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. The current project illustrates these issues using several such non-hypothesis-driven projects from the authors' 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. (publisher abstract modified)
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