Of microbes and whales

At the end of January, the International Society for Microbial Ecology (ISME) journal put out a list: “Readers’ Choice: The best of The ISME Journal 2019” . I don’t know about you (my fellow scientists also with 35+ chrome tabs open to papers to read), but I often feel behind on reading and worry I missed something during the week’s madness. I am also a list person, so this caught my eye and reminded me of a paper from December about two of my favorite things: microbes and whales.

Before we dive (forgive me) into the whale story, I want to note this brief list covers ALL sorts of things from the role of viruses in antibiotic resistance (Debroas and Siguret, 2019), to the microbes responsible for methane production in livestock (Greening et al, 2019), to deep sea archaea that live under the sea floor (Carr et al., 2019). Also, while ideally all of these articles would be open access, at least the majority (12/17) are. Glancing at these article titles reminded me of all the weird and nifty ways the microbial world influences everything around us…okay back to the bowheads.

Whales play an important role in cycling nutrients in the ocean by eating tons of little critters and then pooping scarce nutrients right back into the sea from whence they came. Miller and colleagues point out that sperm whale poop has been shown to stimulate primary production in the Southern Ocean, if you need a visual…here you go. While it’s clear that whale “digesta” (as it’s politely called in the article) is important in biogeochemical cycling…it’s tricky to study.

Bowhead whale GI tract diagram and the 9 sites sampled as well as a comparison of the whale microbiome and what lipids (the lipidome) are present at all sites. (Figure 1 – Miller et al., 2019).

Miller and co-authors, wanted to understand what possible role the microbes might have in relation to the tricky things that whales digest, specifically lipids, and more specifically lipids known as wax esters. All 126 digesta samples were collected by hand by Alaskan Eskimos during subsistence hunts. Thanks to this opportunity generously granted to the researchers by the Alaskan Native whaling captains of the Barrow Whaling Captains Association [http://www.aewc-alaska.org/home.html] to obtain otherwise impossible samples, they were able to study the microbial community from 9 (!!) distinct regions of the gastrointestinal (GI) tract of 38 whales over the course of four years.

Core microbial taxa represented in each GI tract sample. Showing that different members dominate at distinct sites. (after Figure 2 – Miller et al., 2019).

The authors showed that the microbial communities in the GI tract are possibly helping in the digestion of wax esters. This difficult fat to digest is incidentally concentrated in itty bitty crustaceans (like krill), a main food source for bowhead whales. Thanks to sampling many sites along the GI tract, the authors sorted out which bacteria were most abundant where as well as look at the concentration and types of different lipids along the way. Ultimately, they identified where in the gut the wax esters dropped off in concentration and were able to correlate certain bacterial abundance levels with this drop.

Studying whales isn’t easy, and there is much to learn about the enzymes that break down wax esters, exactly how whales digest these abundant lipids is still unknown. I particularly appreciated the section of “Considerations” that the authors include acknowledging multiple variables that could have impacted the study. If you are looking for another light read on the article, check this out from Woods Hole. This paper is an interesting in-depth step towards understanding nutrient cycling of a super abundant compound in the ocean…and you might learn more than expected about the whale GI tract.


Miller, C.A., Holm, H.C., Horstmann, L., George, J.C., Fredricks, H.F., Van Mooy, B.A. and Apprill, A., 2019. Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion. The ISME Journal, pp.1-14. https://doi.org/10.1038/s41396-019-0549-y

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