Defining microbiome function


Why does a microorganism associate with a host? What function does it perform? Such questions are difficult to unequivocally address and remain hotly debated. This is partially because scientists often use different philosophical definitions of ‘function’ ambiguously and interchangeably, as exemplified by the controversy surrounding the Encyclopedia of DNA Elements (ENCODE) project. Here, I argue that research studying host-associated microbial communities and their genomes (that is, microbiomes) faces similar pitfalls and that unclear or misapplied conceptions of function underpin many controversies in this field. In particular, experiments that support phenomenological models of function can inappropriately be used to support functional models that instead require specific measurements of evolutionary selection. Microbiome research also requires uniquely clear definitions of ‘who the function is for’, in contrast to most single-organism systems where this is implicit. I illustrate how obscuring either of these issues can lead to substantial confusion and misinterpretation of microbiome function, using the varied conceptions of the holobiont as a current and cogent example. Using clear functional definitions and appropriate types of evidence are essential to effectively communicate microbiome research and foster host health.

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Fig. 1: The relationship between CR and SE functions.


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I thank the members of the Klassen lab and J. P. Gogarten for their helpful feedback on earlier versions of this manuscript. Funding for this work was provided by NSF IOS-1656475 and the University of Connecticut. These funders had no role in the conceptualization, design, data collection, analysis, decision to publish or preparation of the manuscript.

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Correspondence to Jonathan L. Klassen.

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Klassen, J.L. Defining microbiome function. Nat Microbiol 3, 864–869 (2018).

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