# Culture and Metagenomic Insights into the Ear Microbiota in Dogs with Healthy Ears and Otitis Externa

## TL;DR

This study explores the ear microbiota in dogs with healthy ears and otitis externa, revealing microbial shifts and antimicrobial resistance patterns.

## Contribution

The study combines culture-based and metagenomic approaches to provide a comprehensive view of canine ear microbiota and antimicrobial resistance.

## Key findings

- Staphylococcus pseudintermedius is a predominant species in both healthy and OE-affected dogs.
- Metagenomic analysis shows higher abundance of Bacteroides fragilis in healthy dogs and S. pseudintermedius in OE.
- AMR profiling reveals diverse resistance determinants, including methicillin resistance-associated genes.

## Abstract

Microbiota refers to the living microorganisms present in a specific environment, such as the oral or gut microbiota, and in various parts of the body, including the oral cavity, intestines, skin, and ear canal. The ear canal microbiota of dogs with healthy and otitis externa (OE) poses a significant risk to human health due to the presence of important pathogenic microorganisms (Staphylococcus spp., Pseudomonas aeruginosa, and Escherichia coli). The present study aimed to investigate the ear microbiota of dogs with and without OE using bacterial culture-based techniques and shotgun metagenomic sequencing, and to assess antimicrobial resistance and virulence-associated genetic signatures through read-based analysis. Bacterial culture-based results highlight the polymicrobial nature of the canine ear canal, while metagenomic profiling reveals heterogeneous, pathogen-dominated communities in OE, predominantly characterized by Staphylococcus pseudintermedius.

The canine ear microbiota plays an important role in ear health, and dysbiosis is associated with otitis externa (OE) and antimicrobial resistance (AMR). This study aims to investigate the ear microbiota of dogs with healthy ears and OE using bacterial culture-based methods and shotgun metagenomic sequencing, and to screen for AMR and virulence-associated genetic signatures. Ear swab specimens from 100 healthy and 100 OE-affected dogs were analyzed. The isolates obtained via bacterial culture were identified by MALDI-TOF MS and 16S rRNA sequencing. Metagenomic analysis was performed via Illumina shotgun sequencing. The most commonly defined species in healthy dogs in culture were Staphylococcus pseudintermedius (24.5%) and Staphylococcus epidermidis (5.7%); in dogs with OE, the most commonly defined species were S. pseudintermedius (30.5%), and Clostridium perfringens (4.5%). In healthy samples, metagenomic analysis revealed higher relative abundances of Bacteroides fragilis (15.8%) and Ezakiella coagulans (8.2%), while S. pseudintermedius (38.7%) dominated in OE. AMR profiling demonstrated diverse resistance determinants, including efflux pump systems and methicillin resistance-associated genes. In conclusion, the present study shows that S. pseudintermedius is a predominant member of canine ear microbiota, with higher presence in OE highlighting microbial shifts, and demonstrates that combining culture and metagenomic analyses provides a concise view of microbial communities and clinical relevance.