Background/Question/Methods The realized niches of plants are largely defined by their microbiome and, together, the plant and the microbiome form a holobiont that responds to and adapts to environmental pertubation. Drought is one of the most important factors affecting the sustainability of agriculture and, although it is worsened by global change its effects may be lessened by the use of microbes that confer drought tolerance. Development of a unified theoretial framework on the response and adaption of microbiomes to drought would help advance drought science. Results/Conclusions We advocate developing a unified framework that begins with Vellend’s four basic processes of microbial community assembly (selection, dispersal, diversification and drift) and integrates the several frameworks have been proposed for microbial response to stress. These frameworks include: the Resistance-Resilience-Redundant (RRR) framework that explicitly decomposes different componments of the stability of microbiome to stress; the Competitor-Stress-tolerator-Ruderal (CSR) and high Yield-resource Aquisition-Stress tolerance (YAS) frameworks that focus on the tradeoff of functional traits in response to stress and disturbance; the Stress-Gradient hypothesis (SGH) that examines the biotic interaction in response to stress; and the Cry-For-Help (CRH) model that focuses on how the host regulates its microbiome in response to stress. We also advocate that harnessing microbiome for modern agriculture may be fostered by intergation of a multi-Omics approach, advanced ecological theory, and modern informatic technology. Finally, we show our progress on understanding the response of the sorghum microbiome to drought that has emerged from collaboratively investigating the fungal mycobiome, the bacterial microbiome, the meta-genome and meta-transcriptome, and the host sorghum transcriptome and metabolome.