Proximity ligation technology captures physical interactions between DNA molecules in 3D using next-generation sequencing. It can be used to determine which DNA molecules were next to each other in physical space and therefore inside the same cell. This information can be used to deconvolve complex microbial communities, by separating DNA sequences into their respective genomes. Importantly, this method captures connections between host and phage genomes in vivo and therefore the host-range of phages can be determined directly in mixed populations.
Our new tool, "ProxiPhage" uses proximity ligation data to de novo reconstruct phage genomes and link them to their hosts directly from microbiome samples. This method routinely recovers large numbers of novel phages from diverse sample types and can also be applied to other mobile elements, such as plasmids. In this talk, we will discuss the technology, how it works, and show both published and unpublished data centered on our microbiome and phage discovery efforts.