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Applied and Environmental Microbiology, December 2005, p. 8825-8835, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.8825-8835.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Development and Evaluation of Genome-Probing Microarrays for Monitoring Lactic Acid Bacteria{dagger}

Jin-Woo Bae,1 Sung-Keun Rhee,2 Ja Ryeong Park,1 Won-Hyong Chung,1 Young-Do Nam,1 Insun Lee,3 Hongik Kim,3 and Yong-Ha Park1,3*

Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Eundong 52, Yusong, Daejeon, South Korea,1 Department of Microbiology, Chungbuk National University, Cheongju, South Korea,2 proBionic Corporation, Korea Research Institute of Bioscience and Biotechnology, Eundong 52, Yusong, Daejeon, South Korea3

Received 8 June 2005/ Accepted 27 August 2005

The genome-probing microarray (GPM) was developed for quantitative, high-throughput monitoring of community dynamics in lactic acid bacteria (LAB) fermentation through the deposit of 149 microbial genomes as probes on a glass slide. Compared to oligonucleotide microarrays, the specificity of GPM was remarkably increased to a species-specific level. GPM possesses about 10- to 100-fold higher sensitivity (2.5 ng of genomic DNA) than the currently used 50-mer oligonucleotide microarrays. Since signal variation between the different genomes was very low compared to that of cDNA or oligonucleotide-based microarrays, the capacity of global quantification of microbial genomes could also be observed in GPM hybridization. In order to assess the applicability of GPMs, LAB community dynamics were monitored during the fermentation of kimchi, a traditional Korean food. In this work, approximately 100 diverse LAB species could be quantitatively analyzed as actively involved in kimchi fermentation.

* Corresponding author. Mailing address: proBionic Corp., Korea Research Institute of Bioscience and Biotechnology, Eundong 52, Yusong, Daejeon 305-333, South Korea. Phone: 82 42 860 4620. Fax: 82 42 860 4678. E-mail: yhpark{at}kribb.re.kr.

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

Applied and Environmental Microbiology, December 2005, p. 8825-8835, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.8825-8835.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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