UCSF

The human microbiome comprises a plethora of interacting bacteria. The composition of the microbiome has been correlated with conditions such as inflammatory bowel disease, colon cancer, diabetes and obesity. Manipulating the composition and function of the microbiome has huge potential for improving the human condition. Because the microbiome is an interacting, cooperating consortium, understanding how bacteria interact and assemble in communities is key to engineering a synthetic microbiome. In this thesis an exploration of the building of microbial communities is presented in two-fold.

First, bacterial members of the human microbiome are identified based on their prevalence and variation among many subjects. These bacterial species could function as potential starting points for exploring building a synthetic microbiome optimized for human health.

Second, a novel method in droplet-microfluidics is presented that uses two-dimensional droplet constriction and high-speed fluorescent particle detection to accurately count and sort droplets with sub-micron particles. This technology can be used to build defined communities of bacteria at a relevant scale, in high-throughput, with many replicates and with single cell control.

As synthetic biology strives to understand life by building it, these studies aim to provide new tools and resources for the study of microbial interactions and the assembly dynamics of their communities. Applications of this work could potentially lead to the engineering of key members of the microbiome into a synthetic consortium individually optimized for human health.