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

mSystems. 2017 Oct 10;2(5). pii: e00119-17. doi: 10.1128/mSystems.00119-17. eCollection 2017 Sep-Oct. Apprill A1, Miller CA1, Moore MJ2, Durban JW3, Fearnbach H4, Barrett-Lennard LG5,6. Author information 1 Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA. 2 Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA. 3 Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California, USA. 4 SR3 SeaLife Response, Rehabilitation, and Research, Mukilteo, Washington, USA. 5 Coastal Ocean Research Institute, Vancouver Aquarium, Vancouver, BC, Canada. 6 Zoology Department, University of British Columbia, Vancouver, BC, Canada. Abstract 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. IMPORTANCE 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. KEYWORDS: SSU rRNA gene; bacteria; drone; humpback whale; microbiome PMID: 29034331 PMCID: PMC5634792 DOI: 10.1128/mSystems.00119-17 Free PMC Article