Towards a conceptual framework of microbiome-mediated host defense

Abstract

Microbiomes are essential for the health of plants and animals, contributing to nutrient acquisition, metabolic regulation, and host health. Disruptions in the composition or function of these microbial communities, referred to as dysbiosis, are frequently associated with declining host health. Although plant and animal microbiomes have traditionally been studied in separate disciplines, growing evidence suggests that common ecological and molecular principles underpin microbiome assembly, stability, and host defense across both systems. In this perspective, we bring together recent advances in animal, plant and soil microbiomes research to explore how interactions between microorganisms and their hosts contribute to health. Particular attention is given to microbial metabolites and effector molecules, which can mediate communication, recognition, and functional reorganization within microbial communities. We propose that these interactions are driven by recognition-based processes analogous to immune modulation across animals, plants, and soils, enabling microbial communities to sense health threats and coordinate protective responses. By integrating concepts across kingdoms and ecosystems, we propose a conceptual framework in which disease-protective functions emerge from dynamic interactions among microorganisms and their hosts. This perspective postulates that microbiomes possess community-level, immune-like properties, offering a unifying conceptual basis for understanding how complex microbial ecosystems contribute to health and resilience across kingdoms and ecosystems.