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Implementation of Random Bacterial Genomic DNA Microarray Chip (RBGDMC) for Screening of Dominant Bacteria in Complex Cultures

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Abstract

The random bacterial genomic DNA microarray chip (RBGDMC), which was fabricated using random genomic DNA fragments obtained from the fragmentation of bacterial genome by using four different pairs of restriction enzymes, was found to discriminate bacterial species in the same genus and resulted in the determination of dominant bacteria in enriched cultures. The identification of a dominant bacterial species was successfully conducted in the co-culture of three different bacteria using the RBGDMC. In addition, the analysis of the chip data could confirm if any of the selected bacteria is the most abundant or if some bacteria were enriched and became the dominant species within the consortium after the samples were prepared from the repeated cultures of real sludge in a complex medium. This study shows the successful implementation of the RBGDMC for the identification and monitoring of dominant bacteria in complex environmental bacterial communities simply without any PCR amplification of the target nucleic acids.

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Acknowledgments

This work was supported by a grant (code no. 20080401034020) from the BioGreen 21 Program, Rural Development Administration, Republic of Korea. The authors are grateful for this support.

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Authors and Affiliations

  1. Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea

    Byoung Chan Kim

  2. College of Life Sciences and Biotechnology, Korea University, 5-1 Anam-dong, Seongbuk-gu, Seoul, 136-701, Republic of Korea

    Ji Hyun Park & Man Bock Gu

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  1. Byoung Chan Kim
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  2. Ji Hyun Park
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Correspondence to Man Bock Gu.

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Kim, B.C., Park, J.H. & Gu, M.B. Implementation of Random Bacterial Genomic DNA Microarray Chip (RBGDMC) for Screening of Dominant Bacteria in Complex Cultures. Appl Biochem Biotechnol 162, 2284–2293 (2010). https://doi.org/10.1007/s12010-010-9002-4

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