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Baleen Whale Shares Gut Microbiome Features with Land Herbivores, Carnivores

NEW YORK (GenomeWeb) – A Harvard University-led team has characterized gut microbial communities in baleen whales and found that they overlap with those of land animals.

The researchers, who published their findings online in Nature Communications today, used a combination of 16S ribosomal RNA gene sequencing and metagenomic sequencing data to characterize microbial community members and microbial gene repertoires in fecal samples from baleen whales off Canada's Bay of Fundy. They then compared these gut microbiomes with those found in whale or dolphin species that have teeth, as well as those of various terrestrial mammals.

The team's results hint that the fish- and crustacean-consuming baleen whales carry gut microbial communities that share functions with gut microbiomes from terrestrial carnivores and herbivores, though their overall composition differs from those described in such land mammals.

"As in previous surveys of mammalian gut microbiota, our data show correlations with both diet and host phylogeny, depending on which dimensions of the data are being considered," senior author Peter Girguis, an organismic and evolutionary biology researcher at Harvard, and his colleagues wrote.

In the case of the baleen whale, they explained, the gut microbiome seems to be influenced not only by the host's diet but also by the  organization of the animal's multi-chambered foregut.

Cetaceans, such as whales and dolphins, share digestive features with land animals that are evolutionarily related to them,namely so-called artiodactyls, which include cows and hippopotami, the team noted.

But while both cetaceans and artiodactyls have multi-chambered stomachs, their diets are as different as their habitats, prompting interest in the gut microbial communities of whales and dolphins.

For the current study, the researchers focused on baleen whales, which scarf down chitin-shelled crustaceans and small schools of fish by filter feeding.

To determine the microbial members present in these animals' guts, the researchers used Illumina MiSeq or Roche 454 sequencers to analyze the V4 or V1-V3 gene regions, respectively, of the 16S rRNA gene in fecal samples from baleen whales.

They then compared these to new and existing gut microbial community patterns for other animals, including related toothed whale or dolphin species living in the wild or in captivity.

For a subset of the cetacean samples, the team used metagenomic sequencing to look at the overall microbial gene content. It also analyzed the metagenomes of five more cetacean fecal samples and samples from several other terrestrial and aquatic animals.

As in terrestrial mammals profiled previously, microbial communities in the baleen whale gut tended to include many representatives from the Bacteroidetes and Firmicutes phyla, the researchers noted.

Despite these and other coarse-grain similarities, though, the team saw a slew of differences between terrestrial animals and the cetaceans when they drilled down to the level of operational taxonomic units in the gut.

In contrast to the sizeable diversity detected in the guts of herbivore animals living on land, for example, the whales tended to have less diverse gut microbiomes that more closely resembled those in terrestrial carnivores.

On the metagenomic side, too, the team found that whale gut microbiomes tended to contain genes that carnivores on land carry in their guts to aid in processes such as protein digestion and protein production — perhaps reflecting the baleen whale's mainly meat-based diet.

Still, the microbial gene sequence data also revealed metabolic pathway players that are believed to help carry out functions in digestive steps, such as polysaccharide fermentation, that are used by both terrestrial herbivores, for example cows, and the cetaceans.

Though additional research is needed to track microbiome patterns across different sites in the whale's digestive tract, the researchers argued that their findings "highlight the potential impact of the multi-chambered artiodactyl gut on global marine biogeochemistry."

"Using many of the same fermentative pathways and higher microbial taxa that their terrestrial relatives employ to utilize cellulose, the most abundant biopolymer on land," they explained, "whales evolved a process to utilize chitin, the most abundant biopolymer in the sea."