Utilizing Exhaled Breath and Skin Microbiomes in Assessments of At‐Risk Killer Whales ( <scp> <i>Orcinus orca</i> </scp> )

ABSTRACT For at‐risk populations of killer whales ( Orcinus orca ), biological samples can offer information about individual animal status. We hypothesized that low‐yield samples could provide sufficient material for microbiome analysis. We collected and analyzed, with amplicon metabarcoding, breath samples from managed care and free‐ranging killer whales (8 and 14 animals, respectively) and epidermal tissue from free‐ranging killer whales using dart biopsies and suction cups (11 and 30 animals, respectively). Exhaled breath aerosol from free‐ranging whales was distinct from seawater, but breath from managed care whales was not different from pool water. Eight bacterial species detected in breath from all managed care whales displayed elevated relative abundances in free‐ranging whales. Functional analysis revealed increased pathways associated with degradation and metabolism of xenobiotics and biosynthesis of terpenoid and polyketides in managed care whales. Epidermal collection method (biopsy vs. suction cups) produced differences in microbiomes but was still different from seawater microbiomes. Two bacterial species exhibited inverse abundance patterns between two resident killer whale populations. Epidermal microbiome functions were elevated for xenobiotic degradation and metabolism and for antimicrobial activities, consistent with constant exposure to marine environments. Evidence for the potential utility of these microbiomes for identifying whales with a poor survival prognosis was found for free‐ranging whales that were sampled within 6 months of presumed or known death. For at‐risk populations such as Southern Resident killer whales of the northeastern Pacific Ocean, microbiome analysis to help characterize individual animal health may contribute to safe and rational management decisions and policies.