Global Whale Shark (Rhincodon typus) microbiome: regional taxonomic flexibility and functional stability

Whale sharks, the largest fish in the ocean, have a global distribution and are often targeted for shark tourism. The whale shark feeds on phytoplankton, eggs and larvae of vertebrates, such as fish and invertebrates, such as coral. The whale shark has a global distribution, and is therefore an ideal species to investigate the biogeography of host associated microbes. We sampled the skin microbiomes of 120 whale sharks from 5 location around the world. Microbial samples were collected whilst on snorkel using a supersucker device. The device was filled with sterile sea water and flushed the microbes off the skin of the shark from the flank region under the dorsal fin. Microbes were collected in a 0.22 um sterivex and DNA extracted and sequenced on the Illumina platform. Annotation was conducted using Focus and Superfocus, two kmer based programs. The microbial taxonomic diversity varied across geographic regions, whereas the functional diversity showed no difference. The taxonomic make-up of the microbiome was highly distinct at each location. A bray-Curtis analysis showed 5 % similarity between the microbiomes from La Paz, Mexico and Ningaloo, Western Australia, 21 % between Ningaloo, and Oslob, Philippines, with Cancun, Mexico and Tanzania showing 42 % similarity between microbial taxa. Whereas, the microbial functions showed > 83 % similarity between sharks from all regions, suggesting core functional attributes are required for life on the skin of whale sharks and the functions are found in different microbes depending on location.