Table of Contents Author Guidelines Submit a Manuscript
International Journal of Genomics
Volume 2015, Article ID 198560, 15 pages
http://dx.doi.org/10.1155/2015/198560
Research Article

Phylogenomic and Molecular Demarcation of the Core Members of the Polyphyletic Pasteurellaceae Genera Actinobacillus, Haemophilus, and Pasteurella

Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8N 3Z5

Received 5 November 2014; Revised 19 January 2015; Accepted 26 January 2015

Academic Editor: John Parkinson

Copyright © 2015 Sohail Naushad et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. C. Parte, “LPSN—list of prokaryotic names with standing in nomenclature,” Nucleic Acids Research, vol. 42, no. 1, pp. D613–D616, 2014. View at Publisher · View at Google Scholar · View at Scopus
  2. K. Muehldorfer, S. Speck, and G. Wibbelt, “Proposal of Vespertiliibacter pulmonis gen. nov., sp. nov. and two genomospecies as new members of the family Pasteurellaceae isolated from European bats,” International Journal of Systematic and Evolutionary Microbiology, vol. 64, no. 7, pp. 2424–2430, 2014. View at Publisher · View at Google Scholar
  3. S. M. Spinola, M. E. Bauer, and R. S. Munson Jr., “Immunopathogenesis of Haemophilus ducreyi infection (chancroid),” Infection and Immunity, vol. 70, no. 4, pp. 1667–1676, 2002. View at Publisher · View at Google Scholar · View at Scopus
  4. H. Christensen and M. Bisgaard, “Molecular classification and its impact on diagnostics and understanding the phylogeny and epidemiology of selected members of Pasteurellaceoe of veterinary importance,” Berliner und Münchener Tierärztliche Wochenschrift, vol. 123, no. 1-2, pp. 20–30, 2010. View at Google Scholar · View at Scopus
  5. N. Nørskov-Lauritsen, “Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans,” Clinical Microbiology Reviews, vol. 27, no. 2, pp. 214–240, 2014. View at Publisher · View at Google Scholar · View at Scopus
  6. B. Henderson, J. M. Ward, and D. Ready, “Aggregatibacter (Actinobacillus) actinomycetemcomitans: a triple A* periodontopathogen?” Periodontology 2000, vol. 54, no. 1, pp. 78–105, 2010. View at Publisher · View at Google Scholar · View at Scopus
  7. Ø. Angen, R. Mutters, D. A. Caugant, J. E. Olsen, and M. Bisgaard, “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.,” International Journal of Systematic Bacteriology, vol. 49, no. 1, pp. 67–86, 1999. View at Publisher · View at Google Scholar · View at Scopus
  8. J. T. Bossé, H. Janson, B. J. Sheehan et al., “Actinobacillus pleuropneumoniae: pathobiology and pathogenesis of infection,” Microbes and Infection, vol. 4, no. 2, pp. 225–235, 2002. View at Publisher · View at Google Scholar · View at Scopus
  9. B. A. Wilson and M. Ho, “Pasteurella multocida: from zoonosis to cellular microbiology,” Clinical Microbiology Reviews, vol. 26, no. 3, pp. 631–655, 2013. View at Publisher · View at Google Scholar · View at Scopus
  10. S. Pohl, Reklassifizierung der gattung Actinobacillus Brumpt 1910, Haemophilus Winslow et al. 1971 und Pasteurella Trevisan 1887 anhand phänotypischer und molekularer daten, insbesondere der DNS-verwandtschaften bei DNS: DNS-hybridisierung in vitro und vorschlag einer neuen familie, Pasteurellaceae [Inaug. Diss.], Philipps-Universität, Marburg, Germany, 1979.
