Applied Biochemistry and Biotechnology

, Volume 162, Issue 8, pp 2284–2293 | Cite as

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

  • Byoung Chan Kim
  • Ji Hyun Park
  • Man Bock GuEmail author


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.


Random fragmentation Genomic DNA DNA microarray chip Bacteria identification Complex culture 



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.


  1. 1.
    Dearman, B., Marschner, P., & Bentham, R. H. (2006). Methane production and microbial community structure in single-stage batch and sequential batch systems anaerobically co-digesting food waste and biosolids. Applied Microbiology and Biotechnology, 69, 589–596.CrossRefGoogle Scholar
  2. 2.
    Parkes, R. J., & Taylor, J. (1985). Characterization of microbial populations in polluted marine sediments. Journal of Applied Microbiology, 59, 155S–173S.CrossRefGoogle Scholar
  3. 3.
    Wu, L. Y., Thompson, D. K., Li, G. S., Hurt, R. A., Tiedje, J. M., & Zhou, J. Z. (2001). Development and evaluation of functional gene arrays for detection of selected genes in the environment. Applied and Environmental Microbiology, 67, 5780–5790.CrossRefGoogle Scholar
  4. 4.
    Kampfer, P. (1997). Detection and cultivation of filamentous bacteria from activated sludge. FEMS Microbiology Ecology, 23, 169–181.CrossRefGoogle Scholar
  5. 5.
    Langendijk, P. S., Schut, F., Jansen, G. J., Raangs, G. C., Kamphuis, G. R., Wilkinson, M. H. F., et al. (1995). Quantitative fluorescence in-situ hybridization of Bifidobacterium spp. with genus-specific 16S ribosomal-RNA-targeted probes and its application in fecal samples. Applied and Environmental Microbiology, 61, 3069–3075.Google Scholar
  6. 6.
    Ravenschlag, K., Sahm, K., & Amann, R. (2001). Quantitative molecular analysis of the microbial community in marine Arctic sediments (Svalbard). Applied and Environmental Microbiology, 67, 387–395.CrossRefGoogle Scholar
  7. 7.
    Smit, E., Leeflang, P., Gommans, S., van den Broek, J., van Mil, S., & Wernars, K. (2001). Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Applied and Environmental Microbiology, 67, 2284–2291.CrossRefGoogle Scholar
  8. 8.
    Dahllof, I. (2002). Molecular community analysis of microbial diversity. Current Opinion in Biotechnology, 13, 213–217.CrossRefGoogle Scholar
  9. 9.
    Amann, R., Fuchs, B. M., & Behrens, S. (2001). The identification of microorganisms by fluorescence in situ hybridisation. Current Opinion in Biotechnology, 12, 231–236.CrossRefGoogle Scholar
  10. 10.
    Muyzer, G. (1999). DGGE/TGGE a method for identifying genes from natural ecosystems. Current Opinion in Microbiology, 2, 317–322.CrossRefGoogle Scholar
  11. 11.
    Moeseneder, M. M., Arrieta, J. M., Muyzer, G., Winter, C., & Herndl, G. J. (1999). Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Applied and Environmental Microbiology, 65, 3518–3525.Google Scholar
  12. 12.
    Acinas, S. G., RodriguezValera, F., & PedrosAlio, C. (1997). Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microbiology Ecology, 24, 27–40.CrossRefGoogle Scholar
  13. 13.
    Dionisi, H. M., Harms, G., Layton, A. C., Gregory, I. R., Parker, J., Hawkins, S. A., et al. (2003). Power analysis for real-time PCR quantification of genes in activated sludge and analysis of the variability introduced by DNA extraction. Applied and Environmental Microbiology, 69, 6597–6604.CrossRefGoogle Scholar
  14. 14.
    Barlaan, E. A., Sugimori, M., Furukawa, S., & Takeuchi, K. (2005). Electronic microarray analysis of 16S rDNA amplicons for bacterial detection. Journal of Biotechnology, 115, 11–21.CrossRefGoogle Scholar
  15. 15.
    Kelly, J. J., Siripong, S., McCormack, J., Janus, L. R., Urakawa, H., El Fantroussi, S., et al. (2005). DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Research, 39, 3229–3238.CrossRefGoogle Scholar
  16. 16.
    Rhee, S. K., Liu, X. D., Wu, L. Y., Chong, S. C., Wan, X. F., & Zhou, J. Z. (2004). Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Applied and Environmental Microbiology, 70, 4303–4317.CrossRefGoogle Scholar
  17. 17.
    Epstein, J. R., Biran, I., & Walt, D. R. (2002). Fluorescence-based nucleic acid detection and microarrays. Analytica Chimica Acta, 469, 3–36.CrossRefGoogle Scholar
  18. 18.
    Sergeev, N., Distler, M., Courtney, S., Al-Khaldi, S. F., Volokhov, D., Chizhikov, V., et al. (2004). Multipathogen oligonucleotide microarray for environmental and biodefense applications. Biosensors & Bioelectronics, 20, 684–698.CrossRefGoogle Scholar
  19. 19.
    Cao, X., Wang, Y. F., Zhang, C. F., & Gao, W. J. (2006). Visual DNA microarrays for simultaneous detection of Ureaplasma urealyticum and Chlamydia trachomatis coupled with multiplex asymmetrical PCR. Biosensors & Bioelectronics, 22, 393–398.CrossRefGoogle Scholar
  20. 20.
    Xu, J., Miao, H. Z., Wu, H. F., Huang, W. S., Tang, R., Qiu, M. Y., et al. (2006). Screening genetically modified organisms using multiplex-PCR coupled with oligonucleotide microarray. Biosensors & Bioelectronics, 22, 71–77.CrossRefGoogle Scholar
  21. 21.
    Kim, H. J., Park, S. H., Lee, T. H., Nahm, B. H., Kim, Y. R., & Kim, H. Y. (2008). Microarray detection of food-borne pathogens using specific probes prepared by comparative genomics. Biosensors & Bioelectronics, 24, 238–246.CrossRefGoogle Scholar
  22. 22.
    Kim, B. C., Park, J. H., & Gu, M. B. (2004). Development of a DNA microarray chip for the identification of sludge bacteria using an unsequenced random genomic DNA hybridization method. Environmental Science & Technology, 38, 6767–6774.CrossRefGoogle Scholar
  23. 23.
    Kim, B. C., Park, J. H., & Gu, M. B. (2005). Multiple and simultaneous detection of specific bacteria in enriched bacterial communities using a DNA microarray chip with randomly generated genomic DNA probes. Analytical Chemistry, 77, 2311–2317.CrossRefGoogle Scholar
  24. 24.
    Cook, K. L., & Sayler, G. S. (2003). Environmental application of array technology: Promise, problems and practicalities. Current Opinion in Biotechnology, 14, 311–318.CrossRefGoogle Scholar
  25. 25.
    Gracey, A. Y., & Cossins, A. R. (2003). Application of microarray technology in environmental and comparative physiology. Annual Review of Physiology, 65, 231–259.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Institut Pasteur KoreaSeongnam-siRepublic of Korea
  2. 2.College of Life Sciences and BiotechnologyKorea UniversitySeoulRepublic of Korea

Personalised recommendations