Divergent Gut Microbiomes of Toothed and Baleen Whales

The mammalian gastrointestinal tract is inhabited by a multitude of microbial communities, providing functional features the host may not have acquired during their own genomic evolution. Obligate aquatic mammals such as whales, having invaded the water millions of years ago, may represent ideal closed systems with which to study deep time evolutionary associations of the intestinal microbiota. In this study, we explored the distal gut of the bowhead whale (Balaena mysticetus) and the long-finned pilot whale (Globicephala mela), a baleen and a toothed whale, respectively. We show that these two whale species harbor unique gut microbiota, with the pilot whale being highly divergent from terrestrial mammals. The predicted functions of the microbiomes from the two whale species were highly similar to terrestrial mammals, although similar functions are encoded by different microbial assemblages in the two whales, with the bowhead whale appearing more comparable to terrestrial herbivores, and the pilot whale more similar to carnivores. We hypothesize that these differences in microbial flora between whale species are the result of different dietary, environmental, and evolutionary influences, and that their gut microbiomes co-diversified with their marine host to occupy functions that are largely convergent across mammalian phylogeny.