Rapid and thorough lysis of diverse metagenomic samples remains an important challenge in the study of microbial communities using all modern genomic methods. This is also true for Phase Genomics’ ProxiMeta™ platform, which enables accurate metagenomic deconvolution and mobile element host association using Hi-C proximity ligation sequencing. This technology unlocks the ability to track the hosts of antimicrobial resistance and virulence genes borne on mobile elements in settings ranging from healthcare, food production, to agriculture and waste management.

However, to be a useful surveillance tool, ProxiMeta must be amenable to high throughput methods. Representation of diverse organisms found within metagenomic samples can be severely skewed by differential lysis owing to variation in outer membrane and cell wall composition. Differential lysis is typically minimized through a combination of chemical and physical lysis using detergents and physical disruption (bead beating). Bead beating is effective but limits the throughput of metagenomics analysis because it is not compatible with multi-well plates and liquid handling. We overcome this limitation using the Covaris Adaptive Focused Acoustics
TM (AFA) technology showing that it is able to rapidly lyse complex microbial communities composed of diverse organisms including Gram-negative bacteria, Gram-positive bacteria, and fungi. We observe a beta-diversity Jaccard index of >0.9 when comparing results of traditional bead beat lysis and AFA. Furthermore, AFA lysis speeds up the ProxiMeta protocol, saving hours when scaled to 96-well plates, delivering accurate metagenomes and mobile element host identification faster than ever.

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Phase Genomics