Sample Collection
We sampled island foxes and island spotted skunks following live capture in Tomahawk box traps during annual island-wide carnivore monitoring surveys conducted between June 2021 and February 2022. We inserted a Passive Integrated Transponder (PIT) tag in each individual animal for identification purposes and recorded basic demographic information including sex, weight, body condition, reproductive status, and approximate age for each animal. We used sterile BD BBL CultureSwab swabs (BD Biosciences, New Jersey, USA) to collect gut microbiome samples from the perianal area by gentling swabbing a total of 40 times per animal (i.e. , 10 times before rotating the swab 90 degrees). All field capture and handling efforts were conducted in accordance with island-specific permissions and permits and following the guidelines established by the American Society of Mammalogists for the ethical use of wild mammals in research . Samples on Santa Cruz Island were collected under a MOU with the California Department of Fish and Wildlife (CDFW) and Scientific Collecting Permit (No. 008981) issued by CDFW. Samples on Santa Rosa Island were collected under Channel Islands National Park Research Permit # CHIS-2023-SCI-0017. All protocols were further approved by the Princeton University Institutional Animal Care and Use Committees (Princeton IACUC #3073).