Beyond Antibiotics: Why Preserving the Ear Microbiome May Improve Long-Term Otitis Outcomes

If every recurrence of otitis is treated with another antibiotic, are we solving the problem—or simply resetting the cycle?

Recent microbiome research suggests that preserving microbial diversity may become just as important as eliminating pathogens.

Not Every Organism Is the Enemy

Advanced sequencing has identified numerous bacteria in healthy canine ears that were previously overlooked.

Some organisms, including Escherichia coli and Porphyromonas species, may be present in healthy ears without causing disease¹.

This challenges the traditional assumption that detecting bacteria automatically means treatment is required.

Context matters.

It's the overall microbial balance—not merely the presence of bacteria—that determines ear health.

Why Some Dogs Develop Recurrent Malassezia Otitis

Researchers have also discovered that not all Malassezia species behave the same way.

Healthy dogs often harbour species such as²:

• Malassezia globosa
• Malassezia restricta

Dogs with allergic skin disease and recurrent otitis are more likely to develop overgrowth of Malassezia pachydermatis, which appears to be more pathogenic³.

Differences in skin lipids may influence which species become dominant, potentially explaining why certain breeds and individuals experience repeated yeast otitis.

Inflammation Changes the Microbiome

One important finding is that inflammation itself alters microbial populations.

As inflammation increases¹:

• Microbial diversity decreases.
• Opportunistic pathogens become dominant.
• The damaged skin barrier allows persistent colonisation.
• Chronic inflammation becomes self-perpetuating.

This reinforces the importance of controlling inflammation alongside antimicrobial therapy.

Anti-Inflammatory Therapy May Protect the Microbiome

Interestingly, recent studies suggest that some commonly used therapies do more than reduce inflammation.

Treatments such as¹:

• Topical chlorhexidine with miconazole
• Topical mometasone
• Systemic glucocorticoids
• Ciclosporin

have been associated with better preservation of bacterial and fungal diversity while controlling disease.

Although further research is needed, these findings highlight that effective otitis management should focus on restoring ear health—not simply eliminating microorganisms.

Practical Tips for the Clinic

When managing recurrent otitis:

✔ Treat the underlying allergy or primary disease.

✔ Control inflammation early.

✔ Avoid repeated empirical antibiotic use without reassessment.

✔ Use cytology to guide therapy.

✔ Educate owners that preventing recurrence requires long-term disease management, not just treating each flare.

Clinical Pearl

The future of otitis management may not be about finding stronger antibiotics—it may be about protecting the ear's natural microbial balance.

For clinicians, this means shifting from treating infection alone to managing the ear ecosystem.

Reference

1. Nuttall T. Managing recurrent otitis externa in dogs: what have we learned and what can we do better?. Journal of the American Veterinary Medical Association. 2023 Jun 1;261(S1):S10-22. https://www.pure.ed.ac.uk/ws/portalfiles/portal/332390919/JAVMA_otitis_review_2022_unformatted_version_2.pdf 
2. Guillot J, Bond R. Malassezia yeasts in veterinary dermatology: an updated overview. Frontiers in cellular and infection microbiology. 2020 Feb 28;10:79. https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.00079/pdf 
3. Maddens E, Takeaways K. Dog Yeast Infection: Causes, Symptoms & Vet-Backed Treatment Guide. Veterinary Dermatology. 2026 Mar 28. https://vetified.co/blogs/news/dog-yeast-infection-guide