Investigating and Repurposing Natural Horizontal Gene Transfer Mechanisms for Efficient Microbiome Editing

Complex microbiomes employ diverse strategies to control horizontal gene transfer (HGT) and acquisition of new functions. By studying the molecular mechanisms and dynamics of such gene flow, we can both understand the evolution of complex communities and co-opt these mechanisms for precise microbiome editing. To interrogate the factors that can promote HGT in microbial communities, we first synthesize large families of establishment factors and anti-defense genes encoded in mobile genetic elements (MGEs). Then we perform pooled gain-of-function screens to quantify the impact of individual orthologs on conjugation efficiency. Applying this approach to known and putative gene families, we aim to uncover new mechanisms by which MGEs overcome host-encoded barriers to DNA transformation and promote their persistence and dissemination throughout complex ecosystems. In parallel, we have developed a strategy to capture and domesticate plasmids from complex microbiomes, allowing us to harness diverse previously-unaccessed MGE mobilization and replication systems and repurpose them for microbiome editing. Finally, to track the dynamics of MGE dissemination within communities, we are developing a memory-recorder strategy to barcode and record quantitative associations between MGEs and recipient microbes. Together, these strategies should unlock more efficient microbiome editing across diverse taxa and allow us to understand how the MGE arms race impacts horizontal gene transfer in complex microbial communities.