Reclassification of Xylanibacter oryzae Ueki et al. 2006 as Prevotella oryzae comb. nov., with an emended description of the genus Prevotella

References

1. Felsenstein J. 1985; Confidence limits of phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
   [Google Scholar]
2. Guindon S., Gascuel O. 2003; A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704 [View Article][PubMed]
   [Google Scholar]
3. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [View Article][PubMed]
   [Google Scholar]
4. Kitahara M., Tsuchida S., Kawasumi K., Amao H., Sakamoto M., Benno Y., Ohkuma M. 2011; Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces. Int J Syst Evol Microbiol 61:877–881 [View Article][PubMed]
   [Google Scholar]
5. Kitahara M., Sakamoto M., Tsuchida S., Kawasumi K., Amao H., Benno Y., Ohkuma M. 2012; Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces. Int J Syst Evol Microbiol 62:1145–1150 [View Article][PubMed]
   [Google Scholar]
6. Komagata K., Suzuki K. 1988; Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207 [View Article]
   [Google Scholar]
7. Krieg N. R. 2011; Family V. Prevotellaceae fam. nov. In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 4 p. 85 Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B. P., Paster B. J., Ward N. L., Ludwig W., Whitman W. B. New York: Springer;
   [Google Scholar]
8. Kuykendall L. D., Roy M. A., O’Neill J. J., Devine T. E. 1988; Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 38:358–361 [View Article]
   [Google Scholar]
9. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. et al. 2007; clustal w and clustal_x version 2.0. Bioinformatics 23:2947–2948 [View Article][PubMed]
   [Google Scholar]
10. Miller L. T. 1982; Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584–586[PubMed]
    [Google Scholar]
11. Morotomi M., Nagai F., Sakon H., Tanaka R. 2009; Paraprevotella clara gen. nov., sp. nov. and Paraprevotella xylaniphila sp. nov., members of the family ‘Prevotellaceae’ isolated from human faeces. Int J Syst Evol Microbiol 59:1895–1900 [View Article][PubMed]
    [Google Scholar]
12. Paster B. J., Dewhirst F. E., Olsen I., Fraser G. J. 1994; Phylogeny of Bacteroides, Prevotella, and Porphyromonas spp. and related bacteria. J Bacteriol 176:725–732[PubMed]
    [Google Scholar]
13. Posada D. 2008; jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253–1256 [View Article][PubMed]
    [Google Scholar]
14. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
15. Sakamoto M., Ohkuma M. 2010; Usefulness of the hsp60 gene for the identification and classification of Gram-negative anaerobic rods. J Med Microbiol 59:1293–1302 [View Article][PubMed]
    [Google Scholar]
16. Sakamoto M., Ohkuma M. 2012; Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority. Int J Syst Evol Microbiol 62:1241–1244 [View Article][PubMed]
    [Google Scholar]
17. Sakamoto M., Suzuki M., Umeda M., Ishikawa I., 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 [View Article][PubMed]
    [Google Scholar]
18. Sakamoto M., Suzuki N., Okamoto M. 2010a; Prevotella aurantiaca sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 60:500–503 [View Article][PubMed]
    [Google Scholar]
19. Sakamoto M., Suzuki N., Benno Y. 2010b; hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes . Int J Syst Evol Microbiol 60:2984–2990 [View Article][PubMed]
    [Google Scholar]
20. Shah H. N., Collins D. M. 1990; Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides . Int J Syst Bacteriol 40:205–208 [View Article][PubMed]
    [Google Scholar]
21. Shimodaira H. 2002; An approximately unbiased test of phylogenetic tree selection. Syst Biol 51:492–508 [View Article][PubMed]
    [Google Scholar]
22. Shimodaira H., Hasegawa M. 1999; Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114–1116 [View Article]
    [Google Scholar]
23. Shimodaira H., Hasegawa M. 2001; consel: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246–1247 [View Article][PubMed]
    [Google Scholar]
24. Silvestro D., Michalak I. 2010; raxmlGUI: a graphical front-end for RAxML. Available at http://sourceforge.net/projects/raxmlgui/
25. Stamatakis A. 2006; RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690 [View Article][PubMed]
    [Google Scholar]
26. Ueki A., Akasaka H., Suzuki D., Hattori S., Ueki K. 2006; Xylanibacter oryzae gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, xylanolytic bacterium isolated from rice-plant residue in flooded rice-field soil in Japan. Int J Syst Evol Microbiol 56:2215–2221 [View Article][PubMed]
    [Google Scholar]
27. Ueki A., Akasaka H., Satoh A., Suzuki D., Ueki K. 2007; Prevotella paludivivens sp. nov., a novel strictly anaerobic, Gram-negative, hemicellulose-decomposing bacterium isolated from plant residue and rice roots in irrigated rice-field soil. Int J Syst Evol Microbiol 57:1803–1809 [View Article][PubMed]
    [Google Scholar]
28. Willems A., Collins M. D. 1995; 16S rRNA gene similarities indicate that Hallella seregens (Moore and Moore) and Mitsuokella dentalis (Haapsalo et al.) are genealogically highly related and are members of the genus Prevotella: emended description of the genus Prevotella (Shah and Collins) and description of Prevotella dentalis comb. nov.. Int J Syst Bacteriol 45:832–836 [View Article][PubMed]
    [Google Scholar]