Surveillance of Exhibit Associated Aquatic Viruses Using Next Generation Sequencing Technologies
IAAAM 2016
William Van Bonn1,2,3*; Yiseul Kim3; Tiong Gim Aw3; Frank Oliaro1; Joan Rose3
1A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL, USA; 2Department of Veterinary Clinical Medicine, University of Illinois, Urbana-Champaign, IL, USA; 3Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, USA


The influence of the built environment on resident microbial communities and the resulting health and welfare implications for humans continues to be the subject of intense research focus.1 Altered microbial community profiles, sometimes referred to as dysbiosis, are increasingly correlated with health problems in human individuals.2 Aquaria represent unique built aquatic environments and little to nothing is known about the influence of microbial communities or disturbances of microbial communities on resident animal health. Aquaria also provide excellent test platforms to further investigate these complex interrelationships.

Many investigators are now publishing characterizations of animal associated microbiota including fishes and marine mammals.3,4 Most of these early data are limited in longitudinal resolution and predominantly focus on the bacterial members of complex microbiomes. We undertook a pilot survey of seven aquarium systems with differing physiochemical and resident animal profiles to search for viral nucleic acid using a metagenomic method developed for detecting viral nucleic acids in ballast waters from transoceanic merchant vessels. One system included in the surveillance plan is a seasonal touch tank exhibit. This system was sampled at the beginning and end of the season.

Briefly, viruses were concentrated from 60-liter of water using hollow fiber ultrafiltration. The concentrated viral samples were passed through 0.22-μm filters to remove bacterial and eukaryotic cells and DNase treatment to remove any naked nucleic acids prior to viral nucleic acid extraction. To enable subsequent detection of both DNA and RNA viruses, extracted nucleic acids were randomly primed for cDNA synthesis. The amplification products were pooled for sequencing using an Illumina HiSeq 2500 platform. Bioinformatics analysis was carried out using facilities of the High Performance Computer Center at Michigan State University to assess the viral ecology of aquarium water.

Metagenomic sequencing of water collected from different aquarium systems generated about 276 million sequence reads and showed great advantages in determining diversity of viruses due to its unprecedented sequencing depth. This dataset will be analyzed with our previous bioinformatics pipeline including for viral identification.5 Our results are important as they inform our future efforts to understand the role viruses and viral community dynamics play in the microbiomes of aquatic systems.


We enthusiastically thank the Fishes department aquarists and Marine Mammals staff for coordination of sample collecting and the technicians of the Environmental Quality and Clinical laboratories at Shedd Aquarium for sample collecting and processing. This work was supported in part by a generous gift from the Grainger Foundation.

* Presenting author

Literature Cited

1.  Balter M. Taking stock of the human microbiome and disease. Science. 2012;336:1246–1247.

2.  Vangay P, Ward T, Gerber, JS, Knights D. Antibiotics, pediatric dysbiosis, and disease. Cell Host Microbe. 21015;17(5):553–564.

3.  Wong S, Rawls J. Intestinal microbiota composition in fishes is influenced by host ecology and environment. Mol Ecol. 2012;21:3100–3102.

4.  Bik E, Costello EK, Switzer AD, et al. 2016. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun. 2016:7:1–13.

5.  Kim Y, Aw TG, Teal TK, Rose JB. Metagenomic investigation of viral communities in ballast water. Environ Sci Technol. 2015;49:8396–8407.


Speaker Information
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William Van Bonn, DVM
A. Watson Armour III Center for Animal Health and Welfare
John G. Shedd Aquarium
Chicago, IL, USA

Department of Veterinary Clinical Medicine
University of Illinois
Urbana-Champaign, IL, USA

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