ProxiMeta Metagenome Deconvolution Platform

The ProxiMeta Metagenome Deconvolution Platform, developed by Phase Genomics, combines proximity ligation (Hi-C) data with shotgun sequencing to assemble high-quality metagenomes and associate mobile genetic elements with their hosts. It is designed for researchers working with complex microbial communities who want strain-resolution insights without relying on 16S-based techniques, traditional binning, or culturing of microbes.

The platform covers the full sample-to-analysis workflow, starting from a crude metagenomic sample and ending with analyzed, genome-resolved data. The entire process is typically completed within one month. Library preparation does not require high-molecular-weight DNA extraction or microbial culturing, and the 8-step Hi-C library prep can be completed in two working days with approximately three hours of hands-on time. Sequencing is performed on any Illumina sequencer, with approximately 50 to 100 million paired-end reads required per dual-indexed proximity ligation library.

Core Features and Benefits

• Assembles high-quality genomes directly from mixed microbial samples, including both novel and known microbes
• Associates plasmids, phages, and antimicrobial resistance genes (ARGs) with their host microbes
• Does not require high-molecular-weight DNA extraction or culturing
• Compatible with short-read Illumina sequencing
• Available as an 8-pack ProxiMeta Kit with cloud-based ProxiMeta Analysis included
• Generates proximity-assembled genomes (PAGs) assessed for completeness, contamination, and novelty

ProxiMeta Workflow Steps

1. Start with a crude metagenomic sample (no culturing or HMW DNA extraction required)
2. Perform proximity ligation (Hi-C) library preparation using the ProxiMeta Hi-C Library Prep Kit — completable in 2 working days with ~3 hours hands-on time, with multiple safe stopping points
3. Prepare shotgun sequencing library using a suitable kit (recommendations available from Phase Genomics)
4. Sequence on any Illumina platform (~50–100 million paired-end reads per sample)
5. Upload data to the cloud-based ProxiMeta analysis platform at proximeta.phasegenomics.com
6. Receive genome-resolved metagenomic analysis including genome assemblies, mobile element attribution, and taxonomic annotation

Key Applications

• Metagenome assembly: Generates proximity-assembled genomes (PAGs) for both prokaryotic and eukaryotic microbiome members; uses direct physical evidence of co-location within the same cell rather than binning, producing more complete and less contaminated genome assemblies
• Mobile element host attribution: Links plasmids, transposons, and antibiotic resistance genes to their host organisms, providing insight into horizontal gene transfer in complex microbial communities
• Phage-host attribution: Crosslinks phage and viral DNA to bacterial host DNA during library prep, enabling accurate assignment of phages to their hosts through analysis of chimeric junction sequences
• Antibiotic resistance surveillance: Identifies and attributes AMR genes to specific host microbes within a community

ProxiMeta Explorer — Interactive Analysis Platform

• Cloud-based, interactive platform for genome-resolved metagenomic analysis
• Supports analysis of single samples or large datasets comprising dozens to hundreds of samples
• Provides taxonomic annotation and abundance calculations
• Tracks genomes across time points, conditions, and sample groups
• Links phages, plasmids, and AMR genes to host microbes and displays connection networks
• Outputs well-organized data frames compatible with downstream analysis tools
• Allows download of genomes for bacteria, archaea, viruses, and plasmids, including raw data
• Customizable analyses and reports
• Included with ProxiMeta Kit purchase or service project

All ProxiMeta Kits are offered as bundles that include free online metagenome deconvolution analysis. Phase Genomics also offers service projects for users without prior experience in shotgun library preparation and sequencing, and provides support for data interpretation and additional analyses upon request.