Background and Aims: The loss of long-range sequence contiguity in the process of NGS sequencing is an obstacle to understanding the structure and function of genomes and metagenomes. This obstacle negatively affects both clinical research efforts and virtually all microbiome-centric projects as much genetic information cannot be reconstructed from complex mixed microbial communities without culturing the constituent microbes. Methods and Results: The chromosome conformation capture method, Hi-C, restores chromosome-scale contiguity to large genome assemblies and enables the deconvolution of numerous genomes from mixed samples such as complex microbial communities. Hi-C captures genomic proximity interactions through in vivo crosslinking, followed by proximity-ligation and sequencing. Since the crosslinks occur inside intact cells, any two loci that interact by Hi-C must have originated in the same cell, and this data can be used to deconvolute high quality genomes directly from mixed populations. We have developed a metagenomic discovery platform that exploits Hi-C proximity-ligation data and have applied it to a number of diverse sample types. Our ProxiMeta Hi-C extracts large numbers of genomes directly from microbiome samples without culturing, which can also associate plasmids and phage with hosts and separate strains without culturing. Conclusions: We will discuss the application of Hi-C data to a number of diverse microbiome samples. For example, we have been able to discover hundreds of novel strains and species from fecal and infected samples, as well as identify novel plasmid/phage host interactions.We have been able to identify the host for a number of AMR genes within novel species, underscoring the value of proximity-ligation data to microbiome research.