The importance of microbiomes in host biology guides an intriguing convergence of micro- and macrobiological worlds. Consequently, the multidisciplinary framework of holobiont biology has emerged to integrate modes of genomic and functional variation that emphasize the centrality of microorganisms to the biosphere and the science of microbiome- based solutions for wide-ranging host activities, spanning agricultural production, conservation biology, and human diseases. The terms holobiont (the collection of host and associated microbial cells) and hologenome (all multispecies genetic material in the holobiont) are important to this conceptual change because they unify microbial symbiosis into the structure, function, and evolution of macroorganisms. Host organisms are thus defined to contain other organisms—viruses, bacteria, protozoa, and fungi—and their genomes. The functional relevance of these host-microbe associations will vary from inconsequential to harmful or essential, depending on the interactive milieu of members in the holobiont system.