Data_Sheet_1_Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses.PDF

Chronic otitis media with effusion (COME) is a common childhood disease characterized by an accumulation of fluid behind the eardrum. COME often requires surgical intervention and can also lead to significant hearing loss and subsequent learning disabilities. Recent characterization of the middle ear fluid (MEF) microbiome in pediatric patients has led to an improved understanding of the microbiota present in the middle ear during COME. However, it is not currently known how the MEF microbiome might vary due to other conditions, particularly respiratory disorders. Here, we apply an amplicon sequence variant (ASV) pipeline to MEF 16S rRNA high-throughput sequencing data from 50 children with COME (ages 3–176 months) undergoing tube placement. We achieve a more detailed taxonomic resolution than previously reported, including species and genus level resolution. Additionally, we provide the first report of the functional roles of the MEF microbiome and demonstrate that despite high taxonomic diversity, the functional capacity of the MEF microbiome remains uniform between patients. Furthermore, we analyze microbiome differences between children with COME with and without a history of lower airway disease (i.e., asthma or bronchiolitis). The MEF microbiome was less diverse in participants with lower airway disease than in patients without, and phylogenetic β-diversity (weighted UniFrac) was significantly different based on lower airway disease status. Differential abundance between patients with lower airway disease and those without was observed for the genera Haemophilus, Moraxella, Staphylococcus, Alloiococcus, and Turicella. These findings support previous suggestions of a link between COME and respiratory illnesses and emphasize the need for future study of the middle ear and respiratory tract microbiomes in diseases such as asthma and bronchiolitis.

慢性渗出性中耳炎（Chronic otitis media with effusion, COME）是一种常见的儿童疾病，其特征为鼓膜后方积液。该疾病常需手术干预，还可导致显著听力损失及后续学习障碍。近期针对儿科患者中耳积液（middle ear fluid, MEF）微生物组（microbiome）的表征研究，提升了我们对慢性渗出性中耳炎发病阶段中耳内定植微生物群的认知。然而目前尚不清楚中耳积液微生物组是否会因其他病症，尤其是呼吸道疾病，而发生改变。
本研究针对50名接受鼓膜置管术的慢性渗出性中耳炎患儿（年龄3~176月龄）的中耳积液16S核糖体RNA（16S rRNA）高通量测序数据，采用扩增子序列变异（amplicon sequence variant, ASV）分析流程。本研究获得了比此前报道更为精细的分类学分辨率（taxonomic resolution），可达种和属水平。此外，本研究首次报道了中耳积液微生物组的功能特征，并证实尽管分类学多样性较高，但不同患者的中耳积液微生物组功能潜能仍保持一致。
进一步，本研究分析了伴与不伴下呼吸道疾病（lower airway disease）病史的慢性渗出性中耳炎患儿之间的微生物组差异。下呼吸道疾病包括哮喘（asthma）与毛细支气管炎（bronchiolitis）。结果显示，合并下呼吸道疾病的受试者其中耳积液微生物组多样性低于无此类病史的患者；基于下呼吸道疾病状态的系统发育β多样性（phylogenetic β-diversity），以加权UniFrac（weighted UniFrac）作为分析指标，存在显著差异。嗜血杆菌属（Haemophilus）、莫拉菌属（Moraxella）、葡萄球菌属（Staphylococcus）、异球菌属（Alloiococcus）及图里菌属（Turicella）的相对丰度在伴与不伴下呼吸道疾病的患者间存在显著差异。
本研究结果支持了此前关于慢性渗出性中耳炎与呼吸道疾病存在关联的观点，并强调未来需针对哮喘、毛细支气管炎等疾病开展中耳及呼吸道微生物组的相关研究。