Mapping Microbial Communities across Space and Time

Microbial ecosystems often rely on intricate spatial interactions and temporal processes to perform community-wide functions and maintain population stability. Methods to delineate spatial and temporal information in microbial communities are currently very limited. In this talk, I will describe two new technologies in this arena. First, we developed an unbiased culture-independent method to map the spatial co-associations of microbiota in complex consortia. Borrowing from macroecology, we devised a microbial plot-sampling and statistical reconstruction method called Metagenomic Plot-sampling by sequencing (MaP-seq) to delineate interspecies associations in the mammalian gastrointestinal microbiome, at micron-scale spatial resolution. Second, we developed temporal recording in arrays by CRISPR expansion (TRACE), a framework to store temporal information (both environmental and biological) directly into the genomes of a bacterial population. Using TRACE, we devised a “biological tape recorder” that can stably chronicle temporal and lineage information of cells over multiple days. Together, these approaches to uncover the spatiotemporal organization of microbial communities will lead to better understanding of complex natural ecosystems and new strategies to program microbial sentinels and actuators for a variety of biotechnological applications.