Shark Microbiome

The microbiome is emerging as a significant player in organism’s health, and we are investigating the microbiome of the largest fish in the ocean, the whale shark and other sharks from around the world. The skin of sharks is constructed of dermal denticles, which possess the same features as teeth. These ‘skin teeth’ provide reduced fluid friction and thus increase swimming efficiency, but the effect on the microbiome is an unanswered question in science.
Our first assessment was of a Thresher shark. We showed that shark skin promotes a microbiome that is low in β-diversity, highly divergent from the water column, with specific functions that suggest high heavy metal loads (Doane et. al., 2017). These microbiome characteristics are inverse to those of mucus covered organisms. Our non-invasive sampling procedure being applied to various species of sharks has obtained several shark cells, and we were able to sequence and process the full mitochondrial genome, providing a new record for science and qualifying the phylogenetic position of the thresher shark (Doane et. al., 2018).
The high level of heavy metal genes in the microbiome may be a biproduct of sharks being at the top of the food chain and therefore, at each level of the food web heavy metals bio-accumulate, therefore the shark has the highest level. Alternatively the thresher sharks may have been in a location that had high levels of pollution. To tease apart these two possibilities, we will investigate whether sharks that have different lifestyles, i.e. eat invertebrates and small organisms, like the whale shark and the leopard shark compared with the thresher shark have microbiomes with lower proportions of heavy metal gene. We will also collect the microbiomes from sharks across locations away from human activity and high heavy metal loads to see whether location is causing the high level of heavy metal genes. If all sharks have high level of heavy metal genes in their microbiome, it may suggest that the microbes are using these genes to penetrate the dermal denticles.

We have a major project to investigating whale shark microbiomes across multiple locations to increase knowledge of microbial and shark biogeography. Whale sharks have been sampled from Cancun Mexico, La Paz Mexico, Mafia Island Tanzania. In June we will sample whale sharks in Exmouth Western Australia and Oslob the Philippines. This research has been made possible by a private donor to SDSU and as part of the research we have enabled three undergraduates and four graduates to experience the beauty of these animals and participated in a research expedition. In addition, our research has been made possible by our collaborators; Dr. Deni Ramirez from Mexico, Rafael de la Parra from Mexico, Dr. Simon Pierce from Africa, Dr. Richard Pillans from Australia, and Dr. Gonzalo Araujo from the Philippines.

Whale shark sampling – Cancun, Mexico

During July 2017 the Dinsdale lab traveled down to Cancun, Mexico to take microbial skin samples from whale sharks. This whale shark aggregation can be found a couple miles off the coast of Cancun and is the largest whale shark aggregation in the world. Whale sharks travel here to feed on millions of tuna eggs and swim slow enough, while they eat, that we are able to take microbial skin samples. We take these samples using a dual chambered syringe called the SuperSucker (featured in the video). To use the Supersucker, first sterile seawater is loaded into the SuperSucker, and then the SuperSucker is pressed against the side of the whale shark, which creates a seal separating the skin sample area from the surrounding water. Finally, the sterile seawater washes the microbes off the shark’s skin and back into the chamber. On the boat we ran the water samples the SuperSucker collected through filters that stored the microbial DNA until it could be processed. Special thanks to Rafael de la Parra and Deni Ramirez for their help and wisdom!


SEM image of the skin surface of a Leopard shark (Triakis semifasciata). The individual scale like structures are called dermal denticles, which are a teeth like structure covering the skin of the shark.
Whale shark swimming in La Paz Bay in Baja Sul, Mexico
Mike sampling the skin microbiome of the Whale shark
Michael Doane (left) and Dovi Kacev (right) aboard the Outerbanks participating in the annual common thresher shark survey of the California Bight that NOAA Southwest Fisheries Division supp    orts.