What is the ear microbiome?
Composition of the ear microbiome
The protective role of the ear microbiome
Microbial imbalance and ear disease
The future of ear care: Microbiome-based diagnostics and therapies
References
Further reading
From protective cerumen and resident microbes to striking shifts in bacterial and fungal communities, emerging sequencing research is uncovering a complex microbial ecosystem within the ear that may reshape our understanding of ear health and disease.
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What is the ear microbiome?
The ear microbiome refers to microbial communities associated with the ear, including those of the skin-lined external auditory canal and microorganisms detected in the middle ear space or in middle-ear effusions; bacteria and fungi are the best-characterized components, while the viral component remains poorly defined.1,3,4,6 Recent advances in next-generation sequencing (NGS) technologies have enabled the characterization of the ear microbiome, particularly of microorganisms that cannot be cultured by conventional laboratory methods, using approaches such as bacterial 16S rRNA and fungal internal transcribed spacer (ITS) sequencing.1,2,5,6
The ear canal is a narrow, skin-lined passage approximately 2.5–3 cm long, with cartilaginous and bony portions.5,7 The ear canal is lined by skin directly overlying bone or cartilage and continuous with the eardrum.2,5,7
The external-ear microbiome shares some overlap with the skin microbiome, but is shaped by the canal's enclosed anatomy and the presence of cerumen. Its composition varies substantially among individuals and may be influenced by factors including age, environment, and cerumen type.1,2,3,5 Studies have identified a healthy external-ear core microbiome, whereas a pediatric chronic otitis media with effusion (COME) study reported no core middle-ear-effusion microbiome, underscoring that "normal" ear communities differ by anatomical site and disease context.1,6
The relevance of the ear microbiome and cerumen in otolaryngology research has grown considerably, with studies reporting disease-associated shifts in microbial composition in otitis externa and otitis media rather than a single uniform pattern of dysbiosis. Differences in sampling sites, prior antimicrobial exposure, cohort characteristics, and sequencing methods also complicate comparisons between studies.1,2,4,5 Understanding this ecosystem is essential, as it has direct implications for the diagnosis, management, and prevention of ear infections.
A schematic summary of factors that increase the risk of outer ear infections (otitis externa), highlighting environmental factors (e.g., water exposure and humidity), mechanical damage to the ear canal epithelium, disturbances in cerumen composition, and microbial imbalance, all of which contribute to impaired local immune defense.3
Composition of the ear microbiome
In a large NGS-based study comparing adults with and without ear infection, Cutibacterium acnes dominated the healthy bacteriome, with an average relative abundance of 51.8%.1 Other studies have reported similar results, with Staphylococcus species like S. auricularis and S. capitis/caprae, Corynebacterium otitidis, and Alloiococcus otitidis1,4,6 also abundant in ear-associated microbial communities.1,3,5
In Burton et al., healthy ear bacteriomes were dominated by Firmicutes and Actinobacteria, while Proteobacteria was significantly enriched in the otitis externa group.1 In this cohort, Pseudomonas aeruginosa was the most abundant species, followed by C. acnes and then S. aureus, with eight established otopathogens among the top fifteen most abundant species.1 Case-control sequencing studies of acute and chronic otitis externa have also reported lower bacterial diversity in diseased ear canals than in healthy controls. However, Burton et al. found no significant difference in bacteriome alpha diversity among healthy, otitis externa, and otitis media groups, highlighting variation across cohorts and analytical approaches.1,2,5
Among fungi, the phylum Basidiomycota dominates healthy ear microbiomes, specifically Malassezia arunalokei, Malassezia restricta, and Malassezia globosa.1 In Burton et al.'s otitis externa group, Ascomycota was significantly enriched, as were Aspergillus species and Candida albicans.1 In chronic otitis externa, higher relative abundances of Aspergillus and Candida were also observed, although overall fungal beta diversity did not differ significantly between patients and healthy controls.5
The viral component of the ear microbiome remains poorly defined. However, varicella-zoster virus is an established cause of herpes zoster oticus, but its role as a pathogen should not be interpreted as evidence that it forms part of a stable resident ear virome.3
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The protective role of the ear microbiome
One major function of the ear microbiome is colonization resistance, as established commensal communities prevent infection by pathogenic microorganisms.3 For example, co-occurrence analyses have reported a negative association between Malassezia restricta and the otopathogen Aspergillus in otitis externa, a pattern consistent with a possible protective role for Malassezia but not proof of direct microbial antagonism.1
Commensal bacteria that colonize the ear canal skin contribute to epithelial homeostasis and interact with innate immune pathways.2,3 Changes in community composition may create conditions that permit opportunistic organisms to adhere to and disrupt the epithelial barrier, promoting inflammation.2,3
The external auditory canal is further reinforced by cerumen, which contains host-derived antimicrobial components including human beta-defensins, cathelicidin LL-37, lactoferrin, secretory leukoprotease inhibitor, lysozyme, immunoglobulins, and antimicrobial lipids.3 Its acidic and hydrophobic properties also inhibit microbial growth and limit water penetration into the canal.3,7
Microbial imbalance and ear disease
Together, the microbiome and cerumen constitute an integrated defense system in the external auditory canal, and disruption of either component increases susceptibility to infections.3,7 Otitis media encompasses a spectrum of conditions ranging from acute otitis media to chronic otitis media with effusion, but these conditions are not microbiologically or clinically equivalent: acute otitis media involves acute middle-ear inflammation, otitis media with effusion is characterized by middle-ear fluid without signs of acute infection, and chronic otitis media with effusion refers to persistence of this effusion for at least three months.4
The most frequently implicated bacteria in childhood otitis media include Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. Recently, NGS-based studies have identified Turicella otitidis, Alloiococcus otitidis, and Staphylococcus auricularis as other species implicated in otitis media.1,6 However, the pathogenic status of organisms such as Alloiococcus and Turicella remains debated because they may also occur as commensal or health-associated organisms, and chronic otitis media with effusion shows marked patient-to-patient microbiome variation.4,6
Chronic inflammation in otitis media causes epithelial metaplasia in the middle ear, where the squamous epithelium is replaced by pseudostratified columnar epithelium. This increases the concentration of goblet cells, leading to excess mucin production and persistent middle ear effusion. The mucin MUC5B has been observed in 94.5% of middle ear effusions, whereas MUC5AC has been detected in 65.5%. Samples containing MUC5AC showed a predominance of Haemophilus, whereas this predominance was absent in samples containing only MUC5B.4 In children with chronic otitis media with effusion, concurrent asthma or bronchiolitis was associated with lower bacterial diversity and altered abundances of Haemophilus, Moraxella, Staphylococcus, Alloiococcus, and Turicella; these observations demonstrate association rather than causation. Despite high taxonomic diversity in this COME cohort, predicted functional profiles were similar across patients and showed no significant associations with clinical variables.6
Microbial imbalance is equally central to otitis externa, an infection of the external auditory canal with a lifetime prevalence of approximately 10%. Under normal conditions, the ear canal is characterized by a mildly acidic pH and hydrophobic cerumen, which suppress pathogen overgrowth. Disruption of these conditions due to water exposure, trauma, or skin disease facilitates colonization by Pseudomonas aeruginosa and Staphylococcus aureus and chronic inflammation.7 Sequencing of chronic otitis externa has additionally shown reduced bacterial richness and evenness, greater relative abundance of Staphylococcus and Corynebacterium, and lower relative abundance of Cutibacterium compared with healthy controls.5
Oral antibiotics are prescribed in at least 25% of otitis cases in cited datasets.1 However, uncomplicated acute otitis externa is generally managed with cleansing and topical antiseptic or antimicrobial treatment; systemic antibiotics are mainly reserved for infection extending beyond the ear canal or selected high-risk patients. Prolonged antibiotic exposure is also a recognized predisposing factor for fungal otitis externa.7 Long-term use of hearing aids can alter the ear-canal environment and microbial composition; observational evidence suggests that hearing-aid type may influence organisms associated with infection, but available evidence does not establish inevitable dysbiosis.3
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The future of ear care: Microbiome-based diagnostics and therapies
Whereas conventional culture-based methods can under-detect fastidious organisms, including some Malassezia and anaerobic Cutibacterium species, targeted polymerase chain reaction (PCR) panels are typically limited to approximately 8–20 microbial targets.1 In contrast, NGS can provide broader taxonomic profiling and reveal polymicrobial bacterial and fungal communities that targeted testing may miss. Depending on the sequencing approach, identification may extend to the species level, but taxonomic detection alone does not establish antimicrobial susceptibility or prove that a detected organism is causing disease.1,4
In one study, 35% of otitis media patients harbored a single bacterial pathogen at a relative abundance of over 80%. Although 15% were infected with a single dominant fungal pathogen, using a separate threshold of at least 10% relative abundance, approximately 35% of otitis media patients had both bacterial and fungal pathogens present.1 This degree of individualization highlights the value of patient-specific profiling over empirical, population-level treatment assumptions.
