PAPM EAGER: High-throughput experimental methods to link mobile genetic elements with their bacterial hosts

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The horizontal transfer of genes between bacteria is the main mechanism by which antibiotic resistance spreads, yet little is known about this process in natural bacterial communities. The so-called "flexible" DNA, the portion of the genome that has been horizontally acquired, allows bacteria to rapidly adapt to changing environmental conditions by incorporating novel functions. In addition to antibiotic resistance, functions carried on this flexible DNA can include virulence factors, mercury resistance, carbohydrate metabolism or catabolic genes useful in bioremediation. In some cases, organisms' genomes can consist of upwards of 50% flexible DNA, such as in certain strains of Escherichia coli and Pseudomonas fluorescens. Ultimately, this can expand an organism's niche, provide a competitive edge against other organisms, or change its relationship with its host. Surprisingly, comparative microbiome studies have overall ignored the mobile gene pool as a source for variation, surveying mainly the species present or absent across different conditions or cohorts. This is mainly due to limitations of current technologies used to characterize bacterial communities. To address this need, the investigators propose to develop tools that enable analysis of the flexible DNA. Using these tools, they can then examine the ecology and dynamics of the horizontal transfer of these genes. This research will catalyze discovery across all fields of microbiology around the resiliency of bacterial communities in response to perturbation, barriers to gene flow between specific organisms and the role of horizontal gene transfer in organismal evolution. There are important implications for human health, namely the spread of antibiotic resistance. The PI is committed to incorporating horizontal gene transfer and data from this project into curriculum of a course entitled Engineering the Microbiome. Studying horizontally transferred DNA presents several challenges. These genes may be found in multiple organisms and the flexible portion of a genome may not always be physically linked to the rest of an organism's genome, as in the case of phage or plasmids. The investigators propose developing several new single-cell methods that can detect mobile genetic elements and the identities of their host bacteria. They will develop these methods so that they can be high-throughput and comprehensive, testing all of the mobile genes in a sample simultaneously, rather than focusing on a single gene or a single species. Using the newly developed technologies, they will perform several proof-of-concept experiments to examine variation in mobile gene carriage and probe the dynamics of horizontal gene transfer in natural microbial communities.