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Unlocking the potential of metagenomics through replicated experimental design

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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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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