Abstract: The microbial communities, or microbiomes, residing in the mammalian gut are inherently dynamic, changing due to many factors including host maturation, alteration of the diet, and exchange of microbes with the environment or other hosts. Recent advances in high-throughput technologies in experimental biology, such as DNA sequencing, are enabling collection of unprecedented amounts of microbiome data. I will discuss both computational and experimental projects in my lab for analyzing and generating longitudinal microbiome datasets. In particular, I will describe our work on nonparametric Bayesian models for analyzing time-series of microbial sequencing count data, and a synthetic biology experimental system for high-throughput improvement of fitness of micro-organisms during the dynamic process of gut colonization.