Date of Award


Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)


Environmental Sciences/Environmental, Earth & Ocean Sciences

First Advisor

Michael Tlusty

Second Advisor

Jennifer Bowen

Third Advisor

Charles Innis


All species of sea turtles are threatened or endangered, with various diseases and conditions affecting populations around the world. Understanding healthy populations as well as populations beset by disease conditions, such as fibropapillomatosis and cold-stunning, could lead to helpful tools in the conservation management and medical treatment needed to protect these species. Microbial communities, or the microbiome, at different body sites of sea turtles likely play important roles in the health of these animals, from aiding in digestion to immune system regulation. Disruption of these communities, either through disease and/or environmental factors, may play a role in disease processes and recovery in sea turtle species.

Given the importance of microbial communities in health and disease, my dissertation sought to: 1) characterize the microbiome of two species of sea turtles, Kemp’s ridley and green turtles, from the same habitat in the wild, 2) characterize the microbiome of cold-stunned Kemp’s ridley turtles through rehabilitation, and 3) investigate the respiratory microbiome of Kemp’s ridley turtles in relation to radiographic lung abnormalities and diagnostic tools. To carry out these objectives, I used sequencing of the 16S rRNA gene to identify microbial community composition of various body sites from sea turtles for each experiment. In wild turtles, I identified distinct core microbes from the oral cavity and cloaca of two species of healthy, wild caught sea turtles. In stranded turtles, I characterized the same body sites, oral cavity and cloaca, throughout rehabilitation and found shifts in the microbial community composition throughout hospitalization, including alterations due to antibiotic therapy. I also found that the microbiome did not correlate with disease condition or physiological abnormalities in stranded cold-stunned turtles. Since lung abnormalities are prevalent in cold-stunned turtles, I also examined the respiratory microbiome through tracheal washes and necropsy samples. I found that lungs contained a diverse and variable microbial community and identified limitations of tracheal washes as a diagnostic tool. Taken together, these results contribute to understanding the microbiome of sea turtles across disease states and environmental conditions by identifying the microbial community composition at different body sites, through different methods, and based on different disease conditions.