TY - JOUR
T1 - Are microbiome studies ready for hypothesis-driven research?
AU - Tripathi, Anupriya
AU - Marotz, Clarisse
AU - Gonzalez, Antonio
AU - Vázquez-Baeza, Yoshiki
AU - Song, Se Jin
AU - Bouslimani, Amina
AU - McDonald, Daniel
AU - Zhu, Qiyun
AU - Sanders, Jon G.
AU - Smarr, Larry
AU - Dorrestein, Pieter C.
AU - Knight, Rob
N1 - Funding Information:
This work was supported in part by National Institute of Justice Award 2015-DN-BX-K047 , the Alfred P. Sloan Foundation , and the National Institutes of Health .
Publisher Copyright:
© 2018 Elsevier Ltd
PY - 2018/8
Y1 - 2018/8
N2 - Hypothesis-driven research has led to many scientific advances, but hypotheses cannot be tested in isolation: rather, they require a framework of aggregated scientific knowledge to allow questions to be posed meaningfully. This framework is largely still lacking in microbiome studies, and the only way to create it is by discovery-driven, tool-driven, and standards-driven research projects. Here we illustrate these issues using several such non-hypothesis-driven projects from our own laboratories, including spatial mapping, the American Gut Project, the Earth Microbiome Project (which is an umbrella project integrating many smaller hypothesis-driven projects), and the knowledgebase-driven tools GNPS and Qiita. We argue that an investment of community resources in infrastructure tasks, and in the controls and standards that underpin them, will greatly enhance the investment in hypothesis-driven research programs.
AB - Hypothesis-driven research has led to many scientific advances, but hypotheses cannot be tested in isolation: rather, they require a framework of aggregated scientific knowledge to allow questions to be posed meaningfully. This framework is largely still lacking in microbiome studies, and the only way to create it is by discovery-driven, tool-driven, and standards-driven research projects. Here we illustrate these issues using several such non-hypothesis-driven projects from our own laboratories, including spatial mapping, the American Gut Project, the Earth Microbiome Project (which is an umbrella project integrating many smaller hypothesis-driven projects), and the knowledgebase-driven tools GNPS and Qiita. We argue that an investment of community resources in infrastructure tasks, and in the controls and standards that underpin them, will greatly enhance the investment in hypothesis-driven research programs.
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U2 - 10.1016/j.mib.2018.07.002
DO - 10.1016/j.mib.2018.07.002
M3 - Review article
C2 - 30059804
AN - SCOPUS:85050460316
SN - 1369-5274
VL - 44
SP - 61
EP - 69
JO - Current Opinion in Microbiology
JF - Current Opinion in Microbiology
ER -