Microbes are everywhere in nature and they live in diverse communities that show remarkable metabolic capabilities and robustness. On the other hand, disruption of microbiome homeostasis and associated changes in the community’s structure/function underlies numerous health or environmental issues. My lab has been developing methods and tools rooted in engineering to study microbial communities in order to discover the underlying cellular and molecular mechanisms. In particular, we have pioneered a technological pipeline, based on nanoliter-scale microfluidic droplets, to co-cultivate sub-communities and characterize interactions between community members. A number of technological modules have been created and the pipeline is being applied to the investigation of a range of health or environment related microbiomes. A second distinct yet complementary research thrust in my lab, inspired by naturally occurring synergistic microbial communities, has been the design and construction of synthetic microbial consortia for microbial engineering and biochemical production. One application focus has been synthesis of fuels and chemicals from lignocellulosic biomass. For instance, we designed and optimized a consortium consisting of a cellulolytic fungus capable of hydrolyzing hemicellulose and cellulose (main components of lignocellulosic biomass) into mono and oligosaccharides and a genetically engineered bacterium for converting mono and oligosaccharides into isobutanol, an advanced biofuel. The general framework of engineering defined co-cultures of coordinated specialists also offers exciting new opportunities for the efficient and flexible production of many valuable chemicals from other non-conventional bio-feedstocks.