Metagenomic analysis of the middle ear microbiome: A next-generation sequencing approach in pediatric patients with and without effusion

Objectives

Otitis media with effusion (OME) is one of the most common causes of reversible hearing loss in childhood. In recent years, host-microbiota interactions and alterations in microbiota composition associated with health and disease have gained increasing attention in the context of OME. This study aimed to investigate the bacterial microbiota composition of middle ear cavity (MEC) samples obtained from pediatric patients with and without OME. Microbiome differences were analyzed according to clinical groups and variables such as age and gender.

Methods

16S rRNA-based metagenomic sequencing was performed on MEC samples (n = 80) and nasopharyngeal samples (n = 20) obtained from 80 children—40 diagnosed with bilateral or unilateral OME (OME group) and 40 undergoing cochlear implant surgery without any history of otitis media (control group). The study cohort included 37 males and 43 females, aged between 2 and 11 years (mean age: 5.2 years).

Results

Sequencing analysis revealed that the phyla Firmicutes and Proteobacteria were dominant in MEC samples. In the OME group, Firmicutes were significantly more abundant, whereas Proteobacteria levels were reduced. At the genus level, Alloiococcus was significantly enriched in the OME group, while genera considered potentially protective, such as Lactobacillus and Propionibacterium, were significantly decreased. Age was not significantly associated with microbial richness or evenness, suggesting stability of microbiota composition across age groups. However, a significantly higher relative abundance of Ralstonia was observed in female patients, suggesting that gender-related hormonal or immunological differences may influence the middle ear microbiota.

Conclusion

This study identifies a distinct microbiota profile associated with OME and suggests that host factors, particularly gender, may contribute to shaping the microbial and immunological landscape of the middle ear. These findings also indicate that the microbial environment in OME may shift toward a low-diversity, pathobiont-dominant state.