Characterising the gut microbiomes of two baleen whales with different feeding and migratory strategies

Mammalian gut microbiomes are essential for supporting digestion, nutrient absorption and overall host health. While diet and phylogeny are the two main influences on gut microbial composition, other factors, including life history and environment also contribute. Here, we characterised and compared the gut bacterial microbiomes of two baleen whale species with contrasting life histories: the Brydes whale (Balaenoptera edeni brydei), a non-migratory, year-round generalist forager; and the southern right whale (Eubalaena australis; SRW), a seasonally migrating species with a specific diet of krill and copepods. We found that each species harboured distinct gut microbiomes with potential links to their different feeding and migratory strategies. The Brydes whale gut microbiome bore a strong resemblance to that of toothed whales, with relatively lower bacterial richness and diversity and a high proportion of Proteobacteria. The core microbiome of these whales included taxa supporting a protein-rich diet and year-round foraging lifestyle, e.g. Carnobacterium and Faecalitalea. In contrast, the SRW harboured a gut microbiome similar to other baleen whale species, with a higher richness and diversity and dominated by Firmicutes and Bacteroidetes. SRWs were also sampled at different stages in the migratory cycle and correspondingly differed in the composition of their gut microbiomes. The SRW core microbiome featured taxa associated with lipid metabolism, e.g. Erysipelotrichaceae and Coriobacteriia, reflecting a lipid-rich diet and reliance on blubber reserves during migration. Our findings suggest that migratory behaviour and foraging patterns key aspects of cetacean life history may substantially influence gut microbiome structure and function.