Woods Hole, Mass. (Nov. 12, 2025) A new study published today in The ISME (International Society for Microbial Ecology) Journal marks the first time scientists have shown a connection between respiratory microbes and the health of a free-ranging whale population.
The study, Respiratory microbiomes reflect whale health opens the door to effective ways to monitor and protect the critically endangered North Atlantic right whale, whose population has dwindled to fewer than 400 individuals.
Between 2016 and 2024, researchers from the Woods Hole Oceanographic Institution (WHOI), University of St Andrews , New England Aquarium , SR³, and Whale and Dolphin Conservation , collected 103 respiratory samples from 85 North Atlantic right whales using drones. The researchers found that the microbial matter whales exhale through their blowholes carry valuable information about their health, including distinct, individual microbial patterns that can be linked to characteristics such as robust versus thin whales, among other health metrics.
As the drone flies over a whale as it exhales, it holds a petri dish in the exhalation to collect a sample of the breath. Using drones provides a stable, quiet platform, minimizing stress and disturbance to the animal, and allows permitted researchers to access areas or animals that are difficult and dangerous to reach. Microbial samples were paired with multiple health indexes, including photogrammetric body condition data, visual health assessments, and estimates from a long-term health and survival model. By combining microbiology, drone-based imaging, and long-term ecological datasets, researchers show how interdisciplinary methods can expand understanding of whale health.
"This is a major step forward in developing new approaches for monitoring wildlife health," said Carolyn Miller , a large whale biologist at WHOI and a lead author of the study. "By studying the microbes in their breath, we can begin to develop a non-invasive diagnostic tool that tells us how whales are doing without ever having to touch them."
The study underscores the importance of long-term North Atlantic right whale datasets, including photo-identification catalogs and health assessments as critical baselines for testing new health indicators.
Enrico Pirotta, co-lead author, and statistical ecologist at the Centre for Research into Ecological and Environmental Modelling, University of St Andrews, UK said, "Being able to measure whale health is a critical step towards assessing the effects of multiple stressors on these animals and, ultimately, come up with management solutions that can ensure their conservation."
"This first of its kind study provides a new window into the biology of some of the ocean's most endangered species," said Amy Apprill , co-author, and associate scientist at WHOI. "This technique shows promise as a non-invasive "health checkup" for whales, made possible by drones and microbiome science."
"As right whales face threats from ship strikes, fishing gear, and ocean changes, having better tools to monitor their health is essential," added Miller. "Breath samples may hold a key to protecting the species."
The research was conducted with support from Strategic Environmental Research and Development Program, Office of Naval Research, NOAA, and SR³.
