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).