HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Supplementary sequence alignment Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by Xu, D. Articles by Côté, J.-C. Search for Related Content PubMed PubMed Citation Articles by Xu, D. Articles by Côté, J.-C. Agricola Articles by Xu, D. Articles by Côté, J.-C.

Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3' end 16S rDNA and 5' end 16S–23S ITS nucleotide sequences

Agriculture and Agri-Food Canada, Research Centre, 430 Gouin Blvd, St-Jean-sur-Richelieu, Quebec, Canada J3B 3E6

Correspondence
Jean-Charles Côté
cotejc{at}agr.gc.ca

The nucleotide sequences of the 3' end of the 16S rDNA and the 16S–23S internal transcribed spacer (ITS) of 40 Bacillaceae species were determined. These included 21 Bacillus, 9 Paenibacillus, 6 Brevibacillus, 2 Geobacillus, 1 Marinibacillus and 1 Virgibacillus species. Comparative sequence analysis of a 220 bp region covering a highly conserved 150 bp sequence located at the 3' end of the 16S rRNA coding region and a conserved 70 bp sequence located at the 5' end of the 16S–23S ITS of the 40 species and six sequences available in GenBank were used to infer the phylogenetic relationships between all 46 taxa. When a maximal distance (D_max, where D refers to the number of nucleotide substitutions per site) of 0·31 was introduced as a threshold to determine groupings, 10 phylogenetically distinct clusters were revealed. Twenty-six Bacillus species were separated in seven groups (I, II, III, IV, V, VI and X), but Bacillus circulans remained ungrouped. All six Brevibacillus species under study were in Group VII. The nine Paenibacillus species fell into two distinct groups (VIII and IX). Species with D_max values within 0·05 were considered to be very closely related. These were Bacillus psychrophilus and Bacillus psychrosaccharolyticus in Group II; ‘Bacillus maroccanus’ and Bacillus simplex in Group II; Bacillus amyloliquefaciens, Bacillus atrophaeus, Bacillus mojavensis and Bacillus subtilis in Group VI; Bacillus fusiformis and Bacillus sphaericus in Group VI; Brevibacillus brevis and Brevibacillus formosus in Group VII; Paenibacillus gordonae and Paenibacillus validus in Group VIII; and Bacillus anthracis, Bacillus cereus, Bacillus mycoides and Bacillus thuringiensis in Group X. The phylogenetic classification presented here is, in general, in agreement with current classifications based on phenotypic and molecular data. Our findings suggest, however, that in some cases, further divisions or, conversely, further groupings might be warranted. Should current classifications be re-examined in the light of our results, D_max values of 0·31 and 0·05, as exemplified here, may prove useful threshold values for the grouping of Bacillaceae into taxa akin to genera and species, respectively. These D_max thresholds may also reveal, in a different way, bacterial species for which further characterization might be warranted for proper classification and/or reassignment.

Published online ahead of print on 19 September 2002 as DOI 10.1099/ijs.0.02346-0.

The GenBank accession numbers for the 16S rDNA and 16S–23S ITS of different strains of Bacillus and related genera used in this work are AF478062–AF478111.

This article has been cited by other articles:

				N. A. Logan, O. Berge, A. H. Bishop, H.-J. Busse, P. De Vos, D. Fritze, M. Heyndrickx, P. Kampfer, L. Rabinovitch, M. S. Salkinoja-Salonen, et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria Int J Syst Evol Microbiol, August 1, 2009; 59(8): 2114 - 2121. [Abstract] [Full Text] [PDF]

				T. Hoshino, T. Nakabayashi, K. Hirota, T. Matsuno, R. Koiwa, S. Fujiu, I. Saito, O. B. Tkachenko, H. Matsuyama, and I. Yumoto Paenibacillus macquariensis subsp. defensor subsp. nov., isolated from boreal soil Int J Syst Evol Microbiol, August 1, 2009; 59(8): 2074 - 2079. [Abstract] [Full Text] [PDF]

				D. Xu and J.-C. Cote Sequence Diversity of Bacillus thuringiensis Flagellin (H Antigen) Protein at the Intra-H Serotype Level Appl. Envir. Microbiol., September 1, 2008; 74(17): 5524 - 5532. [Abstract] [Full Text] [PDF]

				X. Hu, W. Fan, B. Han, H. Liu, D. Zheng, Q. Li, W. Dong, J. Yan, M. Gao, C. Berry, et al. Complete Genome Sequence of the Mosquitocidal Bacterium Bacillus sphaericus C3-41 and Comparison with Those of Closely Related Bacillus Species J. Bacteriol., April 15, 2008; 190(8): 2892 - 2902. [Abstract] [Full Text] [PDF]

				P. E. Saikaly, M. A. Barlaz, and F. L. de los Reyes III Development of Quantitative Real-Time PCR Assays for Detection and Quantification of Surrogate Biological Warfare Agents in Building Debris and Leachate Appl. Envir. Microbiol., October 15, 2007; 73(20): 6557 - 6565. [Abstract] [Full Text] [PDF]

				S. J. Bent, J. D. Pierson, L. J. Forney, R. Danovaro, G. M. Luna, A. Dell'Anno, and B. Pietrangeli Measuring Species Richness Based on Microbial Community Fingerprints: the Emperor Has No Clothes Appl. Envir. Microbiol., April 1, 2007; 73(7): 2399 - 2401. [Full Text] [PDF]

				K. Hatayama, H. Shoun, Y. Ueda, and A. Nakamura Tuberibacillus calidus gen. nov., sp. nov., isolated from a compost pile and reclassification of Bacillus naganoensis Tomimura et al. 1990 as Pullulanibacillus naganoensis gen. nov., comb. nov. and Bacillus laevolacticus Andersch et al. 1994 as Sporolactobacillus laevolacticus comb. nov. Int J Syst Evol Microbiol, November 1, 2006; 56(Pt 11): 2545 - 2551. [Abstract] [Full Text] [PDF]

				D. Xu and J.-C. Cote Sequence Diversity of the Bacillus thuringiensis and B. cereus Sensu Lato Flagellin (H Antigen) Protein: Comparison with H Serotype Diversity. Appl. Envir. Microbiol., July 1, 2006; 72(7): 4653 - 4662. [Abstract] [Full Text] [PDF]

				S. L. Helfinstine, C. Vargas-Aburto, R. M. Uribe, and C. J. Woolverton Inactivation of Bacillus Endospores in Envelopes by Electron Beam Irradiation Appl. Envir. Microbiol., November 1, 2005; 71(11): 7029 - 7032. [Abstract] [Full Text] [PDF]

				J. Heyrman, N. A. Logan, M. Rodriguez-Diaz, P. Scheldeman, L. Lebbe, J. Swings, M. Heyndrickx, and P. De Vos Study of mural painting isolates, leading to the transfer of 'Bacillus maroccanus' and 'Bacillus carotarum' to Bacillus simplex, emended description of Bacillus simplex, re-examination of the strains previously attributed to 'Bacillus macroides' and description of Bacillus muralis sp. nov. Int J Syst Evol Microbiol, January 1, 2005; 55(1): 119 - 131. [Abstract] [Full Text] [PDF]

				A. Matarante, F. Baruzzi, P. S. Cocconcelli, and M. Morea Genotyping and Toxigenic Potential of Bacillus subtilis and Bacillus pumilus Strains Occurring in Industrial and Artisanal Cured Sausages Appl. Envir. Microbiol., September 1, 2004; 70(9): 5168 - 5176. [Abstract] [Full Text] [PDF]