Metagenomic Applications for Environmental Health Surveillance: A One Health Case Study from the Pacific Northwest Ecosystem

Younfblood Jessica, Wallance James, Cullen Alison, Elaine M. Faustman


The marine environment is the largest, most diverse and influential ecosystem on Earth. Still largely unexplored, the foundation for further ocean exploration begins with the most abundant and productive life forms in the ocean, the microbial community. Microbes are essential to all life and play an intimate role in ecosystem function and environmental health. Microbial community composition and function are important metrics that can be used to monitor and predict environmental changes highly relevant to global health. Standard lab techniques used for environmental microbial assessment are limited in scope and high throughput, comprehensive approaches offer a tremendous opportunity to expand our estimates and monitoring of microbial diversity. Metagenomics in combination with 454-pyrosequencing, marine metadata and bioinformatics analysis offers a sensitive approach to evaluate intact community genomes for the novel detection and characterization of microbial populations. Metagenomic studies reveal community composition, functional potential and environmental preferences that suggest key species and roles necessary in sustaining a functioning, healthy environment. In addition to its ecological relevance, metagenomic profiling creates translational research opportunities for monitoring environmentally hosted, human health determinants. In this case study based in Washington State’s Puget Sound estuary revealed the high reproducibility and discriminatory capabilities of metagenomic profiling and a comparative analysis of metagenomes exposed significant differences in microbial diversity and antibiotic resistance determinants across a gradient of anthropogenic impact. Our results demonstrate the power of metagenomics for understanding one health.


Metagenomics, Environmental Health, Antibiotic Resistance, Microbial Community, Marine Environment

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Amann, R. I., et al. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1): 143-169.

Babson, A., et al. (2006). Seasonal and interannual variability in the circulation of Puget Sound, Washington: A box model study. Atmos Ocean 49.

Gianoulis, T. A., et al. (2009). Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A 106(5): 1374-1379.

Herr, D. and G. Galland (2009). The Ocean and Climate Change. Tools and Guidelines for Action. IUCN. Gland, Switzerland.

Nogales, B., et al. (2011). Anthropogenic perturbations in marine microbial communities. FEMS Microbiol Rev 35(2): 275-298.

Port, J. A., et al. (2013). Metagenomic Frameworks for Monitoring Antibiotic Resistance in Aquatic Environments. Environ Health Perspect.

Port, J. A., et al. (2012). Metagenomic profiling of microbial composition and antibiotic resistance determinants in Puget Sound. PLoS One 7(10): e48000.

Rusch, D. B., et al. (2007). The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5(3): e77.

Tringe, S. G., et al. (2005). Comparative metagenomics of microbial communities. Science 308(5721): 554-557.

Turnbaugh, P. J., et al. (2007). The human microbiome project. Nature 449(7164): 804-810.

Youngblood, J. (2013). Longitudinal Approaches for Metagenomic Characterization of the Puget Sound for Environmental Health Surveillance, University of Washington.