1887

Abstract

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies, including DNA–DNA similarity, G+C content and representative phylogeny of bacteria. At present, DNA–DNA hybridizations are still considered the gold standard in species descriptions. However, this method is time-consuming and troublesome, and datasets can vary significantly between experiments as well as between laboratories. For the same reasons, full matrix hybridizations are rarely performed, weakening the significance of the results obtained. The authors established a universal sequencing approach for the three genes , and for the , and determined if the sequences could be used for predicting DNA–DNA relatedness within the family. The sequence-based similarity values calculated using a previously published formula proved most useful for species and genus separation, indicating that this method provides better resolution and no experimental variation compared to hybridization. By this method, cross-comparisons within the family over species and genus borders easily become possible. The three genes also serve as an indicator of the genome G+C content of a species. A mean divergence of around 1 % was observed from the classical method, which in itself has poor reproducibility. Finally, the three genes can be used alone or in combination with already-established 16S rRNA, and gene-sequencing strategies in a multisequence-based phylogeny for the family . It is proposed to use the three sequences as a taxonomic tool, replacing DNA–DNA hybridization.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.28991-0
2006-09-01
2020-08-08
Loading full text...

Full text loading...

/deliver/fulltext/micro/152/9/2537.html?itemId=/content/journal/micro/10.1099/mic.0.28991-0&mimeType=html&fmt=ahah

