Metagenomic Investigation of the Whale Gut Microbiome

All exposed surfaces of the animal body are inhabited by a multitude of microbial communities, referred to as the microbiome, that provide functional features the host may not need as part of their own genomic evolution. Comparative studies of mammalian microbiomes are key for understanding not only the composition, function, and evolution of these microbial symbionts, but also the possible codiversification of the microbiota and their hosts. Metagenomic sequencing can assemble the collective genomes of the microbiomes of multiple organisms, and identify overlapping or species-specific microbial diversity and some of the distinctive functional attributes encoded in these microbiomes. We explored the gut microbiomes of two marine mammals, a baleen and a toothed whale, that differ in their feeding strategies, digestive anatomy, and physiology. Based on 16S rRNA amplicon and shotgun genomic sequencing on distal gut samples, we show that these two whale species harbor unique gut microbiomes, with the pilot whale highly divergent from terrestrial mammals. On the other hand, at a superficial level, the functional potential of the microbiomes from the two whales are highly similar to terrestrial mammals, although functions may be encoded from different microbial assemblages in the two whales, with the pilot whale appearing more similar to carnivores. We hypothesize that the difference in microbial flora between the marine species is a result of different dietary, environmental, and evolutionary influences, and that their gut microbiomes co-diversified with their hosts to occupy functions largely convergent across mammalian phylogeny.