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Reviews of metagenomics analysis oftenemphasize the interdisciplinary and tech-nical aspects of data analysis (Knief, 2014;Sharpton, 2014). How might these rec-ommendations be implemented for futureprojects? In this opinion, I provide someareas to consider, especially in experimen-tal design and full-data-cycle planning,and in expertise areas of value to metage-nomics projects. This opinion is struc-tured as a hypothetical conversation thatreviews state-of-the art in these areas andbrings out the various aspects of metage-nomics project design.Let’s consider an example project inplant-microbe metagenomics—analysis ofmicrobial metagenome functional genesthat predict plant yield differences in ahorticultural crop species. I’ve framed adiscussion of key points as a conversa-tion, perhaps at the third or fourth meet-ing, after participants have described theirrange of expertise.

A biologist, a statistician, and a bioinformatician walk into a conference roomâ€¦ and walk out with a great metagenomics project plan