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Biogeochemistry

Of whales and cows: the baleen whale microbiome revealed

J.G. Sander, A.C. Beichmann, J. Roman, J.J. Scott, D. Emerson, J. McCarthy, and P.R. Girguis. Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nature Communications. 22 September 2015. DOI: 10.1038/ncomms9285.

The Illuminated Ruminant.

The Illuminated Ruminant.

We are animals, and our cells are eukaryotic cells, but our bodies are host to upwards of ten times more bacterial cells, also known as our “microbiome”. The microbiome of our guts is particularly important in helping our bodies to access energy stored in the food we eat—without it we would starve. So, how is an individual’s gut microbiome determined? That “your gut microbiome is what you eat” shouldn’t come as too much of surprise, as an organism needs to be able to extract nutrients from the foods it ingests. On the other hand, the way that microbiomes have been inherited through evolutionary time is less intuitive, since the composition of the microbiome has everything to do with environment and nothing to do with the inherited genetic code of the host organism. One way to study this so-called “phylogenetic inertia” is to examine the microbiomes of two distantly related groups of animals with distinct diets. It so happens that whales and cows are related by a common terrestrial ancestor, but while cows are exclusively herbivorous, whales are strictly carnivorous. Hence, a comparative study of their respective microbiomes could tell scientists something about the role of phylogenetic inertia in shaping the gut microbiome.

So, asked a team of U.S. researcher led by Jon G. Sanders, how does the microbiome of a whale compare to that of terrestrial mammals (both herbivores and carnivores)? The study reported recently Nature Communications shows both expected parallels with the microbiomes terrestrial carnivores, as well as some surprising similarities between the gut microbiomes of baleen whales and terrestrial herbivores (like cows).

To obtain samples used in their study, Sanders et al. first scoured the Atlantic Ocean, fishing fresh whale poop from off the side of a ship. With samples in hand from three Atlantic whales, and then some Pacific poop courtesy kindly collaborators, they extracted the DNA content of the poop, and sent it out for sequencing. As a first pass, they performed a community-level analysis to determine what bacterial species were present in the surveyed baleen whale gut microbiome. As expected, the diversity of baleen whale microbiomes different markedly from those of terrestrial mammals.  Indeed, the baleen whale microbiome shared only about ten percent in common with species identified in terrestrial microbiomes. Surprisingly, that slice of the baleen whale microbiome showed more similarity to microbiomes of terrestrial herbivores than it did to terrestrial carnivores, despite the whale’s strictly carnivorous diet.

Sander et al. next shifted from the question of “who’s who?” in the microbiome to “what do they do?”. Consistent with the whale’s carnivorous diets, Sanders and co-workers found genes encoding for enzymes that are involved in break down of proteins. What caused more of a stir were the similarities they found between baleen whales and terrestrial herbivores in enzymes involved in carbon metabolism and fermentation. Cows rely heavily on fermentation as a means of digesting the polysaccharide cellulose, which is the main structural component of plant cell walls.  By analogy, baleen whales consume a diet rich in the marine counterpart of cellulose, chitin, which makes up the shells of zooplankton.  Indeed, making the most of their food makes a great deal of sense for animals that swim thousands of miles every year.

Sanders et al. conclude that the similarities between the whale gut microbiome and that of cows may arise from a conserved gut morphology. Both baleen whales and cows possess a conserved foregut. In cows this foregut is established to serve as a fermentative chamber for the breakdown of cellulose. In baleen whales, it would appear that this ancestrally-derived feature was adapted to extract energy from the cellulose of the sea—chitin. Taking a step back, Sanders et al. further speculate that the whale microbiome may serve an important function in the global carbon cycle by breaking down difficult-to-digest chitin into simpler carbon building blocks that can be mineralized back into carbon dioxide that is in turn utilized by photosynthetic organisms and so on and so forth back to chitin—to think it all started with some stink-y whale poops!

 

Abrahim El Gamal
Abrahim is a PhD student at Scripps Institution of Oceanography in San Diego where he studies marine chemical biology.

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