Beyond timescale separation: An eco-evolutionary consumer-resource theory of host-microbe symbioses

Symbiotic associations between microorganisms and hosts are universal and dynamic. However, current ecological and evolutionary theory often simplistically analyzes hosts and symbionts as either separate or fully integrated entities. This entrenchment obscures a central research challenge: to understand symbioses across varying degrees of interaction, integration, and functional dependence. We posit that major advances will emerge from theoretical models that explicitly capture eco-evolutionary feedbacks linking host and microbial community interaction structure, biotic resource availability, and selection across biological levels. We show how extending consumer-resource theory to incorporate evolutionary processes can overcome limitations in separation of timescales approaches, advancing our understanding of the evolution, adaptability, and persistence of variable host-microbe symbioses. By coupling ecological and evolutionary dynamics across scales, this framework can guide both basic understanding and applied approaches in symbiosis research.