Results/Conclusions: Applying a quantitative genetics framework to understanding structure-function relationships in host-microbe systems requires first that functional traits at the system-level be identified. Such traits would be the product of some combination of host and microbiota genetics interacting with the external environment, and for those traits evolving adaptively would be linked to fitness at the level of the host-microbe system. Total variation in such traits (VT) can be partitioned into that explained by variation in host genetics (VG), by variation in the microbiota (VM), and by environmental variation (VE). The quantities VG / VT and VM / VT are the proportions of total variation in a host-microbe trait that are explained by host genetic and microbiota variation, and together comprise an analog of “heritability” (h2) in traditional quantitative genetics. This conceptualization of host genetic and microbiota components of heritability (h2G and h2M) suggests that well developed quantitative genetic theory and empirical approaches can be extended to better model and quantify microbial structure-function relationships in host-microbe systems. A particularly promising approach is measuring the response of a system-level function to artificial selection in order to calculate heritability and identify co-evolving host genetic and microbiota contributions to adaptive system-level traits.