Dysbiotic microbiomes and the collapse of plant health

Dysbiosis, the disruption of plant-associated microbial communities, is increasingly recognized as a driver of impaired plant health. Notably, plant dysbiosis parallels disruptions of the human gut microbiome, where imbalances similarly contribute to host dysfunction and disease. Here, we discuss the current understanding of plant dysbiosis by integrating host-microbiome interactions and emerging analytical methods. Dysbiosis can extend beyond local compartments, affecting systemic processes such as immunity and nutrient acquisition. Advances in sequencing and quantitative metrics now enable its measurement at the population level, while experimental evidence shows that restoring microbial balance can recover plant function. We highlight translational strategies, including microbiome-informed breeding (Microbiome genes or M genes), synthetic microbial communities (SynComs), and soil microbial priming, to enhance plant resilience. We propose a three-tiered framework for studying and interpreting plant microbiome dysbiosis that integrates compositional profiling, functional omics, and host-performance assessment, and we introduce the concept of functional dysbiosis. We also outline how host-genome-informed M-gene selection, metabolite monitoring, and rationally defined microbial community (SynCom) design can translate this framework into practical crop management strategies.