Jansen, Marissa2025-03-212025-03-212025-03-20https://hdl.handle.net/11299/270501Advisors: Geoff Miller and James ForesterCoyotes (Canis latrans) are currently occupying urban areas where they were previously absent due to habitat loss and the high availability of anthropogenic food sources in cities. In the Twin Cities Metro Area, coyotes have successfully colonized the urban area. Due to the difficulty of capturing these urban coyotes, it’s beneficial to study the coyotes non-invasively, such as by analyzing their readily available scat. This study aimed to examine the bacterial communities and endoparasites present in urban coyote scat samples, and potential differences between the inner and outer sections of samples. In this study, five coyote scat samples were randomly selected from five different areas around the Twin Cities Metro Area, and the inner core and outer crust sections were analyzed separately. DNA was extracted following a modified protocol for scat samples through the Qiagen DNeasy Blood and Tissue Kit, quantified via Qubit, and subjected to Quality Control (QC) tests at UMGC before being analyzed in CZID. Fluorometric quantification revealed variable DNA yields, with some samples failing due to low concentration. Eight samples met sequencing thresholds and were analyzed for bacterial composition in CZID. The results from sequencing indicate a mix of gut, diet-derived, and environmental bacteria, with a notable outlier being Schistosoma japonicum. A one-way ANOVA test was utilized to compare the bacterial diversity across the sample sections and showed no statistically significant differences (F(7, 312) = 1.18, p = 0.315), however, the t-test results indicate that there were statistically significant differences between the inner and outer sample values for only two of the scat samples. The findings from this study provide insights into urban coyote microbiomes and highlight the potential for using shotgun metagenomic sequencing to analyze scat for ecological and health assessments. Future research could explore the potential microbiome differences between urban and rural coyotes.en-USUrban CoyotesShotgun Metagenomic SequencingMicrobiome analysisScholarly Text or Essay