Unlocking the potential of metagenomics through replicated experimental design

Rob Knight; Janet Jansson; Dawn Field; Noah Fierer; Narayan Desai; Jed A. Fuhrman; Phil Hugenholtz; Daniel Van Der Lelie; Folker Meyer; Rick Stevens; Mark J. Bailey; Jeffrey I. Gordon; George A. Kowalchuk; Jack A. Gilbert

doi:10.1038/nbt.2235

Unlocking the potential of metagenomics through replicated experimental design

Rob Knight, Janet Jansson, Dawn Field, Noah Fierer, Narayan Desai, Jed A. Fuhrman, Phil Hugenholtz, Daniel Van Der Lelie, Folker Meyer, Rick Stevens, Mark J. Bailey, Jeffrey I. Gordon, George A. Kowalchuk, Jack A. Gilbert

Research output: Contribution to journal › Review article › peer-review

215 Scopus citations

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.

Original language	English
Pages (from-to)	513-520
Number of pages	8
Journal	Nature Biotechnology
Volume	30
Issue number	6
DOIs	https://doi.org/10.1038/nbt.2235
State	Published - Jun 2012

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title = "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.",

author = "Rob Knight and Janet Jansson and Dawn Field and Noah Fierer and Narayan Desai and Fuhrman, {Jed A.} and Phil Hugenholtz and {Van Der Lelie}, Daniel and Folker Meyer and Rick Stevens and Bailey, {Mark J.} and Gordon, {Jeffrey I.} and Kowalchuk, {George A.} and Gilbert, {Jack A.}",

note = "Funding Information: 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 Funding Information: Environment Research Council, UK, the Crohn{\textquoteright}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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doi = "10.1038/nbt.2235",

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AU - Field, Dawn

AU - Fierer, Noah

AU - Desai, Narayan

AU - Fuhrman, Jed A.

AU - Hugenholtz, Phil

AU - Van Der Lelie, Daniel

AU - Meyer, Folker

AU - Stevens, Rick

AU - Bailey, Mark J.

AU - Gordon, Jeffrey I.

AU - Kowalchuk, George A.

AU - Gilbert, Jack A.

N1 - Funding Information: 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 Funding Information: 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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AB - 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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Unlocking the potential of metagenomics through replicated experimental design

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