References

  1. Angen O, Mutters R, Caugant D. A, Olsen J. E, Bisgaard M. 1999; Taxonomic relationships of the [ Pasteurella ] haemolytica complex as evaluated by DNA–DNA hybridizations and 16S rRNA sequencing with proposal of Mannheimia haemolytica gen.nov., comb. nov., Mannheimia granulomatis comb. nov., Mannheimia glucosida sp. nov., Mannheimia ruminalis sp. nov. and Mannheimia varigena sp. nov. Int J Syst Bacteriol49:67–86[CrossRef]
    [Google Scholar]
  2. Angen O, Ahrens P, Kuhnert P, Christensen H, Mutters R. 2003; Proposal of Histophilus somni gen. nov., sp. nov. for the three species incertae sedis ‘ Haemophilus somnus ’, ‘ Haemophilus agni ’ and ‘ Histophilus ovis ’. Int J Syst Evol Microbiol53:1449–1456[CrossRef]
    [Google Scholar]
  3. Blackall P. J, Christensen H, Beckenham T, Blackall L. L, Bisgaard M. 2005; Reclassification of Pasteurella gallinarum , [ Haemophilus ] paragallinarum , Pasteurella avium and Pasteurella volantium as Avibacterium gallinarum gen.nov., comb. nov., Avibacterium paragallinarum comb. nov., Avibacterium avium comb. nov. and Avibacterium volantium comb. nov. Int J Syst Evol Microbiol55:353–362[CrossRef]
    [Google Scholar]
  4. Brenner D. J, McWhorter A. C, Knutson J. K, Steigerwalt A. G. 1982; Escherichia vulneris : a new species of Enterobacteriaceae associated with human wounds. J Clin Microbiol15:1133–1140
    [Google Scholar]
  5. Christensen H, Bisgaard M. 2004; Revised definition of Actinobacillus sensu stricto isolated from animals. A review with special emphasis on diagnosis. Vet Microbiol99:13–30[CrossRef]
    [Google Scholar]
  6. Christensen H, Bisgaard M, Olsen J. E. 2002; Reclassification of equine isolates previously reported as Actinobacillus equuli , variants of A. equuli , A. suis or taxon 11 of Bisgaard and proposal of two subspecies of A. equuli : A. equuli subsp. equuli and A. equuli subsp. haemolyticus . Int J Syst Evol Microbiol52:1569–1576[CrossRef]
    [Google Scholar]
  7. Christensen H, Bisgaard M, Bojesen A. M, Mutters R, Olsen J. E. 2003a; Genetic relationships among avian isolates classified as Pasteurella haemolytica , ‘ Actinobacillus salpingitidis ’ or Pasteurella anatis with proposal of Gallibacterium anatis gen. nov., comb. nov. and description of additional genomospecies within Gallibacterium gen. nov. Int J Syst Evol Microbiol53:275–287[CrossRef]
    [Google Scholar]
  8. Christensen H, Foster G, Christensen J. P, Pennycott T, Olsen J. E, Bisgaard M. 2003b; Phylogenetic analysis by 16S rDNA gene sequence comparison of avian taxa of Bisgaard and characterization and description of two new taxa of Pasteurellaceae . J Appl Microbiol95:354–363[CrossRef]
    [Google Scholar]
  9. Christensen H, Bisgaard M, Aalbaek B, Olsen J. E. 2004a; Reclassification of Bisgaard taxon 33 with proposal of Volucribacter psittacicida gen.nov., sp. nov. and Volucribacter amazonae sp. nov. as new members of Pasteurellaceae . Int J Syst Evol Microbiol54:813–818[CrossRef]
    [Google Scholar]
  10. Christensen H, Kuhnert P, Olsen J. E, Bisgaard M. 2004b; Comparative phylogenies of the housekeeping genes atpD , infB and rpoB and the 16S rRNA gene within the Pasteurellaceae . Int J Syst Evol Microbiol54:1601–1609[CrossRef]
    [Google Scholar]
  11. Davies R. L. 2004; Genetic diversity among Pasteurella multocida strains of avian, bovine, ovine and porcine origin from England and Wales by comparative sequence analysis of the 16S rRNA gene. Microbiology150:4199–4210[CrossRef]
    [Google Scholar]
  12. Donachie W, Lainson F. A, Hodgson J. C. 1995; Haemophilus, Actinobacillus, and Pasteurella New York: Plenum;
    [Google Scholar]
  13. Fleischmann R. D, Adams M. D, White O.7 other authors 1995; Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science269:496–512[CrossRef]
    [Google Scholar]
  14. Gautier A. L, Dubois D, Escande F, Avril J. L, Trieu-Cuot P, Gaillot O. 2005; Rapid and accurate identification of human isolates of Pasteurella and related species by sequencing the sodA gene. J Clin Microbiol43:2307–2314[CrossRef]
    [Google Scholar]
  15. Gevers D, Cohan F. M, Lawrence J. G.8 other authors 2005; Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol3:733–739[CrossRef]
    [Google Scholar]
  16. Goodfellow M, Manfio G. P, Chun J. 1997; Towards a practical species concept for cultivable bacteria. In Species: the Units of Biodiversity pp 25–59 Edited by Claridge M. F., Dawah H. A., Wilson M. R.. London: Chapman and Hall;
    [Google Scholar]
  17. Hedegaard J, Okkels H, Bruun B, Kilian M, Mortensen K. K, Norskov-Lauritsen N. 2001; Phylogeny of the genus Haemophilus as determined by comparison of partial infB sequences. Microbiology147:2599–2609
    [Google Scholar]
  18. Hong S. H, Kim J. S, Lee S. Y.7 other authors 2004; The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens . Nat Biotechnol22:1275–1281[CrossRef]
    [Google Scholar]
  19. Korczak B, Christensen H, Emler S, Frey J, Kuhnert P. 2004; Phylogeny of the family Pasteurellaceae based on rpoB sequences. Int J Syst Evol Microbiol54:1393–1399[CrossRef]
    [Google Scholar]
  20. Korczak B. M, Stieber R, Emler S, Burnens A. P, Frey J, Kuhnert P. 2006; Genetic relatedness within the genus Campylobacter inferred from rpoB sequences. Int J Syst Evol Microbiol56:937–945[CrossRef]
    [Google Scholar]
  21. Kuhnert P, Boerlin P, Emler S, Krawinkler M, Frey J. 2000; Phylogenetic analysis of Pasteurella multocida subspecies and molecular identification of feline P. multocida subsp. septica by 16S rRNA gene sequencing. Int J Med Microbiol290:599–604[CrossRef]
    [Google Scholar]
  22. Kuhnert P, Frey J, Lang N. P, Mayfield L. 2002; A phylogenetic analysis of Prevotella nigrescens , Prevotella intermedia and Porphyromonas gingivalis field strains reveals a clear species clustering. Int J Syst Evol Microbiol52:1391–1395[CrossRef]
    [Google Scholar]
  23. Kuhnert P, Korczak B, Falsen E, Straub R, Hoops A, Boerlin P, Frey J, Mutters R. 2004; Nicoletella semolina gen.nov., sp.nov., a new member of Pasteurellaceae isolated from horses with airway disease. J Clin Microbiol42:5542–5548[CrossRef]
    [Google Scholar]
  24. May B. J, Zhang Q, Li L. L, Paustian M. L, Whittam T. S, Kapur V. 2001; Complete genomic sequence of Pasteurella multocida , Pm70. Proc Natl Acad Sci U S A98:3460–3465[CrossRef]
    [Google Scholar]
  25. Moller K, Fussing V, Grimont P. A. D, Paster B. J, Dewhirst F. E, Kilian M. 1996; Actinobacillus minor sp. nov., Actinobacillus porcinus sp. nov., and Actnobacillus indolicus sp. nov., three new V factor-dependent species from the respiratory tract of pigs. Int J Syst Bacteriol46:951–956[CrossRef]
    [Google Scholar]
  26. Mutters R, Mannheim W, Bisgaard M. 1989; Taxonomy of the group. In Pasteurella and Pasteurellosis pp 3–34 Edited by Adlam C., Rutter J. M.. London: Academic Press;
    [Google Scholar]
  27. Norskov-Lauritsen N, Christensen H, Okkels H, Kilian M, Bruun B. 2004; Delineation of the genus Actinobacillus by comparison of partial infB sequences. Int J Syst Evol Microbiol54:635–644[CrossRef]
    [Google Scholar]
  28. Olsen I, Dewhirst F. E, Paster B. J, Busse H. J. 2005; Family Pasteurellaceae. In Bergey's Manual of Systematic Bacteriology Edited by Garrity R.. New York: Springer;
    [Google Scholar]
  29. Olsen I, Moller K. 2005; Genus Actinobacillus Brumpt 1919, 849[sup]AL[/sup]. In Bergey's Manual of Systematic Bacteriology Edited by Garrity R.. New York: Springer;
    [Google Scholar]
  30. Pohl S. 1981; DNA relatedness among members of Haemophilus , Pasteurella and Actinobacillus. In Haemophilus , Pasteurella and Actinobacillus p. 253 Edited by Kilian M., Frederiksen W., Biberstein E. L.. London: Academic Press;
    [Google Scholar]
  31. Stackebrandt E, Frederiksen W, Garrity G. M.10 other authors 2002; Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol52:1043–1047[CrossRef]
    [Google Scholar]
  32. Thompson J. D, Gibson T. J, Plewniak F, Jeanmougin F, Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res25:4876–4882[CrossRef]
    [Google Scholar]
  33. Wayne L. G, Brenner D. J, Colwell R. R.9 other authors 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol37:463–464[CrossRef]
    [Google Scholar]
  34. Zeigler D. R. 2003; Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol53:1893–1900[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.28991-0
Loading
/content/journal/micro/10.1099/mic.0.28991-0
Loading

Data & Media loading...

Most cited this month 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