Building the World’s Largest Plasmid-Host Interaction Network Using Proximity Ligation Technology

Plasmids are mediators of horizontal gene transfer (HGT) and serve as both a reservoir and vector for the spread of antimicrobial resistance (AMR) and virulence genes. They are also a valuable tool in synthetic biology, enabling the transformation and engineering of diverse microorganisms. However, plasmid-host relationships in nature have proven challenging to identify without culture-based methods. This culturability requirement restricts the microbial diversity that can be surveyed, and the applicability of these plasmids to engineering of more complex communities.

Proximity ligation sequencing is a powerful metagenomic approach for associating plasmids with their hosts directly in native microbial communities. It captures, in vivo, physical interactions between the host microbial genome and the genetic material of plasmids. These linkages offer direct evidence that plasmid sequences were present within an intact host cell; however, unlike culturing experiments, proximity-ligation does not require the propagation of living bacterial cells. The application of this technology to hundreds of complex microbiome samples has yielded thousands of novel plasmid genomes with host assignments, along with large numbers of new microbial genomes. Through broad-scale use of proximity ligation sequencing, we are creating a global-scale database of highly diverse plasmid-host interactions from samples across the world. We will present published and unpublished work highlighting the power of this approach in the field of metagenomic discovery, and its potential in fueling efforts to develop plasmid vectors for microbial engineering across the tree of life.