Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae

References

1. Angen Ø., 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 Bacteriol 49:67–86 [CrossRef]
   [Google Scholar]
2. Angen Ø., 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 Microbiol 53:1449–1456 [CrossRef]
   [Google Scholar]
3. Bisgaard M. 1993; Ecology and significance of Pasteurellaceae in animals. Zentbl Bakteriol 279:7–26 [CrossRef]
   [Google Scholar]
4. Christensen H., Bisgaard M. 2003 The genus Pasteurella . In The Prokaryotes: an Evolving Electronic Resource for the Microbiological Community , release 3.13 Edited by Dworkin M., Lyons C. New York: Springer; http://141.150.157.117 : 8080/prokPUB/index.htm
   [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 Microbiol 99:13–30 [CrossRef]
   [Google Scholar]
6. Christensen H., Olsen J. E. 1998; Phylogenetic relationships of Salmonella based on DNA sequence comparison of atpD encoding the β subunit of ATP synthase. FEMS Microbiol Lett 161:89–96
   [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 Microbiol 53:275–287 [CrossRef]
   [Google Scholar]
8. Christensen H., Foster G., Christensen J. P., Olsen J. E., Bisgaard M. 2003b; Characterization of bacteria associated with birds including phylogenetic analysis by 16S rRNA sequence comparison and the description of two new taxa of Pasteurellaceae . J Appl Microbiol 95:354–363 [CrossRef]
   [Google Scholar]
9. Christensen H., Bisgaard M., Aalbæk B., Olsen J. E. 2004; Reclassification of Bisgaard taxon 33, with proposal of Volucribacter psittacicida gen.nov., sp. nov. and Volucribacter amazonae sp. nov. as new members of the Pasteurellaceae . Int J Syst Evol Microbiol54813–818 [CrossRef]
   [Google Scholar]
10. Dauga C. 2002; Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae : a model molecule for molecular systematic studies. Int J Syst Evol Microbiol 52:531–547
    [Google Scholar]
11. De Ley J., Mannheim W., Mutters R. 7 other authors 1990; Inter- and intrafamilial similarities of rRNA cistrons of the Pasteurellaceae . Int J Syst Bacteriol 40:126–137 [CrossRef]
    [Google Scholar]
12. Dewhirst F. E., Paster B. J., Olsen I., Fraser G. J. 1992; Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences. J Bacteriol 174:2002–2013
    [Google Scholar]
13. Dewhirst F. E., Paster B. J., Olsen I., Fraser G. J. 1993; Phylogeny of the Pasteurellaceae as determined by comparison of 16S ribosomal ribonucleic acid sequences. Zentbl Bakteriol 279:35–44 [CrossRef]
    [Google Scholar]
14. Doolittle W. F. 1999; Phylogenetic classification and the universal tree. Science 284:2124–2128 [CrossRef]
    [Google Scholar]
15. Felsenstein J. 1995 phylip (Phylogeny Inference Package), version 3.5c. Distributed by the author Department of Genetics, University of Washington; Seattle, USA:
    [Google Scholar]
16. Foster G., Ross H. M., Malnick H., Willems A., Hutson R. A., Reid R. J., Collins M. D. 2000; Phocoenobacter uteri gen. nov., sp. nov. a new member of the family Pasteurellaceae Pohl (1979) 1981 isolated from a harbour porpoise ( Phocoena phocoena . Int J Syst Evol Microbiol 50:135–139 [CrossRef]
    [Google Scholar]
17. Fox G. E., Wisotzkey J. D., Jurtshuk P. Jr 1992; How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170 [CrossRef]
    [Google Scholar]
18. Frey J., Kuhnert P. 2002; RTX toxins in Pasteurellaceae . Int J Med Microbiol 292:149–158 [CrossRef]
    [Google Scholar]
19. Garcia-Vallvé S., Romeu A., Palau J. 2000; Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 10:1719–1725 [CrossRef]
    [Google Scholar]
20. Garrity G. M., Holt J. G. 2001; The road map to the Manual . In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol 1 pp  119–166 Edited by Boone D. R., Castenholz R. W., Garrity G. M. New York: Springer;
    [Google Scholar]
21. Guettler M. V., Rumler D., Jain M. K. 1999; Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing strain from the bovine rumen. Int J Syst Bacteriol 49:207–216 [CrossRef]
    [Google Scholar]
