We captured birds in urban parks and peri-urban forests in the cities of Lugano and Zurich. The urban sites were located in an urban forest (Lugano) and in a cemetery (Zurich), and the bird assemblages were comparable with those of the surrounding forests.
We captured individual birds during sessions lasting multiple days using mist-nets, concentrating the activities within 3-4 hours after sunrise and before sunset. We extracted birds from nets using single-use nitrile gloves and gently wiped their body parts with a dry foam swab MW940 (Medical Wire & Equipment), which was then placed in a screw-capped tube (2 ml), which was previously filled with 1 ml ethanol puriss. (Sigma-Aldrich) under sterile conditions.Then, we marked each bird with an alphanumeric leg band, identified the species, determined the sex and age whenever possible, measured for relevant biometrics (e.g. wing chord), the amount of body fat and pectoral muscle (i.e. body condition), and weighed.
Afterwards, we placed each bird in a disposable paper bag within a cotton bag that ensured respiration and left it for few minutes in a safe and calm place to allow for defecation and the collection of faecal samples. The faecal sample was collected from insectivorous and omnivorous birds, and few granivorous birds that are known to occasionally eat invertebrates, such as the house sparrow Passer domesticus.
After releasing the bird, we stored the faecal sample in a screw-capped tube (2 ml), which was previously filled with 1 ml ethanol puriss. (Sigma-Aldrich) under sterile conditions. We wore single-use nitrile gloves and used sterile toothpicks to collect solid samples. The tubes were initially stored in the refrigerator during the field campaign and no later than seven days after collection at -20°C until prepared for DNA extraction.
DNA extraction and library preparation was performed at WSL Phytopathology facilites, Sequencing was performed at Lausanne Genomic Technologies Facility (University of Lausanne; https://wp.unil.ch/gtf/) on an AVITI benchtop sequencing system (Element Biosciences). Bioinformatics was performed at the Genetic Diversity Center (ETH Zurich) using a custom pipeline.