A Comparison of Standard Clinical Microbiology Diagnostic Techniques to High Throughput Sequencing Using 16s rRNA Gene Analysis in Wild, Sea Side and Aquarium Bottlenose Dolphins (Tursiops truncatus), and the Water They Inhabit
IAAAM 2019
Michael T. Walsh1*; Brent Whitaker2; Yong Ge3; Minghao Gong3; Pat Clough4; Randall S. Wells1,5; Shelly Marquardt6; Laurie Adler1; Rachael Dailey1; Maria Jose Robles Malagamba8; Bikash Sahay3; Craig Pelton1; Mansour Mohamadzadeh3
1Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA; 2National Aquarium, Baltimore, MD, USA; Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD, USA;3Department of Infectious Disease and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA; 4Dolphin Research Center, Grassy Key, FL, USA; 5Chicago Zoological Society’s Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA; 6Clearwater Marine Aquarium, Clearwater, FL, USA; 7Delphinus, Quintana Roo, Mexico


The relevance of bacterial population involvement in health and disease of animals and humans has been relatively recent following the early development of microbiology in the mid-19th century. The information gained from clinical cultures is often incomplete due to cost and the resources needed, limits set on species tested, drugs available in sensitivity panels, and availability to detect anaerobic organisms. The implications of the relationship between emerging microbiota research and health including immune system support, digestion, protection from pathogenic bacteria,2,3,4,5 and an appropriate balanced bacterial flora6 in each body site is thought to be extremely important. To better document and compare bacterial populations of interest in bottlenose dolphins, samples were collected from skin, blow, gastric, fecal and urogenital sites from dolphins from an aquarium, seaside pens, and Sarasota Bay during health examinations.1 These were analyzed by standard cultures techniques at Micrim Labs Inc. and were compared to parallel samples assessed by PCR amplification of a hypervariable region (V3–V4) of the bacterial 16s rRNA gene for each sample followed by sequencing on an Illumina MiSeq platform.2 Water samples were also obtained from each location for microbiota. Results showed a surprising variation between populations and environments compared to standard culture techniques and the need to consider anaerobes as a major component of normal flora and therapy. Veterinarians should consider the technique’s potential for future inclusion in clinical applications as normal ranges are determined, prices go down and this area better explains numerous aspects of the animal’s bacterial populations.


The authors would like to express their deep gratitude to the researchers, water quality personnel, veterinarians and staff members at the National Aquarium, Dolphin Research Center, Clearwater Marie Aquarium and the Sarasota Dolphin Research Program for their dedication and support for this project. This project was financially supported by the John Ben Snow Foundation, Syracuse NY.

Micrim Labs Inc. 800 E Cypress Creek Rd # 202, Fort Lauderdale, FL 33334

*Presenting author

Literature Cited

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2.  Bik EM, Costello EK, Switzer, AD, Callahan BJ, Holmes SP, Wells RS, Carlin KP, Jensen ED, Venn-Watson S, Relman DA. 2016. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nature Commun. 7:10516 doi: 10.1038/ncomms 10516.

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4.  Shulzhenko N, Morgun A, Hsiao W, Battle M, Yao M, Gavrilova O, Orandle M, Mayer L, Macpherson AJ, McCoy KD, Fraser-Liggett C, Matzinger P. 2011. Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut. Nature Medicine, 17(12), 1585–93. doi:10.1038/nm.2505.

5.  Tlaskalova-Hogenova H, Stepankova R, Hudcovic T, Tuckova L, Cukrowska B, Lodinova-Zadnikova R, Kozakova H, Rossmann P, Bartova J, Sokol D, Funda D.P, Borovska D, Rehakova Z, Sinkora J, Hofman J, Drastich P, Kokesova A. 2004. Commensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseases. Immunol Lett. 93:97–108.

6.  Diaz MA, Bik EM, Carlin KP, Venn-Watson SK, Jensen ED, Jones SE, Gaston EP, Relman DA, Versalovic J. 2013. Identification of Lactobacillus strains with probiotic features from the bottlenose dolphin (Tursiops truncatus). J. Appl. Microbiol. 115:1037–1051.


Speaker Information
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Michael T. Walsh
Aquatic Animal Health Program
College of Veterinary Medicine
University of Florida
Gainesville, FL, USA

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