The host-microbiome dimension of ecological regime shifts

Rising climate and local pressures increase the risk of regime shifts, yet despite progress, thresholds remain difficult to identify early enough to take action. We argue that this shortfall reflects a host-centric view that largely omits host-associated microbiomes, which can shape resilience by modulating stress tolerance, aiding recovery, and stabilizing alternative states through inhibitory chemical interactions. We propose a research agenda that integrates host-associated microbiomes into regime-shift ecology by combining novel microbiome manipulations in laboratory and field settings with regime-shift mapping tools, while simultaneously developing microbiome-based early warning indicators. Reframing regime-shift theory through a host-associated microbiome lens can provide practical tools to anticipate collapse, improve monitoring, and inform timely interventions, thereby supporting more adaptive and robust conservation under accelerating global change.