Developmental progression of the nasopharyngeal microbiome during childhood and association with the lower airway microbiome.
Developmental progression of the nasopharyngeal microbiome during childhood and association with the lower airway microbiome.
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儿童期鼻咽微生物组的发育进展及其与下呼吸道微生物组的关联。
DOI：
10.1101/2023.09.18.23295747
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
John,AudreyROdom
中科院分区：
文献类型：
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作者：
Hernandez-Leyva,ArielJ;Rosen,AnneL;Tomera,ChristopherP;Lin,ElainaE;Akaho,ElikplimH;Blatz,AllisonM;Otto,WilliamR;Logan,Joey;Young,LisaR;Harris,RebeccaM;Kau,AndrewL;John,AudreyROdom
上呼吸道（URT）和下呼吸道（LRT）具有不同的环境和影响微生物定植的反应，但研究它们之间的关系在技术上具有挑战性。我们的目的是确定类群殖民城市轨道交通和轻轨之间的关系，并探讨其与儿童时期的发展。方法我们采用V4 16 S rDNA测序技术对183名20周龄至18岁的受试者的鼻咽拭子和气管吸出物进行分析。这些样本是在2020年费城儿童医院20周的择期手术前收集的，来自参加一项调查SARS-CoV-2潜在宿主的研究的其他健康受试者。在提取、测序和质量控制后，我们研究了剩余的124个鼻咽拭子和98个气管抽吸物，包括85个受试者匹配的样本对。V4 16 S rDNA测序显示，鼻咽部由少数高度丰富的类群定殖，而气管吸出物具有多种微生物的组装。虽然没有分类群共同出现在同一受试者的URT和LRT中，但URT中的微生物组群与LRT中的微生物组群相关。URT中确定的聚类与整个儿童期发育的受试者年龄相关。解释跨网站的类群集群之间的相关性可能会建议从第三个网站，如口咽，或主机外部，环境特征的相互影响。在生命的前18年中确定上呼吸道微生物群发育模式表明，在幼儿期观察到的模式可能会延伸到生命早期窗口之外。
Background The upper (URT) and lower (LRT) respiratory tract feature distinct environments and responses affecting microbial colonization but investigating the relationship between them is technically challenging. We aimed to identify relationships between taxa colonizing the URT and LRT and explore their relationship with development during childhood. Methods We employed V4 16S rDNA sequencing to profile nasopharyngeal swabs and tracheal aspirates collected from 183 subjects between 20 weeks and 18 years of age. These samples were collected prior to elective procedures at the Children’s Hospital of Philadelphia over the course of 20 weeks in 2020, from otherwise healthy subjects enrolled in a study investigating potential reservoirs of SARS-CoV-2. Findings After extraction, sequencing, and quality control, we studied the remaining 124 nasopharyngeal swabs and 98 tracheal aspirates, including 85 subject-matched pairs of samples. V4 16S rDNA sequencing revealed that the nasopharynx is colonized by few, highly-abundant taxa, while the tracheal aspirates feature a diverse assembly of microbes. While no taxa co-occur in the URT and LRT of the same subject, clusters of microbiomes in the URT correlate with clusters of microbiomes in the LRT. The clusters identified in the URT correlate with subject age across childhood development. Interpretations The correlation between clusters of taxa across sites may suggest a mutual influence from either a third site, such as the oropharynx, or host-extrinsic, environmental features. The identification of a pattern of upper respiratory microbiota development across the first 18 years of life suggests that the patterns observed in early childhood may extend beyond the early life window.