The middle ear-nasopharyngeal microbiome axis associated with obstructive Eustachian tube dysfunction in chronic otitis media

ABSTRACT Obstructive Eustachian tube dysfunction (ETD) commonly complicates chronic otitis media (COM), yet microbial factors at the Eustachian tube (ET) openings remain poorly understood. In this prospective cohort study, we characterized the microbiota at both the middle ear (ME) and nasopharyngeal (NP) ET openings in COM patients undergoing ear surgery and examined associations with obstructive ETD over one year of follow-up. Using 16S rRNA gene sequencing and functional inference, we profiled microbial communities from the ME-side ET opening and the torus tubarius on both surgical-side and contralateral nasopharynx. Among 37 patients (18 with ETD, 19 without), ME and NP microbiota differed significantly in composition. Ears with ETD showed increased ME microbial diversity and enrichment of Neobacillus , Agrobacterium , and Sphingomonas . Paired NP-ME analyses indicated an altered NP–ME microbial relationship in ETD, with Neobacillus showing a nasopharyngeal source signal. Functional prediction revealed increased porphyrin metabolism and decreased pyruvate metabolism in ME microbiota with ETD, suggesting a shift toward biofilm formation and altered redox states. Anaerococcus was increased in the nasopharynx of patients with bilateral COM. These findings identify distinct microbial and metabolic features of COM with obstructive ETD, supporting a role for nasopharyngeal-microbial influence on ME pathology. IMPORTANCE Chronic otitis media (COM) is a common and often persistent ear disease, especially when complicated by Eustachian tube dysfunction (ETD). By profiling microbiota at both Eustachian tube openings, this study links upper-airway microbial ecology with middle-ear microbial states in COM and helps clarify where clinically relevant signals may arise along the Eustachian tube pathway. The paired nasopharyngeal–middle ear design revealed that nasopharyngeal microbes may be linked to middle-ear community shifts in COM with obstructive ETD, consistent with a potential upper airway contribution to the middle-ear microbiota, generating testable hypotheses about microbial exchange and persistence. These findings highlight the upper airway microbiome as a potential target for developing new preventive and therapeutic strategies in COM.