DNA Extraction
DNA from tissue, swab, and fecal samples were extracted using the Qiagen DNEasyⓇ Blood and Tissue Kit (Qiagen, Inc). For the cloacal swab samples, we used the manufacturer protocol for Purification of Total DNA from Animal Blood or Cells with the optional pre-treatment for Gram-positive bacteria lysis buffer incubation. For tissue and fecal pellets, we included the optional lysis buffer incubation for 30 min at 37°C. After incubation, Buffer AL and proteinase K were added to the tubes. The samples were then incubated at 56°C for 180 minutes (for tissue) or 90 min (for feces) while shaking at 500 RPM (USA Scientific Mixer HC- 8012-0000, Ocala, FL, USA). From here, the extraction was completed according to the Purification of Total DNA from Animal Blood or Cells protocol, beginning at Step 3 (addition of pure ethanol). An extraction blank was included in each extraction. DNA in all samples and blanks was quantified via Qubit to ensure extraction was successful.