  11. W. Mannheim, S. Pohl, and R. Holländer, “On the taxonomy of Actinobacillus, Haemophilus, and Pasteurella: DNA base composition, respiratory quinones, and biochemical reactions of representative collection cultures (author's transl),” Zentralblatt für Bakteriologie A, vol. 246, no. 4, pp. 512–540, 1979. View at Google Scholar
  12. F. E. Dewhirst, B. J. Paster, I. Olsen, and G. J. Fraser, “Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences,” Journal of Bacteriology, vol. 174, no. 6, pp. 2002–2013, 1992. View at Google Scholar · View at Scopus
  13. I. Olsen, F. E. Dewhirst, B. J. Paster, and H. J. Busse, “Family I. Pasteurellaceae,” in Bergey's Manual of Systematic Bacteriology, D. J. Brenner, N. R. Krieg, G. M. Garrity, and J. T. Staley, Eds., vol. 2, pp. 851–856, Springer, New York, NY, USA, 2nd edition, 2005. View at Google Scholar
  14. F. E. Dewhirst, B. J. Paster, I. Olsen, and G. J. Fraser, “Phylogeny of the Pasteurellaceae as determined by comparison of 16S ribosomal ribonucleic acid sequences,” Zentralblatt für Bakteriologie, vol. 279, no. 1, pp. 35–44, 1993. View at Publisher · View at Google Scholar · View at Scopus
  15. H. Christensen, P. Kuhnert, J. E. Olsen, and M. Bisgaard, “Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae,” International Journal of Systematic and Evolutionary Microbiology, vol. 54, no. 5, pp. 1601–1609, 2004. View at Publisher · View at Google Scholar · View at Scopus
  16. B. Korczak, H. Christensen, S. Emler, J. Frey, and P. Kuhnert, “Phylogeny of the family Pasteurellaceae based on rpoB sequences,” International Journal of Systematic and Evolutionary Microbiology, vol. 54, no. 4, pp. 1393–1399, 2004. View at Publisher · View at Google Scholar · View at Scopus
  17. P. Kuhnert and B. M. Korczak, “Prediction of whole-genome DNA-DNA similarity, determination of G + C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA),” Microbiology, vol. 152, no. 9, pp. 2537–2548, 2006. View at Publisher · View at Google Scholar · View at Scopus
  18. H. Christensen, P. Kuhnert, H. J. Busse, W. C. Frederiksen, and M. Bisgaard, “Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae,” International Journal of Systematic and Evolutionary Microbiology, vol. 57, no. 1, pp. 166–178, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. M. P. D. Bonaventura, E. K. Lee, R. DeSalle, and P. J. Planet, “A whole-genome phylogeny of the family Pasteurellaceae,” Molecular Phylogenetics and Evolution, vol. 54, no. 3, pp. 950–956, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. H. S. Naushad and R. S. Gupta, “Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades,” Antonie van Leeuwenhoek, vol. 101, no. 1, pp. 105–124, 2012. View at Publisher · View at Google Scholar · View at Scopus
  21. N. Nørskov-Lauritsen and M. Kilian, “Reclassification of Actinobacillus actinomycetemcomitans, Haemophilus aphrophilus, Haemophilus paraphrophilus and Haemophilus segnis as Aggregatibacter actinomycetemcomitans gen. nov., comb. nov., Aggregatibacter aphrophilus comb. nov. and Aggregatibacter segnis comb. nov., and emended description of Aggregatibacter aphrophilus to include V factor-dependent and V factor-independent isolates,” International Journal of Systematic and Evolutionary Microbiology, vol. 56, no. 9, pp. 2135–2146, 2006. View at Publisher · View at Google Scholar · View at Scopus
  22. P. J. Blackall, H. Christensen, T. Beckenham, L. L. Blackall, and M. Bisgaard, “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,” International Journal of Systematic and Evolutionary Microbiology, vol. 55, no. 1, pp. 353–362, 2005. View at Publisher · View at Google Scholar · View at Scopus
  23. Ø. Angen, P. Ahrens, P. Kuhnert, H. Christensen, and R. Mutters, “Proposal of Histophilus somni gen. nov., sp. nov. for the three species incertae sedis ‘Haemophilus somnus’, ‘Haemophilus agni’ and ‘Histophilus ovis’,” International Journal of Systematic and Evolutionary Microbiology, vol. 53, no. 5, pp. 1449–1456, 2003. View at Publisher · View at Google Scholar · View at Scopus
