Microbial Ecology

, Volume 53, Issue 3, pp 498–506 | Cite as

Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions

  • Michael Wagner
  • Hauke Smidt
  • Alexander Loy
  • Jizhong Zhou


High-throughput technologies are urgently needed for monitoring the formidable biodiversity and functional capabilities of microorganisms in the environment. Ten years ago, DNA microarrays, miniaturized platforms for highly parallel hybridization reactions, found their way into environmental microbiology and raised great expectations among researchers in the field. In this article, we briefly summarize the state-of-the-art of microarray approaches in microbial ecology research and discuss in more detail crucial problems and promising solutions. Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities.


Microbial Community Microbial Community Composition DGGE Banding Microarray Approach Target Nucleic Acid 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Research on DNA microarrays by MW and AL was financed by the German Bundesministerium für Bildung und Forschung in the framework of the BIOLOG I+II program, the Bayerische Forschungsstiftung, the Austrian Science Fund (FWF project P16580-B14), the European Community (Marie Curie Intra-European Fellowship to AL), and the University of Vienna. JZ’s effort was supported by The United States Department of Energy under the Natural and Accelerated Bioremediation Research Program, and the Genomics:GTL program of the Office of Biological and Environmental Research, Office of Science. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for DOE under contract #DE-AC05-96OR22464. Support to HS for array-related research was provided by the Ecogenomics programme of the Netherlands Genome Initiative, the Dutch Science Foundation (NWO-STW), the European Community (FP5:MicrobeDiagnostics, FP6:Aquaterra, FeedforPigHealth, Sedbarcah), The Wageningen Centre for Food Sciences, and the National Institutes of Health (NIH/NIDCR).


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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Michael Wagner
    • 1
  • Hauke Smidt
    • 2
  • Alexander Loy
    • 1
  • Jizhong Zhou
    • 3
  1. 1.Department of Microbial Ecology, Faculty of Life SciencesUniversity of ViennaWienAustria
  2. 2.Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands
  3. 3.Institute for Environmental GenomicsUniversity of OklahomaNormanUSA

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