eBook: New Frontiers in Infectious Disease Research - 18

Filtering Out the Barriers
to Our Understanding of
Microbial Genomics
mNGS has the potential to revolutionize the study, diagnosis,
tracking, and treatment of infectious diseases.
While metagenomic Next Generation Sequencing
(mNGS) is vastly increasing our understanding of
the microbial world, there are still barriers to its
widespread use (Figure 1). Perfecting mNGS largely
depends on a single, critical factor - easily and
effectively eliminating host interference. The ideal
host depletion method must consistently enrich
microbial reads (thereby reducing overall sequencing
costs) without added processing time or workflow
complexity. When resolved, mNGS will have a
more prominent and ubiquitous role in revolutionizing
the study, diagnosis, tracking and treatment
of infectious diseases.
Host depletion techniques
Without any form of depletion, only a small proportion
of sequencing reads correspond to potential
pathogens. This is because genomes of prokaryotic
pathogens are smaller relative to eukaryotic
genomes. Currently, a range of depletion methods
exist, which can be grouped into two categories:
Prior to DNA extraction and Post-DNA extraction.
Figure 1. Benefits and limitations of mNGS
Pre-extraction: Mechanical, chemical or
enzymatic options
Physical approaches include centrifugation and
filtration, which remove host cell components
based on their larger mass and size compared to
microbes. Typically, fast and easy, separation methods
based solely on differential cell sizes are insufficient
because of the significant quantities of host
DNA that remain.
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eBook: New Frontiers in Infectious Disease Research

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