  24. S. Pohl, H. U. Bertschinger, W. Frederiksen, and W. Mannheim, “Transfer of Haemophilus pleuropneumoniae and the Pasteurella haemolytica-like organism causing porcine necrotic pleuropneumonia to the genus Actinobacillus (Actinobacillus pleuropneumoniae comb. nov.) on the basis of phenotypic and deoxyribonucleic acid relatedness,” International Journal of Systematic Bacteriology, vol. 33, no. 3, pp. 510–514, 1983. View at Publisher · View at Google Scholar · View at Scopus
  25. H. Christensen, M. Bisgaard, A. M. Bojesen, R. Mutters, and J. E. Olsen, “Genetic relationship 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 with Gallibacterium gen. nov,” International Journal of Systematic and Evolutionary Microbiology, vol. 53, no. 1, pp. 275–287, 2003. View at Publisher · View at Google Scholar · View at Scopus
  26. P. J. Blackall, A. M. Bojesen, H. Christensen, and M. Bisgaard, “Reclassification of [Pasteurella] trehalosi as Bibersteinia trehalosi gen. nov., comb. nov,” International Journal of Systematic and Evolutionary Microbiology, vol. 57, no. 4, pp. 666–674, 2007. View at Publisher · View at Google Scholar · View at Scopus
  27. R. Mutters, S. Pohl, and W. Mannheim, “Transfer of Pasteurella ureae Jones 1962 to the genus Actinobacillus Brumpt 1910: Actinobacillus ureae comb. nov.,” International Journal of Systematic Bacteriology, vol. 36, no. 2, pp. 343–344, 1986. View at Publisher · View at Google Scholar · View at Scopus
  28. H. Christensen and P. Kuhnert, “International committee on systematics of prokaryotes. Subcommittee on the taxonomy of Pasteurellaceae. Minutes of the meetings, 25 August 2011, Elsinore, Denmark,” International Journal of Systematic and Evolutionary Microbiology, vol. 62, no. 1, pp. 257–258, 2012. View at Publisher · View at Google Scholar · View at Scopus
  29. J. Hedegaard, H. Okkels, B. Bruun, M. Kilian, K. K. Mortensen, and N. Nørskov-Lauritsen, “Phylogeny of the genus Haemophilus as determined by comparison of partial infB sequences,” Microbiology, vol. 147, no. 9, pp. 2599–2609, 2001. View at Google Scholar · View at Scopus
  30. N. Nørskov-Lauritsen, B. Bruun, and M. Kilian, “Multilocus sequence phylogenetic study of the genus Haemophilus with description of Haemophilus pittmaniae sp. nov,” International Journal of Systematic and Evolutionary Microbiology, vol. 55, no. 1, pp. 449–456, 2005. View at Publisher · View at Google Scholar · View at Scopus
  31. V. Cattoir, O. Lemenand, J.-L. Avril, and O. Gaillot, “The sodA gene as a target for phylogenetic dissection of the genus Haemophilus and accurate identification of human clinical isolates,” International Journal of Medical Microbiology, vol. 296, no. 8, pp. 531–540, 2006. View at Publisher · View at Google Scholar · View at Scopus
  32. M. Kilian, “Genus III. Haemophilus,” in Bergey's Manual of Systematic Bacteriology, D. J. Brenner, N. R. Krieg, G. M. Garrity, and J. T. Staley, Eds., vol. 2, pp. 883–904, Springer, New York, NY, USA, 2nd edition, 2005. View at Google Scholar
  33. N. Nørskov-Lauritsen, B. Bruun, C. Andersen, and M. Kilian, “Identification of haemolytic Haemophilus species isolated from human clinical specimens and description of Haemophilus sputorum sp. nov,” International Journal of Medical Microbiology, vol. 302, no. 2, pp. 78–83, 2012. View at Publisher · View at Google Scholar · View at Scopus
  34. R. D. Fleischmann, M. D. Adams, O. White et al., “Whole-genome random sequencing and assembly of Haemophilus influenzae Rd,” Science, vol. 269, no. 5223, pp. 496–512, 1995. View at Publisher · View at Google Scholar · View at Scopus
  35. A. R. Wattam, D. Abraham, O. Dalay et al., “PATRIC, the bacterial bioinformatics database and analysis resource,” Nucleic Acids Research, vol. 42, no. 1, pp. D581–D591, 2014. View at Publisher · View at Google Scholar · View at Scopus
