Date of Award


Document Type

Open Access Thesis

First Advisor

Pamela J. Morris


Cetaceans are proposed as sentinel species for assessing the health of marine ecosystems and human coastal populations. This relationship has been based on similarities in the bioaccumulation of pollutants by cetaceans and humans, as well as their susceptibility to infectious disease. Respiratory disease represents a major cause of mortality in humans and cetaceans, and culture-dependent studies and 16S rDNA gene sequencing have identified known human respiratory pathogens from immunocompromised and healthy dolphins.

To broaden our understanding of the microbial community associated with dolphin upper respiratory tracts (URT), we characterized metagenomes generated from the URT of Atlantic bottlenose dolphins (Tursiops truncatus) from coastal Georgia. Using MG-RAST, we compared dolphin URT metagenomes to metagenomes from healthy human anterior nares, cystic fibrosis (CF) afflicted human lungs, and healthy human lungs. Human and dolphin respiratory metagenomes were dominated by four bacterial phyla (Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes). Ascomycota and Basidiomycota were the only fungal phyla identified in the dolphin URT and human lung, whereas the human nares displayed greater fungal diversity. With mostly unclassified viruses in dolphins, order-level viral comparisons demonstrate similarities between dolphin URT and healthy human lung. However, Genus-level distributions showed differences, with the phage Chlamydiamicrovirus dominating the classified dolphin sequences and absent in the human respiratory metagenomes.

Known cetacean respiratory pathogens were detected in the dolphin and human metagenomes, including bacterial pathogens Staphylococcus aureus, Streptococcus spp., Nocardia spp., and Aeromonas spp.; fungal pathogens Aspergillus spp. and Cryptococcus spp.; and the protozoan Toxoplasma gondii. The bacterial pathogen Erysipelothrix rhusiopathiae and the fungal pathogens Candida glabrata and Ajellomyces dermatitidis were detected exclusively in the dolphin URT. Human adenoviruses A-G were detected in the dolphin URT and adenovirus C in the nares. Additionally, dolphin URT metagenomes were compared with healthy cetartiodactyls (big horn sheep, okapis, pig, giraffe, and cow) and healthy human fecal metagenomes. Bacteroidetes, Actinobacteria, Firmicutes, and Proteobacteria also dominated the fecal metagenomes, although the percentage of Bacteroidetes in human feces double that observed in the dolphin URT and cetartiodactyl fecal metagenomes. Fecal samples had higher fungal diversity and fewer unclassified viruses than the dolphin URT metagenomes.

.Comparison between the dolphin, human and cetartiodactyl metagenomes reveal similarities at higher taxonomic levels. However, dolphin URT microbial community specificity is discernible across genera/species. These results broaden our understanding of the dolphin respiratory microbiome, and represent the first comparison with human respiratory metagenomes. Our findings help to establish a baseline respiratory microflora that can be used to validate the role of cetaceans as sentinels for ecosystem health and indicators of emerging marine mammal and human respiratory pathogens.