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 (faecal) bacterial microbiomes of two baleen whale species with contrasting life histories: the Bryde's whale (Balaenoptera edeni brydei), a non-migratory, year-round generalist forager; and the southern right whale (Eubalaena australis; SRW), a seasonal migrating species with a specialised 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 Bryde's 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 after Firmicutes. 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 had a gut microbiome similar to other baleen whale species, with a higher richness and diversity, and dominated by Firmicutes and Bacteroidetes. 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. We also found that SRWs sampled at different stages in the migratory cycle had significantly different gut microbial compositions. Functional analyses further supported these results, with Bryde's whales being broadly enriched in enzymatic functions including protein digestion and SRWs showing more selective enrichment.

Along with species-specific microbiomes, our findings also suggest that migratory behaviour and foraging patterns - key aspects of cetacean life history - may substantially influence gut microbiome composition. The characterisation of the gut microbiomes of the two whales provides a valuable baseline for the future monitoring of cetaceans and their environments.