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Toward Accurate and Robust Environmental Surveillance Using Metagenomics Open Access (recommended)

Descriptions

Resource type(s)

Article

Keyword

viability
limit of detection
metagenomics
taxonomic resolution
environmental surveillance
quantitative metagenomics

Rights

Attribution 4.0 International

Creator

SHEN, Jiaxian
McFarland, Alexander G
Young, Vincent B
Hayden, Mary K
Hartmann, Erica Marie

Abstract

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 Bibliographic 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.

Related URL

 https://www.frontiersin.org/articles/10.3389/fgene.2021.600111/full

Publisher

FRONTIERS MEDIA SA

Date Created

2021-03-05

Original Identifier

(PMID) 33747038

Language

English

Subject: MESH

Metagenomics
Limit of Detection

Acknowledgments

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

Grants and funding

Searle Leadership Fund

DOI

10.3389/fgene.2021.600111

File Details

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Mime type: application/pdf

File size: 805.9 kB