A Preliminary Investigation of the Gastrointestinal Bacterial Microbiomes of Barred Owls (Strix varia) Admitted to a Wildlife Hospital.

Research on the gut microbiome, which includes microbial communities and genetic material in the gastrointestinal tract, has revealed essential roles beyond digestion, such as immune regulation, metabolism, and homeostasis. However, studies on birds-key ecosystem members-remain limited. Injured wild birds admitted to wildlife hospitals often receive antibiotics that can alter gut microbiota, leading to dysbiosis and promoting antimicrobial-resistant (AMR) bacteria. This study examined how hospitalization and antibiotics influence the cloacal microbiota of barred owls admitted for fracture repair. A total of 17 cloacal swab samples were analyzed using next-generation sequencing targeting 16S rRNA and AMR genes. Across all samples, Bacillota (Firmicutes), Actinomycetota (Actinobacteria), and Pseudomonadota (Proteobacteria) were the most abundant phyla. In non-antibiotic-treated owls, alpha and beta diversity showed no significant changes between admission and release; however, antibiotic-treated owls exhibited significant diversity shifts in these parameters at release. AMR genes were detected in most samples at admission, with some increasing significantly during hospitalization, suggesting an impact of antibiotic exposure. These findings provide insights into how antibiotics used in wildlife rehabilitation affect host microbiota and contribute to AMR gene dissemination.