BACKGROUND Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of microbial communities at the species level along the human respiratory tract. FINDINGS Bronchoalveolar lavage, throat swab, mouth rinse, and nasal swab samples were collected from 5 participants. Bacterial ribosomal operons were sequenced using the Oxford Nanopore MinION to determine the relative abundance of bacterial species in 4 compartments along the respiratory tract. More than 1.8 million raw operon reads were obtained from the participants with ∼600,000 rRNA reads passing quality assurance/quality control (70-95% identify; >1,200 bp alignment) by Discontiguous MegaBLAST against the EZ BioCloud 16S rRNA gene database. Nearly 3,600 bacterial species were detected overall (>750 bacterial species within the 5 dominant phyla: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. The relative abundance of bacterial species along the respiratory tract indicated that most microbes (95%) were being passively transported from outside into the lung. However, a small percentage (<5%) of bacterial species were at higher abundance within the lavage samples. The most abundant lung-enriched bacterial species were Veillonella dispar and Veillonella atypica while the most abundant mouth-associated bacterial species were Streptococcus infantis and Streptococcus mitis. CONCLUSIONS Most bacteria detected in lower respiratory samples do not seem to colonize the lung. However, >100 bacterial species were found to be enriched in bronchoalveolar lavage samples (compared to mouth/nose) and may play a substantial role in lung health.

中文翻译：

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人类呼吸道微生物组的物种水平评估。


背景人类呼吸道微生物组的变化可能对呼吸道疾病的进展有重大影响。然而，很少有研究在人类呼吸道的物种水平上检验微生物群落的相对丰度。结果 从 5 名参与者身上采集了支气管肺泡灌洗液、咽喉拭子、漱口水和鼻拭子样本。使用 Oxford Nanopore MinION 对细菌核糖体操纵子进行测序，以确定呼吸道 4 个区室中细菌种类的相对丰度。根据 EZ BioCloud 16S rRNA 基因数据库，通过不连续 MegaBLAST 从参与者那里获得了超过 180 万个原始操纵子读数，其中约 600,000 个 rRNA 读数通过了质量保证/质量控制（70-95% 识别；>1,200 bp 比对）。总共检测到近 3,600 种细菌（超过 750 种细菌属于 5 个主要门：厚壁菌门、变形菌门、放线菌门、拟杆菌门和梭杆菌门。呼吸道细菌种类的相对丰度表明，大多数微生物 (95%) 都处于被动状态然而，一小部分细菌（<5 id=3>100 种细菌被发现在支气管肺泡灌洗样本中富集（与口腔/鼻子相比），可能对肺部健康发挥重要作用。