Study Identifies Whale Blow Microbiome

Oct. 12, 2017

Drone Collected Samples Provide New Tool for Health Monitoring

Washington, DC - October 10, 2017 - A new study by the Woods Hole Oceanographic Institution (WHOI) and colleagues identified for the first time an extensive conserved group of bacteria within healthy humpback whales' blow—the moist breath that whales spray out of their blowholes when they exhale. The research is published this week in mSystems, an open-access journal of the American Society for Microbiology.

The discovery of this shared respiratory microbiome could serve as an important framework for monitoring the health of this and other whale species. Just like with humans, scientists say the assemblages of microorganisms that live in and on whales—known as microbiomes—may play a crucial role in their overall health, from maintaining a healthy immune system to fighting off disease.

Blow samples were collected from two different humpback populations: 17 from whales in coastal waters off Cape Cod, Ma. and nine from whales in waters around Vancouver Island, Canada. The team then sequenced the genetic material found in the blow samples to determine what kinds of microorganisms are living in a whale’s respiratory tract.

"The pulmonary system is a common site for bacterial infections in whales," says WHOI researcher Amy Apprill, lead author of the study published Oct. 10, 2017. The collaborative research team also included scientists from the National Oceanic and Atmospheric Administration (NOAA), SR3 Sealife Response, Rehabilitation and Research and the Vancouver Aquarium.

"We see evidence of respiratory illnesses frequently in stranded and deceased animals," Apprill adds. "Until now, little has been known about the normal respiratory microbiome of healthy whales."

After collecting their first sample in Patagonia in early 2015, WHOI biologist Michael Moore, NOAA researcher John Durban and SR3’s Holly Fearnbach successfully used a new, minimally intrusive technique, a custom-made, remotely controlled, six-rotor hexacopter, to sample the blows from humpback whales off Cape Cod late that year.

"We were using the drone to take aerial images of the whales, so that we could assess body conditions," says Durban, a coauthor of the paper. "Because of the stable flight performance of our hexacopter, we quickly learned that we could reliably fly through whale blow without disturbing the animals."

"We were surprised to find a microbiome that looked very different from seawater," Apprill says. "That's really exciting because it demonstrates that we are obtaining a clear signal of a microbiome that's coming from the animal."

Apprill and WHOI laboratory colleague Carolyn Miller identified 25 bacterial groups present in all of the whale samples—a conserved or “core” microbiome.

"This strongly suggests that regardless of where the animal lives, or even their age or sex, they have a shared blow microbiome," Apprill says.

Within the core group of 25 microbial species, the researchers found 20 sequences similar to microbes associated with other marine mammals.

"From this study, we have a good idea of what a normal, healthy whale microbiome looks like. Now we need to understand what the microbiome of an unhealthy whale looks like," Apprill says. "This comparison is critical for health monitoring and disease detection."

It may also prove to be crucial to the survival of these endangered whales. The past year has been particularly difficult for both humpbacks and North Atlantic right whales.

"There are very few ways to gather useful data from live large whales at sea," Moore adds. "This tool has the potential to broaden our perspective of large whale health."

Funding for this project was provided through a grant from the Ocean Life Institute at WHOI.


The American Society for Microbiology is the largest single life science society, composed of over 50,000 scientists and health professionals. ASM's mission is to promote and advance the microbial sciences.

ASM advances the microbial sciences through conferences, publications, certifications and educational opportunities. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.


The Woods Hole Oceanographic Institution is a private, non-profit organization on Cape Cod, Mass., dedicated to marine research, engineering, and higher education. Established in 1930 on a recommendation from the National Academy of Sciences, its primary mission is to understand the ocean and its interaction with the Earth as a whole, and to communicate a basic understanding of the ocean's role in the changing global environment. For more information, please visit