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Published March 5, 2021 | Version v1.0.0
Journal Article Open

Toward Accurate and Robust Environmental Surveillance Using Metagenomics

  • 1. ROR icon Northwestern University
  • 2. ROR icon University of Michigan–Ann Arbor
  • 3. ROR icon Rush University Medical Center


Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and the continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out in addressing the need. However, several hurdles remain to be overcome in order to generate actionable interpretations from metagenomic sequencing data for infection prevention. Conceptually and technically, we focus on viability assessment, taxonomic resolution, and quantitative metagenomics, and discuss their current advancements, necessary precautions and directions to further development. We highlight the importance of building solid conceptual frameworks and identifying rational limits to facilitate the application of techniques. We also propose the usage of internal standards as a promising approach to overcome analytical bottlenecks introduced by low biomass samples and the inherent lack of quantitation in metagenomics. Taken together, we hope this perspective will contribute to bringing accurate and consistent metagenomics-based environmental surveillance to the ground.


original_citation: Shen JX, McFarland AG, Young VB, Hayden MK, Hartmann EM. Toward Accurate and Robust Environmental Surveillance Using Metagenomics. Frontiers in Genetics. 2021;12:8.


We would like to thank Jason Romano for his help in making the figure.


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March 30, 2023
October 11, 2023