1887

Abstract

The genus belongs to the family and its members are known to be adapted to a wide range of ecological niches. ATCC 49188 and LUP21 are strains isolated from human clinical and plant root nodule samples, respectively, which share high similarity for phylogenetic markers (i.e 100 % for 16S rRNA, 99.9 % for and 99.35 % for ). In this work, multiple genome average nucleotide identity (ANI) approaches, digital DNA–DNA hybridization (dDDH) and phylogenetic analysis were performed in order to investigate the taxonomic relationship between ATCC 49188, LUP21, and other five type strains from the genus . Whole-genome comparisons demonstrated that LUP21 and the genus type species ATCC 49188, share 97.55 % of ANIb, 98.25 % of ANIm, 97.99 % of gANI, 97.94 % of OrthoANI and 83.9 % of dDDH, which exceed the species delineation thresholds. These strains are also closely related in phylogenies reconstructed from a concatenation of 1193 sequences from single-copy ortholog genes. A review of their profiles revealed that ATCC 49188 and LUP21 do not present pronounced differences at phenotypic and chemotaxonomic levels. Considering phylogenetic, genomic, phenotypic and chemotaxonomic data, should be considered a later heterotypic synonym of .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003465
2019-08-01
2019-12-05
Loading full text...

Full text loading...

References

  1. Trujillo ME, Willems A, Abril A, Planchuelo AM, Rivas R et al. Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov. Appl Environ Microbiol 2005;71:1318–1327 [CrossRef][PubMed]
    [Google Scholar]
  2. Holmes B, Popoff M, Kiredjian M, Kersters K. Ochrobactrum anthropi gen. nov., sp. nov. from human clinical specimens and previously known as group Vd. Int J Syst Bacteriol 1988;38:406–416 [CrossRef]
    [Google Scholar]
  3. Scholz HC, Tomaso H, Al Dahouk S, Witte A, Schloter M et al. Genotyping of Ochrobactrum anthropi by recA-based comparative sequence, PCR-RFLP, and 16S rRNA gene analysis. FEMS Microbiol Lett 2006;257:7–16 [CrossRef][PubMed]
    [Google Scholar]
  4. 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 [CrossRef][PubMed]
    [Google Scholar]
  5. 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 [CrossRef][PubMed]
    [Google Scholar]
  6. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  7. 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 [CrossRef][PubMed]
    [Google Scholar]
  8. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32:929–931 [CrossRef][PubMed]
    [Google Scholar]
  9. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015;43:6761–6771 [CrossRef][PubMed]
    [Google Scholar]
  10. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  11. Kim M, Oh HS, Park SC, 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 [CrossRef][PubMed]
    [Google Scholar]
  12. Meier-Kolthoff JP, Klenk HP, 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 [CrossRef][PubMed]
    [Google Scholar]
  13. Sant'anna FH, Ambrosini A, De Souza R, De Carvalho Fernandes G, Bach E et al. Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification. Front Microbiol 2017;8:8 [CrossRef][PubMed]
    [Google Scholar]
  14. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  15. Smith SA, Dunn CW. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 2008;24:715–716 [CrossRef][PubMed]
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  17. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992;8:275–282 [CrossRef][PubMed]
    [Google Scholar]
  18. Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 2008;9:299–306 [CrossRef][PubMed]
    [Google Scholar]
  19. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012;28:1823–1829 [CrossRef][PubMed]
    [Google Scholar]
  20. Hasegawa M, Kishino H, Yano T, T-a Y. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985;22:160–174 [CrossRef][PubMed]
    [Google Scholar]
  21. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008;25:1307–1320 [CrossRef][PubMed]
    [Google Scholar]
  22. Zurdo-Piñeiro JL, Rivas R, Trujillo ME, Vizcaíno N, Carrasco JA et al. Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int J Syst Evol Microbiol 2007;57:784–788 [CrossRef][PubMed]
    [Google Scholar]
  23. Vital M, Chai B, Østman B, Cole J, Konstantinidis KT et al. Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. ISME J 2015;9:1130–1140 [CrossRef][PubMed]
    [Google Scholar]
  24. Li L, Li YQ, Jiang Z, Gao R, Nimaichand S et al. Ochrobactrum endophyticum sp. nov., isolated from roots of Glycyrrhiza uralensis. Arch Microbiol 2016;198:171–179 [CrossRef][PubMed]
    [Google Scholar]
  25. Kämpfer P, Huber B, Busse HJ, Scholz HC, Tomaso H et al. Ochrobactrum pecoris sp. nov., isolated from farm animals. Int J Syst Evol Microbiol 2011;61:2278–2283 [CrossRef][PubMed]
    [Google Scholar]
  26. Kämpfer P, Scholz HC, Huber B, Falsen E, Busse HJ. Ochrobactrum haematophilum sp. nov. and Ochrobactrum pseudogrignonense sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol 2007;57:2513–2518 [CrossRef][PubMed]
    [Google Scholar]
  27. Lebuhn M, Achouak W, Schloter M, Berge O, Meier H et al. Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. Int J Syst Evol Microbiol 2000;50 Pt 6:2207–2223 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003465
Loading

Supplements

Supplementary File 1

PDF

Most Cited This Month

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