Use of single-point genome signature tags as a universal tagging method for microbial genome surveys

Applied and Environmental Microbiology
Daniel van der LelieJohn Dunn

Abstract

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...Continue Reading

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Citations

Oct 2, 2012·Indian Journal of Microbiology·Sameer A Barghouthi
Jul 4, 2012·Annual Review of Microbiology·Bing MaJacques Ravel
Jan 26, 2008·Environmental Microbiology·Celine LesaulnierDaniel van der Lelie
May 17, 2006·Current Opinion in Biotechnology·Brian D Green, Martin Keller
Jun 12, 2012·Translational Research : the Journal of Laboratory and Clinical Medicine·Roxana J HickeyLarry J Forney
Oct 4, 2008·The Journal of Molecular Diagnostics : JMD·John R ten Bosch, Wayne W Grody

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