This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by van der Lelie, D.
Right arrow Articles by Dunn, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by van der Lelie, D.
Right arrow Articles by Dunn, J.
Agricola
Right arrow Articles by van der Lelie, D.
Right arrow Articles by Dunn, J.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, March 2006, p. 2092-2101, Vol. 72, No. 3
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.3.2092-2101.2006

Use of Single-Point Genome Signature Tags as a Universal Tagging Method for Microbial Genome Surveys{dagger}

Daniel van der Lelie,1* Celine Lesaulnier,1,2 Sean McCorkle,1 Joke Geets,1,3 Safiyh Taghavi,1 and John Dunn1

Brookhaven National Laboratory, Biology Department, Building 463, Upton, New York 11973,1 IRD, UR 101, IFR-BAIM, Université de Provence, ESIL, F-13288 Marseille Cedex 09, France,2 and Universiteit Hasselt, Environmental Sciences, Building D, Universitaire Campus, Diepenbeek B3590, Belgium3

Received 13 May 2005/ Accepted 28 December 2005

We developed single-point genome signature tags (SP-GSTs), a generally applicable, high-throughput sequencing-based method that targets specific genes to generate identifier tags from well-defined points in a genome. The technique yields identifier tags that can distinguish between closely related bacterial strains and allow for the identification of microbial community members. SP-GSTs are determined by three parameters: (i) the primer designed to recognize a conserved gene sequence, (ii) the anchoring enzyme recognition sequence, and (iii) the type IIS restriction enzyme which defines the tag length. We evaluated the SP-GST method in silico for bacterial identification using the genes rpoC, uvrB, and recA and the 16S rRNA gene. The best distinguishing tags were obtained with the restriction enzyme Csp6I upstream of the 16S rRNA gene, which discriminated all organisms in our data set to at least the genus level and most organisms to the species level. The method was successfully used to generate Csp6I-based tags upstream of the 16S rRNA gene and allowed us to discriminate between closely related strains of Bacillus cereus and Bacillus anthracis. This concept was further used successfully to identify the individual members of a defined microbial community.

* Corresponding author. Mailing address: Brookhaven National Laboratory, Biology Department, Building 463, Upton, NY 11973. Phone: (631) 344-5349. Fax: (631) 344-3407. E-mail: vdlelied{at}bnl.gov.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, March 2006, p. 2092-2101, Vol. 72, No. 3
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.3.2092-2101.2006




This article has been cited by other articles:

  • Taghavi, S., Garafola, C., Monchy, S., Newman, L., Hoffman, A., Weyens, N., Barac, T., Vangronsveld, J., van der Lelie, D. (2009). Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees. Appl. Environ. Microbiol. 75: 748-757 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»