Epidermal Microbiome Structure of Leopard Sharks (Triakis semifasciata) Across Spatial and Temporal Scales

The group of micro-organisms that reside on or in the body of an organism, known as a microbiome, are vital for its health. A core microbiome is the set of microbes which can be found within the microbiome of all healthy organisms within a species. Describing the core microbiomes will provide an understanding of the effect of abiotic factors on the microbiome and identify dysbiosis. Here we characterized the taxonomic and functional gene structure of the epidermal microbiome of 32 individual leopard sharks (Triakis semifasciata) from La Jolla, CA (2013, 2015, 2017), Moss Landing, CA (2015), the Birch Aquarium (2018 & 2019), and the Scripps Institute of Oceanography Aquarium (2016). Microbial DNA was extracted from the samples using a Macherey Nagel Tissue Kit, and prepared into libraries using a Swift 2S Plus Kit and PCR a OneTouch kit. The DNA library was shotgun sequenced using a Mi-Seq Illumina sequencer and Mi-Seq v3 Kit and produced 28,418,189 metagenome sequences. The taxonomic annotation was conducted by Focus and the functional gene annotation was performed by Superfocus. We discovered a core microbiome of 10 genera present in 78.12% of the samples, including Helicobacter and Mycoplasma. The β-diversity described as a Bray-Curtis similarity index shows the sharks sharing 52.91% of genera, which was lower than thresher sharks. A PERMANOVA with a Benjamini-Hochberg correction revealed the functions of the microbiome did not remain stable across a temporal scale in La Jolla (p=0.001). Although we have identified a core microbiome, the genetic potential within this core varies over time. Therefore, we suggest that the microbiome is adapting to abiotic conditions by varying the functional genes represented in each microbial taxon. This maintains a core microbiome and health of the shark.