ABSTRACT Metabolism is fundamental to life, and metabolic dysregulation plays a key role in a wide variety of human diseases. In all eukaryotic cells, compartmentation is a crucial component of metabolic regulation, and metabolic pathways are separated within different cellular organelles to generate specific pools of metabolites. However, different cellular organelles also have to work in harmony to coordinate their activities, for maintaining optimal cellular homeostasis and organismal fitness. How this cellular harmony is achieved is a pivotal but unsolved question. I propose that specific metabolites derived from cellular organelles could serve as messengers to communicate between different compartments in the cell. Although metabolomics has identified thousands of metabolites, further pinpointing those “messenger” metabolites and understanding their regulatory network are not feasible with current tools. In this proposal, I propose two technological innovations: 1. Couple isotope-labeling and fluorescence imaging with hyperspectral stimulated Raman scattering (SRS) microscopy. This new microscopy platform will allow us, for the first time to visualize spatiotemporal dynamics of metabolites between organelles, cells and tissues in living organisms. 2. Develop a new imaging/sorting microfluidics system for high-throughput genomic screening with subcellular resolution. This platform will enable us to screen ~100,000 animals per day using either Confocal or SRS microscopy in a quantitative and automatic manner. Based on these two technological innovations, I aim to elucidate lysokine-mediated communication nexus with the nucleus and mitochondria, as well as decipher microbe-host mitochondria communication network. These studies will provide new conceptual understanding of metabolite-mediated communication systems and their crucial roles in orchestrating cellular and organismal homeostasis. I also expect to discover innovative nutraceutical targets for treating metabolic pathologies and promoting healthy aging. Together, this project will yield new insights regarding small molecule chemical imaging, functional metabolomics and high-throughput genomics, and will have high impact on research in the field of metabolism, cell biology and aging biology.