Theses and Dissertations

Defense Date

7-28-2017

Document Type

Thesis

Degree Name

M.S. Marine Biology

First Advisor

Jose Lopez

Second Advisor

Cole Easson

Third Advisor

Mahmood Shivji

Abstract

The microbiome (microbial community) of individuals is crucial when characterizing and understanding processes that are required for organism function and survival. Microbial organisms, which make up an individual’s microbiome, can be linked to disease or function of the host organism. In humans, individuals differ substantially in their microbiome compositions in various areas of the body. The cause of much of the composition diversity is yet unexplained, however, it is speculated that habitat, diet, and early exposure to microbes could be altering the microbiomes of individuals (Human Microbiome Project Consortium, 2012b, 2012a). To date, only one study has reported on microbiome characterization in a shark (Doane et al., 2017; skin microbiome of the common thresher shark). A comparative characterization of microbiomes sampled from different shark species and anatomical locations will allow an understanding of the differences in microbiomes that may be explained by variance in shark habitat and diet. Florida leads as shark bite capitol of the world, with 778 unprovoked bites recorded since 1837, or 4-5 average bites per year. With only a few bites a year, there is not a lot of opportunities to study these bites. What can be studied, however, is how the microbial environment in shark’s teeth is composed. To understand overall microbiome composition, and if microbiomes are distinct from the environment, or specific by species or anatomical location (henceforth location), we characterized microbiomes from the teeth, gill, skin, and cloacal microbiomes of 8 shark species in south Florida (nurse, lemon, sandbar, Caribbean reef, Atlantic sharpnose, blacktip, bull, and tiger) using high throughput DNA sequencing of the 16S rRNA gene V4 region. There was a significant difference in microbial community richness among species, sample location, but not the interaction between species and location. Microbial diversity by location was significantly different for both the Shannon index and Inverse Simpson index. Samples examined by species had no significant difference in microbial community diversity overall for both Shannon and Inverse Simpson indexes. Microbial community diversity of samples by location and species combined significantly differed when submitted to an analysis of variance with the Shannon index, but not the Inverse Simpson index. Teeth microbial communities showed the most diversity based on both Shannon and Inverse Simpson indices. Teeth microbiomes are distinct but also share taxa with the water they inhabit, including potentially pathogenic genera such as Streptococcus (8.0% ± 9.0%) and Haemophilus (2.9% ± 3.3%) in the Caribbean reef shark. The lemon shark teeth hosted Vibrio (10.8% ± 26.0%) and the Corynebacterium genus (1.6%±5.1%). The Vibrio genus (2.8% ± 6.34%), Salmonella enterica (2.6% ± 6.4%), and the genus Kordia (3.1% ± 6.0%) are found in the nurse shark teeth microbial community. Strikingly, the Vibrio genus was represented in the sandbar shark (54.0% ± 46.0%) and tiger shark (5.8% ±12.3%) teeth microbiomes. One OTU related to traditionally non-pathogenic family Phyllobacteriaceae appear to be driving up to 32% of variance in teeth microbiome diversity. We conclude that south Florida sharks host distinct microbiomes from the surrounding environment and vary among species due to differences in microbial community richness. Future work should focus on bacteria found in shark teeth to determine if those present are pathogenic and could provide insights to bite treatment.