;30:2114–2120 [CrossRef]
    [Google Scholar]
  25. 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 [CrossRef]
    [Google Scholar]
  26. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013;29:1072–1075 [CrossRef]
    [Google Scholar]
  27. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–2069 [CrossRef]
    [Google Scholar]
  28. 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 [CrossRef]
    [Google Scholar]
  29. Yoon S-H, Ha S-min, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017;110:1281–1286 [CrossRef]
    [Google Scholar]
  30. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014;9:111–118 [CrossRef]
    [Google Scholar]
  31. Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, Alexander Richter R et al. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 2012;6:1186–1199 [CrossRef]
    [Google Scholar]
  32. Ankenbrand MJ, Keller A. bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 2016;59:783–791 [CrossRef]
    [Google Scholar]
  33. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef]
    [Google Scholar]
  34. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007;35:W182–W185 [CrossRef]
    [Google Scholar]
  35. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ et al. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 2017;45:W36–W41 [CrossRef]
    [Google Scholar]
  36. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012;67:2640–2644 [CrossRef]
    [Google Scholar]
  37. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 2014;52:1501–1510 [CrossRef]
    [Google Scholar]
  38. Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O. PathogenFinder - distinguishing friend from foe using bacterial whole genome sequence data. PLoS One 2013;8:e77302 [CrossRef]
    [Google Scholar]
  39. Zhu D, Xie C, Huang Y, Sun J, Zhang W. Description of Comamonas serinivorans sp. nov., isolated from wheat straw compost. Int J Syst Evol Microbiol 2014;64:4141–4146 [CrossRef]
    [Google Scholar]
  40. Chen W-M, Cho N-T, Yang S-H, Arun AB, Young C-C et al. Aquabacterium limnoticum sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 2012;62:698–704 [CrossRef]
    [Google Scholar]
  41. Hiraishi A, Hoshino Y, Satoh T. Rhodoferax fermentans gen. nov., sp. nov., a phototrophic purple nonsulfur bacterium previously referred to as the "Rhodocyclus gelatinosus-like" group. Arch Microbiol 1991;155:330–336 [CrossRef]
    [Google Scholar]
  42. Spring S, Kampfer P, Ludwig W, Schleifer K-H. Polyphasic characterization of the genus Leptothrix: new descriptions of Leptothrix mobilis sp. nov. and Leptothrix discophora sp. nov. nom. rev. and emended description of Leptothrix cholodnii emend. Syst Appl Microbiol 1996;19:634–643 [CrossRef]
    [Google Scholar]
  43. Takeda M, Kamagata Y, Ghiorse WC, Hanada S, Koizumi J-ichi et al. Caldimonas manganoxidans gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading, manganese-oxidizing thermophile. Int J Syst Evol Microbiol 2002;52:895–900 [CrossRef]
    [Google Scholar]
  44. Elbanna K, Lütke-Eversloh T, Van Trappen S, Mergaert J, Swings J et al. Schlegelella thermodepolymerans gen. nov., sp. nov., a novel thermophilic bacterium that degrades poly(3-hydroxybutyrate-co-3-mercaptopropionate). Int J Syst Evol Microbiol 2003;53:1165–1168 [CrossRef]
    [Google Scholar]
  45. Chou Y-J, Sheu S-Y, Sheu D-S, Wang J-T, Chen W-M. Schlegelella aquatica sp. nov., a novel thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2006;56:2793–2797 [CrossRef]
    [Google Scholar]
  46. Härtig C, Loffhagen N, Harms H. Formation of trans fatty acids is not involved in growth-linked membrane adaptation of Pseudomonas putida. Appl Environ Microbiol 2005;71:1915–1922 [CrossRef]
    [Google Scholar]
  47. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981;45:316–354 [CrossRef]
    [Google Scholar]
  48. Stackebrandt E, Verbarg S, Frühling A, Busse H-J, Tindall BJ. Dissection of the genus Methylibium: reclassification of Methylibium fulvum as Rhizobacter fulvus comb. nov., Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. and Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. and emended descriptions of the genera Rhizobacter and Methylibium. Int J Syst Evol Microbiol 2009;59:2552–2560 [CrossRef]
    [Google Scholar]
  49. Voronina OL, Kunda MS, Ryzhova NN, Aksenova EI, Semenov AN et al. The variability of the order Burkholderiales representatives in the healthcare units. Biomed Res Int 2015;2015:1–9 [CrossRef]
    [Google Scholar]
  50. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018;36:996–1004 [CrossRef]
    [Google Scholar]
  51. Wu D, Jospin G, Eisen JA. Systematic identification of gene families for use as “Markers” for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One 2013;8:e77033 [CrossRef]
    [Google Scholar]
  52. Cullen ME, Wyke AW, Kuroda R, Fisher LM. Cloning and characterization of a DNA gyrase A gene from Escherichia coli that confers clinical resistance to 4-quinolones. Antimicrob Agents Chemother 1989;33:886–894 [CrossRef]
    [Google Scholar]
  53. Heulin T et al. Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia. Int J Syst Evol Microbiol 2003;53:589–594 [CrossRef]
    [Google Scholar]
  54. Lee HJ, Lee SH, Lee S-S, Lee JS, Kim Y et al. Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter. Int J Syst Evol Microbiol 2014;64:1317–1322 [CrossRef]
    [Google Scholar]
  55. Kalmbach S, Manz W, Wecke J, Szewzyk U. Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system. Int J Syst Bacteriol 1999;49:769–777 [CrossRef]
    [Google Scholar]
  56. Suyama T, Shigematsu T, Takaichi S, Nodasaka Y, Fujikawa S et al. Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the beta-subclass of the Proteobacteria. Int J Syst Bacteriol 1999;49 Pt 2:449–457 [CrossRef]
    [Google Scholar]
  57. Rakshak K, Ravinder K, Srinivas TNR, Kumar PA. Caldimonas meghalayensis sp. nov., a novel thermophilic betaproteobacterium isolated from a hot spring of Meghalaya in northeast India. Antonie Van Leeuwenhoek 2013;104:1217–1225 [CrossRef]
    [Google Scholar]
  58. Kang W, Soo Kim P, Hyun D-W, Lee J-Y, Sik Kim H et al. Comamonas piscis sp. nov., isolated from the intestine of a Korean rockfish, Sebastes schlegelii. Int J Syst Evol Microbiol 2016;66:780–785 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004010
Loading
/content/journal/ijsem/10.1099/ijsem.0.004010
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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