Microbial communities play a significant role in maintaining human health. However, understanding the complex relationship between a human host and its resident microbial flora presents a considerable challenge. For example, the total number of microbial cells residing in an individual is estimated to far outnumber the individual's somatic cells. Unfortunately, the identity, distribution, and functional significance of the majority of these microorganisms are unknown. The situation is further complicated by the inability to culture many of these organisms in the laboratory. Here, we propose the development of a microfabricated device that enables the parallel culturing and characterization of individual members of a microbial community. Single cells will first be encapsulated into alginate gel microdroplets to allow for small-scale growth of thousands of isolated cells in parallel. Segregation of a cell into a gel bead will also facilitate subsequent sorting and selection based on the metabolic profile of the cell, which will be assessed using fluorogenic enzyme substrates. By employing a panel of different substrates, a large number of different species can be distinguished based on their metabolic properties. This approach will allow for quantification of the relative distribution and functional capabilities of the different members of the consortia and for subsequent genetic analyses. The scale, throughput capabilities, and sensitivity of the proposed technology address the key challenges facing the analysis of microbial consortia. Demonstration of this "front-end" sample preparation technique will greatly facilitate subsequent genome sequencing and interpretation of the complex relationship between a human host and its resident microbial flora. PUBLIC HEALTH RELEVANCE: Microbial communities play a significant role in maintaining human health by bestowing metabolic capabilities and disease resistance. However, the components, composition, and dynamics of these communities cannot be assessed effectively using current techniques. The proposed research will result in new technology that will facilitate the identification, sorting, and characterization of these microbial communities.