22. Hedegaard J., Steffensen S. A. de A., Nørskov-Lauritsen N., Mortensen K. K., Sperling-Petersen H. U. 1999; Identification of Enterobacteriaceae by partial sequencing of the gene encoding translation initiation factor 2. Int J Syst Bacteriol 49:1531–1538 [CrossRef]
    [Google Scholar]
23. Hedegaard J., Okkels H., Bruun B., Kilian M., Mortensen K. K., Nørskov-Lauritsen N. 2001; Phylogeny of the genus Haemophilus as determined by comparison of partial infB sequences. Microbiology 147:2599–2609
    [Google Scholar]
24. Henz S. R., Auch A. F., Huson D. H., Nieselt-Struwe K., Schuster S. C. 2003; Whole genome-based prokaryotic phylogeny. In Abstracts of the European Conference on Computational Computing Paris: 27–30 September 2003
    [Google Scholar]
25. Huelsenbeck J. P., Chandall K. A. 1997; Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Evol Syst 28:437–466 [CrossRef]
    [Google Scholar]
26. Klenk H. P., Zillig W. 1994; DNA-dependent RNA polymerase subunit B as a tool for phylogenetic reconstructions: branching topology of the archaeal domain. J Mol Evol 38:420–432 [CrossRef]
    [Google Scholar]
27. Korczak B., Christensen H., Emler S., Frey J., Kuhnert P. 2004; Phylogeny of the family Pasteurellaceae based on rpoB sequences. Int J Syst Evol Microbiol 54:1393–1399 [CrossRef]
    [Google Scholar]
28. Laalami S., Putzer H., Plumbridge J. A., Grunberg-Manago M. 1991; A severely truncated form of translational initiation factor 2 supports growth of Escherichia coli . J Mol Biol 220:335–340 [CrossRef]
    [Google Scholar]
29. Ludwig W., Klenk H.-P. 2001; Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol 1 pp  49–65 Edited by Boone D. R., Castenholz R. W., Garrity G. M. New York: Springer;
    [Google Scholar]
30. Ludwig W., Neumaier J., Klugbauer N. 9 other authors 1993; Phylogenetic relationships of Bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes. Antonie van Leeuwenhoek 64:285–305
    [Google Scholar]
31. March P. E., Inouye M. 1985; GTP-binding membrane protein of Escherichia coli with sequence homology to initiation factor 2 and elongation factors Tu and G. Proc Natl Acad Sci U S A 82:7500–7504 [CrossRef]
    [Google Scholar]
32. Møller 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 Actinobacillus indolicus sp. nov., three new V factor-dependent species from the respiratory tract of pigs. Int J Syst Bacteriol 46:951–956 [CrossRef]
    [Google Scholar]
33. Mollet C., Drancourt M., Raoult D. 1997; rpoB sequence analysis as a novel basis for bacterial identification. Mol Microbiol 26:1005–1011 [CrossRef]
    [Google Scholar]
34. Nørskov-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 Microbiol 54:635–644 [CrossRef]
    [Google Scholar]
35. Olsen G. J., Matsuda H., Hagstrom R., Overbeek R. 1994; FastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 10:41–48
    [Google Scholar]
36. Olsen I., Dewhirst F. E., Paster B. J., Busse H.-J. 2004; Family Pasteurellaceae . In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol 2 Edited by Garrity G. R. New York: Springer; (in press
    [Google Scholar]
37. Petersen K. D., Christensen H., Bisgaard M., Olsen J. E. 2001; Genetic diversity of Pasteurella multocida fowl cholera isolates as demonstrated by ribotyping and 16S rRNA and partial atpD sequence comparisons. Microbiology 147:2739–2748
    [Google Scholar]
38. Pohl S. 1981; DNA relatedness among members of Haemophilus , Pasteurella and Actinobacillus . In Haemophilus, Pasteurella and Actinobacillus pp  245–253 Edited by Kilian M., Frederiksen W., Biberstein E. L. London: Academic Press;
    [Google Scholar]
39. Rivera M. C., Jain R., Moore J. E., Lake J. A. 1998; Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci U S A 95:6239–6244 [CrossRef]
    [Google Scholar]
40. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacterial 44:846–849 [CrossRef]
    [Google Scholar]
41. Woese C. 1987; Bacterial evolution. Bacteriol Rev 51:221–271
    [Google Scholar]
42. Zeigler D. R. 2003; Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900 [CrossRef]
    [Google Scholar]