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. 2004 Apr;42(4):1626-30.
doi: 10.1128/JCM.42.4.1626-1630.2004.

Reassessment of sequence-based targets for identification of bacillus species

K S Blackwood  1 , C Y Turenne, D Harmsen, A M Kabani
Affiliations

Reassessment of sequence-based targets for identification of bacillus species

K S Blackwood et al. J Clin Microbiol. 2004 Apr.

Abstract

The Bacillus genus is a large heterogeneous group in need of an efficient method for species differentiation. To determine the current validity of a sequence-based method for identification and provide contemporary data, PCR and sequencing of a 500-bp product encompassing the V1 to V3 regions of the 16S rRNA gene were undertaken using 65 of the 83 type strains of this genus. This region proved discriminatory between most species (70.0 to 100% similarity), the exceptions being clinically relevant B. cereus and B. anthracis as well as nonpathogenic B. psychrotolerans and B. psychrodurans. Consequently, 27 type and clinical strains from the B. cereus group were used to test alternate targets (rpoB, vrrA, and the 16S-23S spacer region) for identification. The rpoB gene proved the best alternate target, with a conserved 4-nucleotide difference between B. cereus and B. anthracis. The high 16S rRNA gene sequence similarities between some strains demonstrated the need for a polyphasic approach to the systematics of this genus. This approach is one focus of the Ribosomal Differentiation of Medical Microorganisms mandate. Accordingly, the 16S rRNA gene sequences generated in this study have been submitted for inclusion into its publicly accessible, quality-controlled database at http://www.ridom_rdna.de/.

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Figures

FIG.1.
FIG.1.
Neighbor-joining phylogenetic tree based on the V1-V3 region of the 16S rRNA gene (E. coli nt 54 to 510) of Bacillus species used in this study. Sequences we were unable to obtain in this study were taken from GenBank (boxed). Three strains (*) had one ambiguous base pair (n). The branching pattern is rooted using A. acidocaldarius as the outlier. Created with Bionumerics (version 2.50).
FIG. 2.
FIG. 2.
B. cereus group members (clinical as well as type strains) used for rpoB gene analysis. The similarity matrix (pairwise comparison) and corresponding phylogenetic tree (neighbor joining) were created with Bionumerics (version 2.5).
See this image and copyright information in PMC

Comment in

  • Polyphasic approach for identifying Bacillus spp.
    Elzi MV, Mallard K, Droz S, Bodmer T. Elzi MV, et al. J Clin Microbiol. 2005 Feb;43(2):1010. doi: 10.1128/JCM.43.2.1010.2005. J Clin Microbiol. 2005. PMID: 15695735 Free PMC article. No abstract available.

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