Phase Genomics, Inc., the leading provider of proximity ligation next generation sequencing (NGS) solutions for genomics and metagenomics, in collaboration with the USDA, National Human Genome Research Institute, Pacific Biosciences, and several university teams, has demonstrated the value of their ProxiMeta™ Metagenome Deconvolution Platform in resolving the biological features of highly complex microbiomes.
The study, published in Genome Biology this past Friday, applied both Illumina short-read and Pacific Biosciences long-read sequencing combined with Phase Genomics’ proximity ligation (Hi-C) based metagenome deconvolution.
Phase Genomics CEO and Co-founder, Ivan Liachko, PhD said, “Our proximity ligation platform provides unique insights into the diversity and biology of complex microbial communities. Our technology enables researchers to track viruses and antibiotic resistance, discover their host organisms, and elucidate their potential vulnerabilities. This offers a new culture-free tool to combat antibiotic resistance in agriculture, health care, and beyond.”
Phase Genomics’ Hi-C proximity ligation platform enabled the identification of 188 novel viral-host interactions in the recent publication and revealed new insights into the biology of how bacteriophages interact with their hosts. A further 94 antimicrobial resistance genes (ARGs) were identified in the sample showcasing the horizontal transfer of mobile elements.
Given the benefits from the combined approach, the paper’s authors concluded with the recommendation that, “…future surveys of complex metagenomic communities include a combination of different DNA sequencing technologies and conformational capture techniques (i.e. Hi-C proximity ligation) in order to best resolve the unique biological features of the community”.
"The direct association of mobile genetic elements with their microbial hosts in complex populations is one of the last remaining technological challenges in the microbiome space,” said Professor Paul Plummer of Iowa State University and Executive Director of the Institute for Antimicrobial Resistance Research and Education. “Proximity ligation is an elegant way to overcome this obstacle and presents a promising key technology in the study of bacteriophage and antibiotic resistance biology within a microbial context." Plummer was not directly involved in the study.
Researchers leveraged Phase Genomics’ technology in another recent study, entitled, “Linking the Resistome and Plasmidome to the Microbiome.” The authors were able to detect both known and novel interactions between ARGs, mobile genetic elements, and host genomes directly from a crude wastewater sample, thereby validating the technology.
Phase Genomics is committed to collaborating on metagenomics projects. Visit the Phase Genomics website or follow them on Twitter for the latest news and information.
ABOUT PHASE GENOMICS – Phase Genomics applies Hi-C and other proximity-ligation methods to enable chromosome-scale genome assembly, metagenomic deconvolution, as well as analysis of structural genomic variation and genome architecture. They offer a comprehensive portfolio of laboratory and computational services and products, including Hi-C kits for plants, animals, microbes, and human samples as well as industry-leading genome and metagenome assembly and analysis software.
Based in Seattle, WA, the company was founded in 2015 by a team of genome scientists, software engineers, and entrepreneurs. The company’s mission is to empower scientists with genomic tools that accelerate breakthrough discoveries.