Precision Profiling of Microbiome-Host Interactions

Despite the centrality of microbes to human health, we know very little about how microbes interact with each other and their environment. This lack of understanding is due to fundamental limitations of existing tools to study microbiomes and microbiome-host interactions. In this talk, I will describe key limitations of existing tools, and I will provide solutions. First, I will discuss the utility of next generation sequencing assays of urinary cell-free DNA for the broad diagnosis of viral and bacterial infections of the urinary tract. Second, I will present a droplet-microfluidics single-cell RNA sequencing technology that enables to catalog the diversity of viral transcripts within infected cells, and at the same time record the cellular response to viral infection. Last, I will discuss a highly multiplexed in-situ hybridization assay that provides a means to map the locations and identities of hundreds of different microbial species in dense microbial communities. I will discuss both translational and basic science applications of these techniques.