Molecular Characterization of the Middle Ear Microbiome in Pediatric Otitis Media with Effusion: Diagnostic and Clinical Implications

Background: Otitis media with effusion (OME) is a highly prevalent pediatric condition and a leading cause of conductive hearing loss in children. Its pathogenesis remains uncertain, and diagnostic and therapeutic challenges make management difficult. Objectives: This review evaluates current evidence on the middle ear microbiome in pediatric OME, focusing on the diagnostic value of 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing and its potential clinical implications. Methods: A literature review was conducted using the PubMed database, including studies published between 2006 and 2026. Eligible studies involved pediatric patients with OME and examined the sources and characteristics of microbiota potentially involved in disease pathogenesis. Microbiome analysis was performed using next-generation sequencing (NGS) techniques. Results: Growing evidence indicates that OME is associated with microbial dysbiosis and biofilm formation rather than a sterile inflammatory process. The most frequently detected genera include Haemophilus, Moraxella, Streptococcus, and Alloiococcus, although substantial variability exists between studies. Pathogens are believed to reach the middle ear through the Eustachian tube from two main reservoirs: the nasopharynx and the adenoids. The potential role of Helicobacter pylori infection and gastroesophageal reflux disease (GERD) in OME pathogenesis remains uncertain and requires further investigation. NGS methods, including 16S rRNA sequencing, demonstrate higher sensitivity than conventional culture techniques, enabling the detection of fastidious and previously unrecognized microorganisms. Evidence also highlights the limited effectiveness of antibiotic therapy in OME, the persistent issue of antibiotic overuse, and the relative advantages of conservative management and microbiome-modulating approaches compared with antibiotics and surgical interventions. Conclusions: Current evidence suggests that OME is closely associated with microbiota dysbiosis and bacterial biofilm formation. Given the limited efficacy of antibiotics, microbiome-focused strategies—particularly probiotics—should be further explored. Molecular diagnostic methods, especially NGS, show clear advantages over traditional culture-based techniques. Future research should further evaluate microbiome modulation as a potential adjunctive or preventive strategy.