We develop and use bioinformatic and genome-enabled approaches to study microbial communities. With the advent of new sequencing technologies, one can sequence billions or trillions of base pairs of DNA for relatively little money. One of the most powerful applications of this new economy is the direct sequencing of microbial DNA and RNA from the environment. The combination of deep sequencing and bioinformatics reveals that even “simple” natural microbial communities are in fact quite complex. The Miller lab is interested in understanding this complexity at a systems level for microbial communities relevant to the environment, bioenergy production, and health and disease.