We have developed a chemical probe technology for function-dependent separation of uncultivated microbes from their native habitat, with potential for subsequent single cell genome sequencing. Our chemical biology approach addresses a DOE grand challenge to discover and study new branches of life and new metabolic activities through massive-scale isolation and sequencing of unexplored microbial 'dark matter'. We have developed a chemical probe-based platform for selectively labeling functional proteins within microbial cells based upon specific functional activities of interest (e.g., drug metabolism in the gut microbiome, bioprocessing for development of alternative energy sources, carbon and nitrogen cycling in soil relevant to climate change and plant/crop performance. Our chemical probes can be deployed directly in living microbial populations within their native habitat. Probes that interact with or are taken up by cells and label proteins can then be appended with fluorophores, thereby enabling the use of flow cytometry to collect cells expressing the targeted activity for subsequent 16S sequencing or even single cell genome sequencing, and can also be parallelized with proteomic analyses.