  36. NCBI, NCBI Genome Database, 2014, http://www.ncbi.nlm.nih.gov/genome/.
  37. NCBI, NCBI Nucleotide Database, 2014, http://www.ncbi.nlm.nih.gov/nuccore/.
  38. R. C. Edgar, “MUSCLE: multiple sequence alignment with high accuracy and high throughput,” Nucleic Acids Research, vol. 32, no. 5, pp. 1792–1797, 2004. View at Publisher · View at Google Scholar · View at Scopus
  39. K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, “MEGA6: molecular evolutionary genetics analysis version 6.0,” Molecular Biology and Evolution, vol. 30, no. 12, pp. 2725–2729, 2013. View at Publisher · View at Google Scholar · View at Scopus
  40. S. J. Foote, J. T. Bossé, A. B. Bouevitch, P. R. Langford, N. M. Young, and J. H. E. Nash, “The complete genome sequence of Actinobacillus pleuropneumoniae L20 (serotype 5b),” Journal of Bacteriology, vol. 190, no. 4, pp. 1495–1496, 2008. View at Publisher · View at Google Scholar · View at Scopus
  41. Z. Xu, Y. Zhou, L. Li et al., “Genome biology of Actinobacillus pleuropneumoniae JL03, an isolate of serotype 3 prevalent in China,” PLoS ONE, vol. 3, no. 1, Article ID e1450, 2008. View at Publisher · View at Google Scholar · View at Scopus
  42. M. P. Di Bonaventura, R. DeSalle, M. Pop et al., “Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700,” Journal of Bacteriology, vol. 191, no. 14, pp. 4693–4694, 2009. View at Publisher · View at Google Scholar · View at Scopus
  43. C. Chen, W. Kittichotirat, Y. Si, and R. Bumgarner, “Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1,” Journal of Bacteriology, vol. 191, no. 23, pp. 7378–7379, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. C. Chen, W. Kittichotirat, W. Chen, J. S. Downey, Y. Si, and R. Bumgarner, “Genome sequence of naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1,” Journal of Bacteriology, vol. 192, no. 10, pp. 2643–2644, 2010. View at Publisher · View at Google Scholar · View at Scopus
  45. T. J. Johnson, C. Fernandez-Alarcon, A. M. Bojesen, L. K. Nolan, D. W. Trampel, and T. Seemann, “Complete genome sequence of Gallibacterium anatis strain UMN179, isolated from a laying hen with peritonitis,” Journal of Bacteriology, vol. 193, no. 14, pp. 3676–3677, 2011. View at Publisher · View at Google Scholar · View at Scopus
  46. I. K. Jordan, A. B. Conley, I. V. Antonov et al., “Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus,” Journal of Bacteriology, vol. 193, no. 20, pp. 5879–5880, 2011. View at Publisher · View at Google Scholar · View at Scopus
  47. F. R. Strouts, P. Power, N. J. Croucher et al., “Lineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptius,” Emerging Infectious Diseases, vol. 18, no. 3, pp. 449–457, 2012. View at Publisher · View at Google Scholar · View at Scopus
  48. J. S. Hogg, F. Z. Hu, B. Janto et al., “Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains,” Genome Biology, vol. 8, no. 6, article R103, 2007. View at Publisher · View at Google Scholar · View at Scopus
  49. A. Harrison, D. W. Dyer, A. Gillaspy et al., “Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: comparative study with H. influenzae serotyped, strain KW20,” Journal of Bacteriology, vol. 187, no. 13, pp. 4627–4636, 2005. View at Publisher · View at Google Scholar · View at Scopus
  50. M. Yue, F. Yang, J. Yang et al., “Complete genome sequence of Haemophilus parasuisSH0165,” Journal of Bacteriology, vol. 191, no. 4, pp. 1359–1360, 2009. View at Publisher · View at Google Scholar · View at Scopus
  51. J. F. Challacombe, A. J. Duncan, T. S. Brettin et al., “Complete genome sequence of Haemophilus somnus (Histophilus somni) strain 129Pt and comparison to Haemophilus ducreyi 35000HP and Haemophilus influenzae Rd,” Journal of Bacteriology, vol. 189, no. 5, pp. 1890–1898, 2007. View at Publisher · View at Google Scholar · View at Scopus
  52. S. H. Hong, J. S. Kim, S. Y. Lee et al., “The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens,” Nature Biotechnology, vol. 22, no. 10, pp. 1275–1281, 2004. View at Publisher · View at Google Scholar · View at Scopus
  53. J. Gioia, X. Qin, H. Jiang et al., “The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny,” Journal of Bacteriology, vol. 188, no. 20, pp. 7257–7266, 2006. View at Publisher · View at Google Scholar · View at Scopus
