Whale snot and drones: What a time to be a microbiologist

"Sampling the blow of a whale used to involve a long stick and a large petri dish"

Like Comment

A new study published in mSystems by the Woods Hole Oceanographic Institution has just trumped any microbiome sampling method you have ever read, while doing important conservation work. 

Researchers flew a drone over the blow of different whales and waited for them to, well, blow. Once covered in whale snot, the drone returned safely to the research ship and the whale swam off, completely unaware that it had just deposited a microbiome sample.

The study has allowed the research team to work out what is a healthy microbiome for a whale blow which, along with a fast and non-invasive sampling method, is important for conservation efforts in the future. 

As important as this is, it is also immensely cool. I'm so jealous that I've never used a drone to collect samples before, maybe one day...

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring


The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales (Megaptera novaeangliae), sampled in the Massachusetts coastal waters off Cape Cod (n = 17) and coastal waters around Vancouver Island (n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community. The blow microbiomes were distinct from the seawater microbiomes and included 25 phylogenetically diverse bacteria common to all sampled whales. This core assemblage comprised on average 36% of the microbiome, making it one of the more consistent animal microbiomes studied to date. The closest phylogenetic relatives of 20 of these core microbes were previously detected in marine mammals, suggesting that this core microbiome assemblage is specialized for marine mammals and may indicate a healthy, noninfected pulmonary system. Pathogen screening was conducted on the microbiomes at the genus level, which showed that all blow and few seawater microbiomes contained relatives of bacterial pathogens; no known cetacean respiratory pathogens were detected in the blow. Overall, the discovery of a shared large core microbiome in humpback whales is an important advancement for health and disease monitoring of this species and of other large whales.


The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present surprising results about the discovery of a large core microbiome that was shared across individual whales from geographically separated populations in two ocean basins. We suggest that this core microbiome, in addition to other microbiome characteristics, could be a useful feature for health monitoring of large whales worldwide.


Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring
Amy Apprill, Carolyn A. Miller, Michael J. Moore, John W. Durban, Holly Fearnbach, Lance G. Barrett-Lennard
mSystems Oct 2017, 2 (5) e00119-17; DOI: 10.1128/mSystems.00119-17

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.