Humpback whale microbiome changes with the seasons

Researchers from the Woods Hole Oceanographic Institution (WHOI), Duke University, and the University of California, Santa Cruz sampled 89 whales under tricky conditions

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When people think of microbiologists, they tend to think of lab coat-wearing geeks with no idea of what constitutes an appropriate dinner table conversation. Sadly, I have done nothing to dispel this stereotype, in fact I was reminded over lunch yesterday how much I was promoting it (apparently the nasal microbiome puts people off their food). When thinking of microbiologists, very few people would imagine a young explorer, hanging over the side of a dinghy in the Antarctic with a crossbow tightly gripped in their hand, aimed carefully at the upper flank of a humpback whale.

But that’s just another day at the office for Amy Apprill and KC Bierlich, who just published a paper titled “Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula” in Applied and Environmental Microbiology. You may think the name Amy Apprill sounds familiar, that’s because a few months ago, she published an article detailing how she used a hexacopter drone to sample the microbiome of whale blowholes. In other words, she is my new hero.

Antarctic Humpback Whale Biopsy from Woods Hole Oceanographic Inst. on Vimeo.

The team used their 68 kg pull crossbow and floating Ceta-Dart darts with 40 mm surgical stainless steel tips ("described as "standard biopsy techniques" in the methods), to sample the skin microbiome of 89 healthy humpback whales. "Humpback whales are a particularly interesting species for microbiome studies because they are found in every ocean," says Bierlich. "They regularly migrate between high-latitude summer feeding grounds and low-latitude winter breeding grounds, which exposes their skin to a wide variety of ocean conditions and environments."  

Analysis of sequencing data revealed that 6 core genera were present in 93% of the healthy whales. However, the composition was affected by the season. "The analyses of skin samples in late summer showed that the whales' microbiome changes, perhaps in response to seasonal shifts in water temperature. But the microbes may also be affected by less predictable changes, such as the amounts of sea ice," says Apprill.

This exciting new study may provide a method to monitor the health of humpback whales, as well as providing information on their lifestyle, such as foraging patterns. They could also serve as sensitive indicators of changes in the ecosystem.


The skin is the first line of defense between an animal and its environment, and disruptions in skin-associated microorganisms can be linked to an animal's health and nutritional state. To better understand the skin microbiome of large whales, high-throughput sequencing of partial small subunit ribosomal RNA genes was used to study the skin-associated bacteria of 89 seemingly healthy humpback whales (Megaptera novaeangliae) sampled along the Western Antarctic Peninsula (WAP) during early (2010) and late (2013) austral summers. Six core genera of bacteria were present in 93% or more of all humpback skin samples. A shift was observed in the average relative abundance of these core genera over time, with the emergence of four additional core genera corresponding to a decrease in water temperature, possibly caused by seasonal or foraging related changes in skin biochemistry that influenced microbial growth, or other temporal-related factors. The skin microbiome differed between whales sampled at several regional locations along the WAP, suggesting that environmental factors or population may also influence the whale skin microbiome. Overall, the skin microbiome of humpback whales appears to provide insight into animal and environmental-related factors and may serve as a useful indicator for animal health or ecosystem alterations.

IMPORTANCE: The microbiomes of wild animals are currently understudied, but may provide information about animal health and/or animal-environmental interactions. In the largest sampling of any marine mammal microbiome, this study demonstrates conservation in the skin microbiome of 89 seemingly healthy humpback whales sampled in the Western Antarctic Peninsula, with shifts in the bacterial community composition related to temporal and regional variability. This study is important because it suggests that the skin microbiome of humpback whales could provide insight into animal nutritional or seasonal/environmental-related factors, which are becoming increasingly important to recognize due to unprecedented rates of climate change and anthropogenic impact on ocean ecosystems.


Appl Environ Microbiol. 2017 Dec 21. pii: AEM.02574-17. doi: 10.1128/AEM.02574-17. [Epub ahead of print]
Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula.
Bierlich KC, Miller C, DeForce E, Friedlaender AS, Johnston DW, Apprill A.

Ben Libberton

Science Communicator, Freelance

I'm a freelance science communicator, formerly a Postdoc in the biofilm field. I'm interested in how bacteria cause disease and look to technology to produce novel tools to study and ultimately prevent infection.