Introduction: The host‐associated microbiome: Pattern, process and function

An explosion of studies in recent years has established the ubiquity of host-associated microbes and their centrality to host biology (McFall-Ngai et al., 2013; Russell, Dubilier, & Rudgers, 2014). Microbes aid in digestion, modulate development, contribute to host immunity, mediate abiotic stress and more. While relationships with host-associated microbes are ubiquitous and important, they are certainly not monolithic. Characterizing the microbial diversity associated with an ever-broadening array of hosts (diverse animals, plants, algae and protists) has shown that essential functions can be performed by microbes that are integrated with the host to varying degrees, ranging from embedded endosymbionts to a variable cast of transient microbes acquired from the environment. The maturing host–microbiome field is now developing a mechanistic understanding of host/microbe relationships across this spectrum and the crosstalk mediating these interactions. Similarly, studies across systems are illuminating the ecological and evolutionary factors that shape host–microbe interactions today and providing hints into the origins of specific relationships. The field of host-associated biology is often motivated by a desire to understand the impact of the microbiome on host organisms (Bordenstein & Theis, 2015; McFall-Ngai et al., 2013) and manipulate the microbiome to improve host health or performance (Busby et al., 2017; McKenzie, Kueneman, & Harris, 2018; Petrosino, 2018). Following from this, a consistent aim is determining which microbial symbionts are likely to most impact the host and should therefore occupy the bulk of our attention. Identifying key microbes and their interactions with the host requires different approaches across systems owing to the vast differences in microbiome diversity. Key microbes are readily apparent in some cases, exemplified by endosymbionts of animals that provide their host with nutritional subsidies (Wernegreen, 2012), such as those harboured by aphids and many other insects (Moran, McCutcheon, & Nakabachi, 2008). For hosts and tissues colonized by diverse microbial consortia—such as animal skin or plant rhizosphere—the observed community is a mix of transient microbes, variably present symbionts and core symbionts. Here, surveys across populations can often be an informative first step in differentiating transients from variable components of the microbiota, and identifying key players as the consistent presence of particular microbes (i.e., the core microbiome) can serve as a proxy for those most likely to contribute key functions (Busby et al., 2017; Shade & Handelsman, 2012). But even this approach may face challenges, as the core microbiome (if it exists) may often fail to Received: 10 April 2018 | Accepted: 16 April 2018 DOI: 10.1111/mec.14706