This project, funded under the HMP “New Computational Tools” initiative, was an exciting interdisciplinary collaboration spanning genomics, evolutionary biology, applied mathematics, and ecology. The three main aims of the project were to develop enriched descriptors of microbial community diversity, to develop methods for describing how human-associated microbial communities vary over time and space, and to develop new methods for tracing the flow of organisms among different communities. The project built on prior work in the Knight lab on the UniFrac metric for comparing microbial communities, in the Martin lab for developing new techniques to integrate evolution and ecology in the microbial world, and in the Brenner lab in analyzing communities and next-generation sequencing.

Several key outcomes of the project and its ARRA supplement were the analysis of detailed spatial and temporal datasets, including the highest-resolution time series spanning multiple body sites collected as...