Lower airway microbiota in COPD and healthy controls

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, the use of inhaled corticosteroids (ICS), and COPD severity is still scarce. 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. 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 con..., , , # Lower airway microbiota in COPD and healthy controls #### This note was written by Solveig Tangedal, on Nov 29th, 2023, and edited on Dec 17th, 2024. We have submitted deidentified participant data (metadata) in .xlsx and .txt format(**COPDvCMetadata.xlsx COPDvCMetadata.txt**), Amplicon sequencing variants (ASV) tables in qza format for all ASVs and for ASVs eligible for differential abundance analyses (**COPDvC_ASV.qza COPDvCAncomASV.qza**) Representative sequences tables in qza format for all ASVs (**COPDvCRepSeq.qza**), Rooted phylogenetic trees in qza format (**COPDvC_rootedtree.qza**), Taxonomy tables in qza format (**COPDvC_Taxonomy.qza**), QIIME 2 code in txt format (**COPDvsControl_Q2_code.txt**), R code in RScript format (**COPDvControl_Rcommand.R**), and the manuscript abstract in docx format (**ABSTRACT.docx**) The MicroCOPD study is a large study, with amplicon (16S rRNA) sequencing of more than 3000 samples over > 30 RUNs. The airways samples number > 2500, and ...慢性阻塞性肺疾病（chronic obstructive pulmonary disease, COPD）患者的下呼吸道微生物群与健康个体的微生物群相比，大概率存在改变。目前关于吸烟、吸入性糖皮质激素（inhaled corticosteroids, ICS）的使用以及COPD严重程度如何影响微生物群的相关信息仍较为匮乏。 在MicroCOPD研究中，研究团队于2012年至2015年间在单中心通过标准化问卷与临床检测收集受试者的特征信息。对97例COPD患者与97例健康对照的保护性支气管肺泡灌洗样本，采用Illumina MiSeq系统进行双端测序。数据通过QIIME 2与R软件进行分析。 分析结果显示，COPD患者的α多样性（Alpha-diversity）低于健康对照组（皮洛均匀度（Pielou evenness）：COPD组为0.76，对照组为0.80，p=0.004；香农熵（Shannon entropy）：COPD组为3.98，对照组为4.34，p=0.01）。β多样性（Beta-diversity）仅在COPD队列中与吸烟状态存在显著关联（加权UniFrac：置换多元方差分析（permutational analysis of variance）R²=0.04，p=0.03）。共有9个菌属在COPD患者与对照之间的丰度存在显著差异…… # COPD患者与健康对照的下呼吸道微生物群 本说明由Solveig Tangedal于2023年11月29日撰写，2024年12月17日修订。本研究已提交去标识化的受试者数据（元数据），格式为.xlsx与.txt（**COPDvCMetadata.xlsx、COPDvCMetadata.txt**）；扩增子序列变异（Amplicon Sequencing Variants, ASV）表涵盖所有ASV及符合差异丰度分析条件的ASV，格式为qza（**COPDvC_ASV.qza、COPDvCAncomASV.qza**）；所有ASV的代表性序列表，格式为qza（**COPDvCRepSeq.qza**）；带根系统发育树，格式为qza（**COPDvC_rootedtree.qza**）；分类学表，格式为qza（**COPDvC_Taxonomy.qza**）；QIIME 2代码，格式为txt（**COPDvsControl_Q2_code.txt**）；R代码，格式为RScript（**COPDvControl_Rcommand.R**）；以及手稿摘要，格式为docx（**ABSTRACT.docx**） MicroCOPD研究为一项大型研究，已对超过3000份样本完成16S rRNA扩增子测序，涵盖超过30次测序运行。气道样本数量超过2500份，……