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Nucleic Acids Research 2005 33(13):e113; doi:10.1093/nar/gni112
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Published online 19 July 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Methods Online

Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes

Jin-Woo Bae1, Sung-Keun Rhee2, Young-Do Nam1 and Yong-Ha Park1,3,*

1Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB) Eundong 52, Yusong, Daejeon, Korea 2Department of Microbiology, Chungbuk National University 12 Gaeshin-dong Heungduk-gu, Cheongju, Korea 3National Research Laboratory of Molecular Ecosystematics, Institute of Probionics, Probionic Corporation, Korea Research Institute of Bioscience and Biotechnology (KRIBB) Eundong 52, Yusong, Daejeon, Korea

*To whom correspondence should be addressed. Tel: +82 42 860 4622; Fax: +82 42 860 4677; Email: yhpark{at}kribb.re.kr

Received May 15, 2005. Revised June 17, 2005. Accepted June 30, 2005.

The generation of microarray probes with specificity below the species level is an ongoing challenge, not least because the high-throughput detection of microorganisms would be an efficient means of identifying environmentally relevant microbes. Here, we describe how suppression subtractive hybridization (SSH) can be applied to the production of microarray probes that are useful for microbial differentiation at the subspecies level. SSH was used to initially isolate unique genomic sequences of nine Salmonella strains, and these were validated in quadruplicate by microarray analysis. The results obtained indicate that a large group of genes subtracted by SSH could serve together, as one probe, for detecting a microbial subspecies. Similarly, the whole microbial genome (not subjected to SSH) can be used as a species-specific probe. The detailed methods described herein could be used and adapted for the estimation of any cultivable bacteria from different environments.


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