Microbial organisms are ubiquitous in nature and often form communities closely associated with their host, referred to as the microbiome. The microbiome has strong influence on species interactions, but microbiome studies rarely take interactions between hosts into account, and network interaction studies rarely consider microbiomes. Here, we propose to use metacommunity theory as a framework to unify research on microbiomes and host communities by considering host insects and their microbes as discretely defined "communities of communities" linked by dispersal (transmission) through biotic interactions. We provide an overview of the effects of heritable symbiotic bacteria on their insect hosts and how those effects subsequently influence host interactions, thereby altering the host community. We suggest multiple scenarios for integrating the microbiome into metacommunity ecology and demonstrate ways in which to employ and parameterize models of symbiont transmission to quantitatively assess metacommunity processes in host-associated microbial systems. Successfully incorporating microbiota into community-level studies is a crucial step for understanding the importance of the microbiome to host species and their interactions.

Biology Centre of the Czech Academy of Sciences Institute of Entomology Ceske Budejovice Czech Republic

Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic

School of Informatics Computing and Cyber Systems Northern Arizona University Flagstaff AZ USA

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Microbiome Structure of a Wild Drosophila Community along Tropical Elevational Gradients and Comparison to Laboratory Lines

Ontogeny, species identity, and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae)