Background The lower airway microbiota in patients with chronic obstructive pulmonary disease (COPD) are likely altered compared with the microbiota in healthy individuals. Information on how the microbiota is affected by smoking, use of inhaled corticosteroids (ICS) and COPD severity is still scarce. Methods In the MicroCOPD Study, participant characteristics were obtained through standardised questionnaires and clinical measurements at a single centre from 2012 to 2015. Protected bronchoalveolar lavage samples from 97 patients with COPD and 97 controls were paired-end sequenced with the Illumina MiSeq System. Data were analysed in QIIME 2 and R. Results Alpha-diversity was lower in patients with COPD than controls (Pielou evenness: COPD=0.76, control=0.80, p=0.004; Shannon entropy: COPD=3.98, control=4.34, p=0.01). Beta-diversity differed with smoking only in the COPD cohort (weighted UniFrac: permutational analysis of variance R2=0.04, p=0.03). Nine genera were differentially abundant between COPD and controls. Genera enriched in COPD belonged to the Firmicutes phylum. Pack years were linked to differential abundance of taxa in controls only (ANCOM-BC (Analysis of Compositions of Microbiomes with Bias Correction) log-fold difference/q-values: Haemophilus −0.05/0.048; Lachnoanaerobaculum −0.04/0.03). Oribacterium was absent in smoking patients with COPD compared with non-smoking patients (ANCOM-BC log-fold difference/q-values: −1.46/0.03). We found no associations between the microbiota and COPD severity or ICS. Conclusion The lower airway microbiota is equal in richness in patients with COPD to controls, but less even. Genera from the Firmicutes phylum thrive particularly in COPD airways. Smoking has different effects on diversity and taxonomic abundance in patients with COPD compared with controls. COPD severity and ICS use were not linked to the lower airway microbiota. Data are available in a public, open access repository. Data are available from the time of publication and without end date at DRYAD depository: . Submitted data include de-identified participant data (metadata) in .xlsx and .txt format, ASV and representative sequences tables, phylogenetic tree (rooted), and taxonomy in .qza format from QIIME 2, QIIME 2 code and R code. The data have been generated by ST and TME. The study protocol is published and linked to in the manuscript.

中文翻译：

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慢性阻塞性肺病和健康对照中的下呼吸道微生物群

背景 与健康个体的微生物群相比，慢性阻塞性肺疾病（COPD）患者的下呼吸道微生物群可能发生改变。关于吸烟、吸入皮质类固醇 (ICS) 的使用和慢性阻塞性肺病严重程度如何影响微生物群的信息仍然很少。方法 在 MicroCOPD 研究中，通过 2012 年至 2015 年单个中心的标准化问卷和临床测量获得参与者特征。使用 Illumina MiSeq 系统对 97 名 COPD 患者和 97 名对照者的受保护支气管肺泡灌洗样本进行双端测序。在 QIIME 2 和 R 中分析数据。结果 COPD 患者的 Alpha 多样性低于对照组（Pielou 均匀度：COPD=0.76，对照=0.80，p=0.004；香农熵：COPD=3.98，对照=4.34，p= 0.01）。仅在 COPD 队列中，β 多样性与吸烟存在差异（加权 UniFrac：方差排列分析 R2=0.04，p=0.03）。 COPD 和对照之间有九个属的丰度存在差异。富含COPD的属属于厚壁菌门。包装年份仅与对照中类群的差异丰度相关（ANCOM-BC（带有偏差校正的微生物组组成分析）对数倍数差异/q值：嗜血杆菌 -0.05/0.048；Lachnoanaerobaculum -0.04/0.03）。与不吸烟患者相比，患有 COPD 的吸烟患者体内不存在奥里杆菌（ANCOM-BC 对数倍数差异/q 值：-1.46/0.03）。我们发现微生物群与 COPD 严重程度或 ICS 之间没有关联。结论 COPD 患者下气道微生物群的丰富度与对照组相同，但均匀度较差。厚壁菌门的属在慢性阻塞性肺病 (COPD) 气道中尤其繁盛。与对照组相比，吸烟对慢性阻塞性肺病患者的多样性和分类丰度有不同的影响。 COPD 严重程度和 ICS 使用与下呼吸道微生物群无关。数据可在公共、开放访问存储库中获取。数据自发布之日起可在 DRYAD 存储库获取，无结束日期：。提交的数据包括 .xlsx 和 .txt 格式的去识别参与者数据（元数据）、ASV 和代表性序列表、系统发育树（有根）以及来自 QIIME 2、QIIME 2 代码和 R 代码的 .qza 格式的分类法。数据由 ST 和 TME 生成。研究方案已发布并在手稿中链接。