Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores

Mammals host gut microbiomes of immense physiological consequence, but the determinants of diversity in these communities remain poorly understood. Diet appears to be the dominant factor, but host phylogeny also seems to be an important, if unpredictable, correlate. Here we show that baleen whales, which prey on animals (fish and crustaceans), harbor unique gut microbiomes with surprising parallels in functional capacity and higher level taxonomy to those of terrestrial herbivores. These similarities likely reflect a shared role for fermentative metabolisms despite a shift in primary carbon sources from plant-derived to animal-derived polysaccharides, such as chitin. In contrast, protein catabolism and essential amino acid synthesis pathways in baleen whale microbiomes more closely resemble those of terrestrial carnivores. Our results demonstrate that functional attributes of the microbiome can vary independently even given an animal-derived diet, illustrating how diet and evolutionary history combine to shape microbial diversity in the mammalian gut.


Toothed whales
In contrast to baleen whales, the toothed whale samples in our dataset were highly variable in taxonomic composition, often dominated by one or two bacterial lineages typically found at lower abundance in other mammalian guts (Fig 1a). Some of these dominant OTUs were perfect matches to sequences previously recovered from marine environmental samples, including the Gammaproteobacteria Pseudoalteromanas and Photobacterium, suggesting the potential for an environmental origin. Some of these sequences also matched a library of bacterial 16S sequences associated with marine copepods, further suggesting the potential impact of environmental bacteria (Supplementary Fig. 2). However, three other dominant OTUs were 99-100% matches to sequences previously recovered from other marine mammals, including Mycoplasma (Tenericutes), Mycobacterium (Actinobacteria), and Cetobacterium (Fusobacteria). In aggregate, the taxonomic composition we observed in toothed whales showed a similar trend to what has previously been reported for piscivorous pinnipeds 1,2 , with an enrichment in Proteobacteria and Fusobacteria relative to terrestrial mammals.
The three toothed whale metagenomes also showed notable differences to the overall pattern of similarity with 16S data, with these samples having dramatically different profiles of predicted functional genes. Taxonomic profiling suggests an extremely high degree of host genomic contamination for these samples: between 20 and 90% of reads matched most closely to eukaryotic sequences in the KEGG database ( Supplementary Fig. 8). Manual inspection of these reads reveals that most match closely to the low-coverage genomic sequence available for the dolphin Trusiops truncatus (Ensembl accession turTru1) or to Bos taurus, suggesting that the sequenced DNA was derived from the host animal rather than undigested food or laboratory contamination. The source of this host DNA is unknown, but may arise from sloughing intestinal epithelia in a midgut that is much longer than in most other mammals 3 .
Together with the high taxonomic variability observed in 16S data from these samples, the high proportion of host sequence suggests that these samples may not be directly comparable to other samples; we have consequently excluded them from further analysis.

Difference among whales
Comparison of whale species within our sample set also showed moderate differences in microbial composition, potentially reflecting differences between diets.
Our Illumina 16S data consisted of seven right whales, which feed primarily upon crustaceans such as calanoid copepods, and five other baleen whales (humpback and sei whales), which consume both vertebrate and invertebrate prey. Compared with right whales, other baleen whales appeared to retain more of the bacterial taxa that were also more abundant in terrestrial mammals, such as Bacilli, Blautia, Coprococcus, and Coprobacillus, than did right right whales (Supplementary Data 2). Diets consisting entirely of invertebrates would be likely to contain higher proportions of fermentable animal polysaccharides (including chitin). Consistent with this, the clade 5 Verrucomicrobia, which were more enriched in baleen whales and terrestrial herbivores than in other mammals, were also significantly more abundant in right whales than in other baleen whales. These overall differences in community composition were especially apparent in an initial 454 dataset of the V1-V3 regions of 16S, with baleen whales grouping separately from both terrestrial samples and from Antarctic seals ( Supplementary Fig. 9).