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‘Omics’ studies have by now deposited massive amounts of data into the databases, and it is now time to return to the question as to what can we actually learn from them. Increased application of the deductive approach in synthetic microbial ecology and synthetic microbiome research will undoubtedly provide exciting new opportunities for advancing our understanding of microbial ecology.

Getting back to the nature of the microbial world: from the description and inductive reasoning to deductive study after ‘meta‐omics’