Metagenomic spaces: a framework to study the effect of microbiome variation on animal ecology and evolution

Microorganisms are essential for the normal functioning of most vertebrates. Hence, identifying and measuring the factors that shape host-associated microbial communities is necessary to understand the ecological and evolutionary implications of host-microbiota associations. We propose a framework, built on the so-called "metagenomic space" concept, which incorporates multiple definitions and quantifiable features relating to the variation of microbial communities that are associated with vertebrate hosts. By drawing on diverse theories and concepts developed in different fields of biology, our framework sets a conceptual landscape that transcends the mere characterization of microbial communities. This provides the basis to study more complex attributes, such as "potential metagenomic space" and "fundamental metagenomic space," "metagenomic plasticity," and "metagenomic evolvability," which we argue are essential for understanding the microbial contribution to vertebrate host ecology and evolution-and hold considerable promise for advancing applied research and innovation. In doing so, we hope to contribute to an improved understanding of the impact of spatiotemporal variation of vertebrate host-microbiota associations, and inspire new approaches to address testable hypotheses related to ecological, evolutionary, and applied processes.