  54. B. J. May, Q. Zhang, L. L. Li, M. L. Paustian, T. S. Whittam, and V. Kapur, “Complete genomic sequence of Pasteurella multocida, Pm70,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 6, pp. 3460–3465, 2001. View at Publisher · View at Google Scholar · View at Scopus
  55. R. C. Edgar, “Search and clustering orders of magnitude faster than BLAST,” Bioinformatics, vol. 26, no. 19, Article ID btq461, pp. 2460–2461, 2010. View at Publisher · View at Google Scholar · View at Scopus
  56. K. Katoh and D. M. Standley, “MAFFT multiple sequence alignment software version 7: improvements in performance and usability,” Molecular Biology and Evolution, vol. 30, no. 4, pp. 772–780, 2013. View at Publisher · View at Google Scholar · View at Scopus
  57. M. N. Price, P. S. Dehal, and A. P. Arkin, “FastTree 2—approximately maximum-likelihood trees for large alignments,” PLoS ONE, vol. 5, no. 3, Article ID e9490, 2010. View at Publisher · View at Google Scholar · View at Scopus
  58. S. Whelan and N. Goldman, “A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach,” Molecular Biology and Evolution, vol. 18, no. 5, pp. 691–699, 2001. View at Publisher · View at Google Scholar · View at Scopus
  59. R. S. Gupta, “Identification of conserved indels that are useful for classification and evolutionary studies,” in Methods in Microbiology, vol. 41, pp. 153–182, Academic Press, 2014. View at Publisher · View at Google Scholar
  60. F. Jeanmougin, J. D. Thompson, M. Gouy, D. G. Higgins, and T. J. Gibson, “Multiple sequence alignment with Clustal X,” Trends in Biochemical Sciences, vol. 23, no. 10, pp. 403–405, 1998. View at Publisher · View at Google Scholar · View at Scopus
  61. E. Stackebrandt and J. Ebers, “Taxonomic parameters revisited: tarnished gold standards,” Microbiology Today, vol. 33, no. 4, p. 152, 2006. View at Google Scholar
  62. K. T. Konstantinidis and E. Stackebrandt, “Defining taxonomic ranks,” in The Prokaryotes, pp. 229–254, Springer, 2013. View at Google Scholar
  63. R. J. Redfield, W. A. Findlay, J. Bossé, J. S. Kroll, A. D. S. Cameron, and J. H. E. Nash, “Evolution of competence and DNA uptake specificity in the Pasteurellaceae,” BMC Evolutionary Biology, vol. 6, article 82, 2006. View at Publisher · View at Google Scholar · View at Scopus
  64. A. Rokas, B. I. Williams, N. King, and S. B. Carroll, “Genome-scale approaches to resolving incongruence in molecular phylogenies,” Nature, vol. 425, no. 6960, pp. 798–804, 2003. View at Publisher · View at Google Scholar · View at Scopus
  65. D. Wu, P. Hugenholtz, K. Mavromatis et al., “A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea,” Nature, vol. 462, no. 7276, pp. 1056–1060, 2009. View at Publisher · View at Google Scholar · View at Scopus
  66. P. Yilmaz, L. W. Parfrey, P. Yarza et al., “The SILVA and 'sll-species living tree project (LTP)' taxonomic frameworks,” Nucleic Acids Research, 2013. View at Publisher · View at Google Scholar
  67. B. Gao, R. Mohan, and R. S. Gupta, “Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria,” International Journal of Systematic and Evolutionary Microbiology, vol. 59, no. 2, pp. 234–247, 2009. View at Publisher · View at Google Scholar · View at Scopus
  68. A. M. Cutiño-Jiménez, M. Martins-Pinheiro, W. C. Lima, A. Martín-Tornet, O. G. Morales, and C. F. M. Menck, “Evolutionary placement of Xanthomonadales based on conserved protein signature sequences,” Molecular Phylogenetics and Evolution, vol. 54, no. 2, pp. 524–534, 2010. View at Publisher · View at Google Scholar · View at Scopus
  69. H. S. Naushad and R. S. Gupta, “Phylogenomics and molecular signatures for species from the plant pathogen-containing order Xanthomonadales,” PLoS ONE, vol. 8, no. 2, Article ID e55216, 2013. View at Publisher · View at Google Scholar · View at Scopus
  70. R. S. Gupta, “Applications of conserved indels for understanding microbial phylogeny,” in Molecular Phylogeny of Microorganisms, A. Oren and R. T. Papke, Eds., pp. 135–150, Caister Academic Press, Norfolk, UK, 2010. View at Google Scholar
  71. H. S. Naushad, B. Lee, and R. S. Gupta, “Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: Identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria,” International Journal of Systematic and Evolutionary Microbiology, vol. 64, no. 2, pp. 366–383, 2014. View at Publisher · View at Google Scholar · View at Scopus
  72. R. S. Gupta, “Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes,” Microbiology and Molecular Biology Reviews, vol. 62, no. 4, pp. 1435–1491, 1998. View at Google Scholar · View at Scopus
