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Unlocking the potential of metagenomics through replicated experimental design

Nature Biotechnology volume 30, pages 513–520 (2012)Cite this article

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Abstract

Metagenomics holds enormous promise for discovering novel enzymes and organisms that are biomarkers or drivers of processes relevant to disease, industry and the environment. In the past two years, we have seen a paradigm shift in metagenomics to the application of cross-sectional and longitudinal studies enabled by advances in DNA sequencing and high-performance computing. These technologies now make it possible to broadly assess microbial diversity and function, allowing systematic investigation of the largely unexplored frontier of microbial life. To achieve this aim, the global scientific community must collaborate and agree upon common objectives and data standards to enable comparative research across the Earth's microbiome. Improvements in comparability of data will facilitate the study of biotechnologically relevant processes, such as bioprospecting for new glycoside hydrolases or identifying novel energy sources.

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Figure 1: Conceptual diagram of why replicated samples, especially across a gradient or along a time series, are critical for interpretation of results.
Figure 2: Importance of metadata-enabled studies.

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Acknowledgements

We wish to thank J. Eisen for his constant support of the Earth Microbiome Project and his help with writing this work. This work was in part supported by the US Department of Energy under contracts DE-AC02-06CH11357 and DE-AC02-05CH11231, the US National Institutes of Health, the Natural Environment Research Council, UK, the Crohn's and Colitis Foundation of America, and the Howard Hughes Medical Institute. We thank J. Reeder, J. Stombaugh, C. Lozupone, D. McDonald, J. Kuczynski and J. Metcalf for comments on drafts.

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Authors and Affiliations

  1. Howard Hughes Medical Institute and Department of Chemistry & Biochemistry, University of Colorado at Boulder, Boulder, Colorado, USA

    Rob Knight

  2. Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Janet Jansson

  3. Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, California, USA

    Janet Jansson

  4. Joint Bioenergy Institute, Emeryville, California, USA

    Janet Jansson

  5. Centre for Ecology & Hydrology, Wallingford, Oxford, UK

    Dawn Field & Mark J Bailey

  6. Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado, USA

    Noah Fierer

  7. Argonne National Laboratory, Argonne, Illinois, USA

    Narayan Desai, Folker Meyer, Rick Stevens & Jack A Gilbert

  8. Department of Biological Sciences, University of Southern California, Los Angeles, California, USA

    Jed A Fuhrman

  9. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences & Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia

    Phil Hugenholtz

  10. RTI, Research Triangle Park, Durham, North Carolina, USA

    Daniel van der Lelie

  11. The Computation Institute, University of Chicago, Chicago, Illinois, USA

    Folker Meyer & Rick Stevens

  12. Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA

    Jeffrey I Gordon

  13. Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands

    George A Kowalchuk

  14. Institute of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands

    George A Kowalchuk

  15. Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA

    Jack A Gilbert

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Correspondence to Rob Knight.

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Knight, R., Jansson, J., Field, D. et al. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol 30, 513–520 (2012). https://doi.org/10.1038/nbt.2235

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