Comparison of ear canal microbiome in rabbits (Oryctolagus cuniculus domesticus) with and without otitis externa using next generation DNA sequencing

Background: Contemporary research has increasingly explored the clinical applicability of next-generation DNA sequencing (NGS) technologies in veterinary medicine, which has provided new and practical opportunities for rabbit otitis externa clinical interventions. The objectives of this study were to characterize the normal external ear canal microbiome of clinically healthy rabbits compared to otitis externa presenting rabbits, and to assess the diagnostic viability of NGS in aural veterinary medicine.Methods: Swabs from the external ear canal of 34 clinically healthy rabbits and 16 rabbits diagnosed with otitis externa were collected. Alongside bioinformatic analysis, library preparation was performed targeting the V1-V3 region of the 16S rRNA bacterial gene and the ITS-2 region for fungal DNA analysis.Results: In the clinically healthy group, the bacterial species with the highest relative abundances were an uncharacterized Phytoplasma from the family Acholeplasmataceae (8.74%) and Staphylococcus epidermidis (5.56%), while in the otitis group the species with the highest relative abundances were Staphylococcus aureus (12.59%), Corynebacterium lactis (9.27%), and Corynebacterium mastitidis (7.92%). Fungal species with the highest relative abundances in the healthy group were a species from the genus Cladosporium (14.46%), while in the otitis externa group the fungal species with the highest relative abundances were a species from the genus Cladosporium (9.89%) and Malassezia restricta (4.76%). Additionally, there was a significantly higher number of different bacterial and fungal species in the clinically healthy group compared to the otitis group (P = 0.00 and P = 0.00, respectively).Conclusions and clinical relevance: This study provided evidence that the rabbit aural microbiome profile is distinctly different between a clinically healthy and an otitis state. It also highlighted new bacterial and fungal organisms of note in rabbits diagnosed with otitis externa compared to those previously thought to be the primary disease-causing organisms. Understanding the microbial population dynamics in the rabbit aural microbiome is particularly critical for helping clinicians recognize, prevent, or revert the progression of otitis.