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Application of Suppressive Subtractive Hybridization to Uncover the Metagenomic Diversity of Environmental Samples

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Environmental Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 410))

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Metagenomics addresses the collective genetic structure and functional composition of a microbial environmental sample without the bias or necessity for culturing the microorganisms from the community in question. Metagenomic studies are now beginning to take advantage of the plethora of complete genome sequences (1,2) and the associated tools, such as bacterial artificial chromosome (BAC) and fosmid vectors, to discover novel genes and survey the structure and function of microbial communities. Complementary and less expensive methods to compare genomes from individual microbes have been utilized in comparative genomic studies. Suppressive subtractive hybridization (SSH) is one such approach, which has been utilized to compare the genomic content of closely related species of bacteria (3 –6). Recently, SSH has also been used as a comparative method to examine the microbial diversity (i.e., species composition) and functional differences (i.e., gene composition) in the genomic content of two different rumen environmental communities (7). Through a series of hybridizations and polymerase chain reaction (PCR) amplifications, metagenomic differences between two environmental samples can be isolated by SSH. Subsequent DNA sequencing and bioinformatic analyses allow the putative identification of these differences.

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Acknowledgments

This work was supported by USDA NRI grant no. 970–326, and by the Agricultural Experimental Station of the University of Illinois. The authors gratefully acknowledge Professor Adrian Egan of the University of Melbourne for spawning this idea at the RRI-INRA meeting in Aberdeen, Scotland.

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Authors and Affiliations

  1. Agtech Products, Inc., Waukesha, WI

    Elizabeth A. Galbraith

  2. Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI

    Dionysios A. Antonopoulos

  3. Departments of Animal Sciences & Pathobiology, Division of Nutritional Sciences, North American Consortium for Genomics of Fibrolytic Ruminal Bacteria, University of Illinois at Urbana-Champaign, Urbana, IL

    Bryan A. White

Authors
  1. Elizabeth A. Galbraith
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  2. Dionysios A. Antonopoulos
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  3. Bryan A. White
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Editors and Affiliations

  1. Center for Advanced Research in Environmental Genomics (CAREG),Department of Biology, University of Ottawa, Ottawa, Canada

    C. Cristofre Martin

  2. Department of Biochemistry, St. George’s University Medical School, St. George’s, Grenada, West Indies

    C. Cristofre Martin

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Galbraith, E.A., Antonopoulos, D.A., White, B.A. (2008). Application of Suppressive Subtractive Hybridization to Uncover the Metagenomic Diversity of Environmental Samples. In: Martin, C.C., Martin, C.C. (eds) Environmental Genomics. Methods in Molecular Biology, vol 410. Humana Press. https://doi.org/10.1007/978-1-59745-548-0_16

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  • DOI: https://doi.org/10.1007/978-1-59745-548-0_16

  • Publisher Name: Humana Press

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