  73. A. Rokas and P. W. H. Holland, “Rare genomic changes as a tool for phylogenetics,” Trends in Ecology and Evolution, vol. 15, no. 11, pp. 454–459, 2000. View at Publisher · View at Google Scholar · View at Scopus
  74. R. S. Gupta and R. Lali, “Molecular signatures for the phylum Aquificae and its different clades: Proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacteriaceae,” Antonie van Leeuwenhoek, vol. 104, no. 3, pp. 349–368, 2013. View at Publisher · View at Google Scholar · View at Scopus
  75. R. S. Gupta, S. Mahmood, and M. Adeolu, “A phylogenomic and molecular signature based approach for characterization of the phylum spirochaetes and its major clades: proposal for a taxonomic revision of the phylum,” Frontiers in Microbiology, vol. 4, article 217, 2013. View at Publisher · View at Google Scholar · View at Scopus
  76. M. Adeolu and R. S. Gupta, “A phylogenomic and molecular marker based proposal for the division of the genus Borrelia into two genera: the emended genus Borrelia containing only the members of the relapsing fever Borrelia, and the genus Borreliella gen. nov. containing the members of the Lyme disease Borrelia (Borrelia burgdorferi sensu lato complex),” Antonie van Leeuwenhoek, vol. 105, no. 6, pp. 1049–1072, 2014. View at Publisher · View at Google Scholar · View at Scopus
  77. V. Bhandari and R. S. Gupta, “Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. Nov. and Petrotogales ord. Nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. Nov., Kosmotogaceae fam. Nov. and Petrotogaceae fam. Nov.) and a new genus Pseudothermotoga gen. Nov. with five new combinations,” Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, vol. 105, no. 1, pp. 143–168, 2014. View at Publisher · View at Google Scholar · View at Scopus
  78. I. Olsen, “Recent approaches to the chemotaxonomy of the Actinobacillus-Haemophilus-Pasteurella group (family Pasteurellaceae),” Oral Microbiology and Immunology, vol. 8, no. 6, pp. 327–336, 1993. View at Publisher · View at Google Scholar · View at Scopus
  79. N. Hayashimoto, M. Ueno, A. Tkakura, and T. Itoh, “Biochemical characterization and phylogenetic analysis based on 16S rRNA sequences for V-factor dependent members of Pasteurellaceae derived from laboratory rats,” Current Microbiology, vol. 54, no. 6, pp. 419–423, 2007. View at Publisher · View at Google Scholar · View at Scopus
  80. R. Mutters, W. Frederiksen, and W. Mannheim, “Taxonomy of the group,” in Pasturella and Pasteurellosis, C. Adlam and J. M. Rutter, Eds., pp. 3–34, Academic Press, London, UK, 1989. View at Google Scholar
  81. K. P. Snipes and E. L. Biberstein, “Pasteurella testudinis sp. nov.: a parasite of desert tortoises (Gopherus agassizi),” International Journal of Systematic Bacteriology, vol. 32, no. 2, pp. 201–210, 1982. View at Publisher · View at Google Scholar · View at Scopus
  82. Ø. Angen, P. Ahrens, and M. Bisgaard, “Phenotypic and genotypic characterization of Mannheimia (Pasteurella) haemolytica-like strains isolated from diseased animals in Denmark,” Veterinary Microbiology, vol. 84, no. 1-2, pp. 103–114, 2002. View at Publisher · View at Google Scholar · View at Scopus
  83. N. Z. Ahmod, R. S. Gupta, and H. N. Shah, “Identification of a Bacillus anthracis specific indel in the yeaC gene and development of a rapid pyrosequencing assay for distinguishing B. anthracis from the B. cereus group,” Journal of Microbiological Methods, vol. 87, no. 3, pp. 278–285, 2011. View at Publisher · View at Google Scholar · View at Scopus
  84. S. Y. Wong, A. Paschos, R. S. Gupta, and H. E. Schellhorn, “Insertion/deletion-based approach for the detection of Escherichia coli O157:H7 in freshwater environments,” Environmental Science & Technology, vol. 48, no. 19, pp. 11462–11470, 2014. View at Google Scholar
  85. B. Gao and R. S. Gupta, “Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria,” Microbiology and Molecular Biology Reviews, vol. 76, no. 1, pp. 66–112, 2012. View at Publisher · View at Google Scholar · View at Scopus
  86. M. Howard-Azzeh, L. Shamseer, H. E. Schellhorn, and R. S. Gupta, “Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives,” Photosynthesis Research, vol. 122, no. 2, pp. 171–185, 2014. View at Publisher · View at Google Scholar · View at Scopus