SPECIAL ISSUE The ecosystem services of animal microbiomes E. A. McKenney 1 | K. Koelle 2 | R. R. Dunn 1 | A. D. Yoder 3 1 Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA 2 Department of Biology, Emory University, Atlanta, GA, USA 3 Duke University, Durham, NC, USA Correspondence Erin A. McKenney, Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA. Email: erinamck@gmail.com Abstract Microbiologists often evaluate microbial community dynamics by formulating func- tional hypotheses based on ecological processes. Indeed, many of the methods and terms currently used to describe animal microbiomes derive from ecology and evo- lutionary biology. As our understanding of the composition and functional dynamics of “the microbiome” grows, we increasingly refer to the host as an ecosystem within which microbial processes play out. Even so, an ecosystem service framework that extends to the context of the host has thus far been lacking. Here, we argue that ecosystem services are a useful framework with which to consider the value of microbes to their hosts. We discuss those “microbiome services” in the specific con- text of the mammalian gut, providing a context from which to develop new hypotheses and to evaluate microbial functions in future studies and novel systems. KEYWORDS ecosystem services, host–microbiome, microbial ecology, microbiome 1 | INTRODUCTION Animals are inhabited by microbial communities that together are referred to as “the microbiome.” These microbiomes can provide both benefits and costs to their host. Here, we argue that the con- cept of ecosystem services is a useful framework within which to consider the value of microbes to their hosts in general, and specifi- cally, provides a framework in which to begin to predict when microbes are most likely to offer “services” to their host in terms of health and reproductive fitness. Our work builds upon and extends recent work in which other investigators have productively bor- rowed ecological frameworks to understand microbiome composition and change (Cho & Blaser, 2012; Christian et al., 2015; Costello, Stagaman, Dethlefsen, Bohannan, & Relman, 2012; Fierer et al., 2012; Leser & Mølbak, 2009; McFall-Ngai et al., 2013; Relman, 2012; Stilling, Bordenstein, Dinan, & Cryan, 2014; Walter & Ley, 2011), but broadens this effort by considering ecosystem services. The host–microbe system is a unique context in which to con- sider ecosystem services, in as much as the host is always under selection to extract more services from the microbes (and shape the microbes in such a way as to provide those services), while the microbes are under selection to extract more benefits from the host. Selection on the host favours variants of host genes associated with greater host fitness. Those gene variants can be associated with host morphologies that favour microbiome services beneficial to the host, which in turn filters the lineages and species present in the host’s microbial community. As a key example, in herbivores that consume high proportions of dietary fibre, selection has favoured complex gut morphologies inhabited by microbial communities that are able to ferment dietary fibre. Such a scenario is highly dynamic, with selec- tion on hosts favouring both host genes associated with certain microbial processes, as well as on the microbes that carry them out. But to further complete the ecological analogy, the microbes are perpetually interacting with each other, often as competitors, or even as predators and prey. This system is complex, and it is this complexity that makes it both interesting and potentially informative for larger questions in ecology and evolution. Here, we discuss “mi- crobiome services” in the specific context of mammalian guts. We provide a context from which to develop new hypotheses and to evaluate microbial functions in future studies and novel systems. Though focused on the gut microbiome, the concepts introduced here are sufficiently general to apply to other host “ecosystems” and to larger questions of symbiotic interactions. Dispersal, diversification, environmental selection and drift have traditionally informed hypotheses about the composition of microbial communities (Costello et al., 2012; Vellend, 2010). While these Received: 1 August 2017 | Accepted: 2 February 2018 DOI: 10.1111/mec.14532 Molecular Ecology. 2018;1–9. wileyonlinelibrary.com/journal/mec © 2018 John Wiley & Sons Ltd | 1