More broadly, personalized ear, nose, and throat (ENT) treatment approaches guided by microbiome profiling remain a research direction rather than an established standard of care. If validated in prospective clinical studies, patient-specific profiling could help distinguish bacterial, fungal, and polymicrobial disease and support more targeted therapy and antimicrobial stewardship.1,3,4 Clinical translation is limited by small cohorts - for example, 14 otitis externa patients and 14 controls in Kim et al. - and demographic differences, including median ages of 30 and 64 years in Burton et al.'s healthy and otitis groups, as well as variation in sampling and sequencing pipelines, low-biomass contamination risk, prior antimicrobial exposure, and uncertainty over whether detected microorganisms are causal pathogens, commensals, or bystanders.1,2,4 Larger longitudinal and interventional studies are needed before microbiome-based diagnostics or microbiome-modifying therapies can be recommended routinely.1,2,4,5,6
References
- Burton, M., Krumbeck, J. A., Wu, G., et al. (2022). The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes. PloS One 17(1); e0262806. DOI: 10.1371/journal.pone.0262806. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0262806.
- Kim, S. K., Han, S. J., Hong, S. J., & Hong, S. M. (2022). Microbiome of Acute Otitis Externa. Journal of Clinical Medicine 11(23); 7074. DOI: 10.3390/jcm11237074. https://www.mdpi.com/2077-0383/11/23/7074.
- Paprocka, P., Spałek, J., Daniluk, T., et al. (2026). The Importance of Ear Canal Microbiota and Earwax in the Prevention of Outer Ear Infections. International Journal of Molecular Sciences 27(2); 622. DOI: 10.3390/ijms27020622. https://www.mdpi.com/1422-0067/27/2/622.
- Nogues, J. C., Pérez-Losada, M., & Preciado, D. (2020). Review of otitis media microbiome studies: What do they tell us?. Laryngoscope Investigative Otolaryngology 5(5); 936-940. DOI: 10.1002/lio2.460. https://onlinelibrary.wiley.com/doi/10.1002/lio2.460.
- Lee, J. S., Lee, S. M., Son, H. S., et al. (2022). Analysis of the Microbiome of the Ear Canal in Normal Individuals and Patients with Chronic Otitis Externa. Annals of Dermatology 34(6); 461-471. DOI: 10.5021/ad.22.153. https://anndermatol.org/DOIx.php?id=10.5021/ad.22.153.
- Kolbe, A. R., Castro-Nallar, E., Preciado, D., & Pérez-Losada, M. (2019). Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses. Frontiers in Cellular and Infection Microbiology 9; 339. DOI: 10.3389/fcimb.2019.00339. https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2019.00339/full.
- Wiegand, S., Berner, R., Schneider, A., et al. (2019). Otitis Externa. Deutsches Arzteblatt International 116(13); 224-234. DOI: 10.3238/arztebl.2019.0224. https://di.aerzteblatt.de/int/archive/article/206313
Further Reading
Last Updated: Aug 26, 2026