Highlights:
- Largest dog cohort to date analyzed for both the bacterial and fungal microbiota in healthy and diseased skin and ears.
- This study uniquely used relative and absolute microbial abundances determining a cutoff for microbial infectious overgrowth.
- Potential novel pathogens causing canine skin and ear infections can be discovered using the NGS-based approach as described.
- NGS-based analysis of infections is a novel diagnostic approach with the potential to significantly reduce patient suffering.
- NGS-based analysis allows real-time microbiome monitoring and may reduce the use of unwarranted antibiotics for infections.