16S–23S rRNA gene internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Porphyromonas

References

1. Boyer S. L., Flechtner V. R., Johansen J. R. 2001; Is the 16S-23S rRNA internal transcribed spacer region a good tool for use in molecular systematics and population genetics? A case study in cyanobacteria. Mol Biol Evol 18:1057–1069 [CrossRef]
   [Google Scholar]
2. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T. J., Higgins D. G., Thompson J. D. 2003; Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497–3500 [CrossRef]
   [Google Scholar]
3. Christensen H., Moller P. L., Vogensen F. K., Olsen J. E. 2000; Sequence variation of the 16S to 23S rRNA spacer region in Salmonella enterica . Res Microbiol 151:37–42 [CrossRef]
   [Google Scholar]
4. Conrads G., Claros M. C., Citron D. M., Tyrrell K. L., Merriam V., Goldstein E. J. C. 2002; 16S–23S rDNA internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Fusobacterium . Int J Syst Evol Microbiol 52:493–499
   [Google Scholar]
5. Finegold S. M., Jousimies-Somer H. 1997; Recently described clinically important anaerobic bacteria: medical aspects. Clin Infect Dis 25:S88–S93 [CrossRef]
   [Google Scholar]
6. Finegold S. M., Vaisanen M. L., Rautio M., Eerola E., Summanen P., Molitoris D., Song Y., Liu C., Jousimies-Somer H. 2004; Porphyromonas uenonis sp. nov., a pathogen for humans distinct from P. asaccharolytica and P. endodontalis . J Clin Microbiol 42:5298–5301 [CrossRef]
   [Google Scholar]
7. Fournier D., Mouton C., Lapierre P., Kato T., Okuda K., Menard C. 2001; Porphyromonas gulae sp. nov., an anaerobic, Gram-negative coccobacillus from the gingival sulcus of various animal hosts. Int J Syst Evol Microbiol 51:1179–1189 [CrossRef]
   [Google Scholar]
8. Graham T. A., Golsteyn-Thomas E. J., Thomas J. E., Gannon V. P. 1997; Inter- and intraspecies comparison of the 16S-23S rRNA operon intergenic spacer regions of six Listeria spp. Int J Syst Bacteriol 47:863–869 [CrossRef]
   [Google Scholar]
9. Guasp C., Moore E. R. B., Lalucat J., Bennasar A. 2000; Utility of internally transcribed 16S–23S rDNA spacer regions for the definition of Pseudomonas stutzeri genomovars and other Pseudomonas species. Int J Syst Evol Microbiol 50:1629–1639 [CrossRef]
   [Google Scholar]
10. Gurtler V., Rao Y., Pearson S. R., Bates S. M., Mayall B. C. 1999; DNA sequence heterogeneity in the three copies of the long 16S–23S rDNA spacer of Enterococcus faecalis isolates. Microbiology 145:1785–1796 [CrossRef]
    [Google Scholar]
11. Iteman I., Rippka R., Tandeau De Marsac N., Herdman M. 2000; Comparison of conserved structural and regulatory domains within divergent 16S rRNA–23S rRNA spacer sequences of cyanobacteria. Microbiology 146:1275–1286
    [Google Scholar]
12. Jousimies-Somer H. R. 1995; Update on the taxonomy and the clinical and laboratory characteristics of pigmented anaerobic gram-negative rods. Clin Infect Dis 20:S187–S191 [CrossRef]
    [Google Scholar]
13. Jousimies-Somer H. 1997; Recently described clinically important anaerobic bacteria: taxonomic aspects and update. Clin Infect Dis 25:S78–S87 [CrossRef]
    [Google Scholar]
14. Jousimies-Somer H., Summanen P. 2002; Recent taxonomic changes and terminology update of clinically significant anaerobic gram-negative bacteria (excluding spirochetes). Clin Infect Dis 35:S17–S21 [CrossRef]
    [Google Scholar]
15. Jousimies-Somer H. R., Summanen P., Finegold S. M. 1995; Bacteroides levii -like organisms isolated from clinical specimens. Clin Infect Dis 20:S208–S209 [CrossRef]
    [Google Scholar]
16. Jousimies-Somer H., Summanen P., Citron D. M., Baron E. J., Wexler H. M., Finegold S. M. (editors) 2002 Wadsworth-KTL Anaerobic Bacteriology Manual , 6th edn. Belmont: Star Publishing;
    [Google Scholar]
17. Lowe T. M., Eddy S. R. 1997; tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964 [CrossRef]
    [Google Scholar]
18. Ludwig W., Strunk O., Westram R. 29 other authors 2004; arb: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [CrossRef]
    [Google Scholar]
19. Motoyama Y., Ogata T. 2000; 16S–23S rDNA spacer of Pectinatus , Selenomonas and Zymophilus reveal new phylogenetic relationships between these genera. Int J Syst Evol Microbiol 50:883–886 [CrossRef]
    [Google Scholar]
20. Nadkarni M. A., Martin F. E., Jacques N. A., Hunter N. 2002; Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148:257–266
    [Google Scholar]
21. Nicholas K. B., Nicholas H. B. J. 1997; GeneDoc: a tool for editing and annotation multiple sequence alignments. Distributed by the authors http://www.psc.edu/biomed/genedoc
22. Page R. D. 1996; TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
    [Google Scholar]
23. Sakamoto M., Suzuki M., Umeda M., Ishikawa L., Benno Y. 2002; Reclassification of Bacteroides forsythus (Tanner et al . 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov.. Int J Syst Evol Microbiol 52:841–849 [CrossRef]
    [Google Scholar]
24. Soller R., Hirsch P., Blohm D., Labrenz M. 2000; Differentiation of newly described Antarctic bacterial isolates related to Roseobacter species based on 16S–23S rDNA internal transcribed spacer sequences. Int J Syst Evol Microbiol 50:909–915 [CrossRef]
    [Google Scholar]
25. Vaisanen M. L., Kiviranta M., Summanen P., Finegold S. M., Jousimies-Somer H. R. 1997; Porphyromonas endodontalis -like organisms from extraoral sources. Clin Infect Dis 25:S191–S193 [CrossRef]
    [Google Scholar]
26. Willems A., Collins M. D. 1995; Reclassification of Oribaculum catoniae (Moore and Moore 1994) as Porphyromonas catoniae comb. nov. and emendation of the genus Porphyromonas . Int J Syst Bacteriol 45:578–581 [CrossRef]
    [Google Scholar]