Data from: Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients

Background: Induced and spontaneous sputum are used to evaluate the airways microbiota. Whether the sputum types can be used interchangeably in microbiota research is unknown. Our aim was to compare microbiota in induced and spontaneous sputum from COPD patients sampled during the same consultation.

Methods: COPD patients from Bergen, Norway, were followed between 2006/2010, examined during the stable state and exacerbations. 30 patients delivered 36 sample pairs. DNA was extracted by enzymatic and mechanical lysis methods. The V3-V4 region of the 16S rRNA gene was PCR-amplified and prepared for paired-end sequencing. Illumina Miseq System was used for sequencing, and Quantitative Insights Into Microbial Ecology (QIIME) and Stata were used for bioinformatics and statistical analyses.

Results: Approximately 4 million sequences were sorted into 1004 different OTUs and further assigned to 106 different taxa. Pair-wise comparison of both taxonomic composition and beta-diversity revealed significant differences in one or both parameters in 1/3 of sample pairs. Alpha-diversity did not differ. Comparing abundances for each taxa identified, showed statistically significant differences between the mean abundances in induced versus spontaneous samples for 15 taxa when disease state was considered. This included potential pathogens like Haemophilus and Moraxella.

Conclusion: When studying microbiota in sputum samples one should take into consideration how samples are collected and avoid the usage of both induced and spontaneous sputum in the same study.

背景：诱导痰（induced sputum）与自发性咳痰（spontaneous sputum）常用于评估气道微生物群。目前尚不明确这两类痰液样本能否在微生物群研究中互换使用。本研究旨在对比同一就诊期间采集的慢性阻塞性肺疾病（Chronic Obstructive Pulmonary Disease, COPD）患者的诱导痰与自发性咳痰中的微生物群组成。

方法：研究纳入来自挪威卑尔根的COPD患者，于2006年至2010年间开展随访，分别在患者病情稳定期与急性加重期进行检查。最终30名患者提供了36份样本对。采用酶解与机械裂解联合方法提取DNA。对16S核糖体RNA（16S rRNA）基因的V3-V4可变区进行聚合酶链式反应（Polymerase Chain Reaction, PCR）扩增，并制备成双端测序文库。使用Illumina MiSeq测序系统完成测序，采用微生物生态定量分析工具（Quantitative Insights Into Microbial Ecology, QIIME）与Stata软件开展生物信息学及统计学分析。

结果：共获得约400万条序列，经聚类得到1004个不同的操作分类单元（Operational Taxonomic Unit, OTU），并进一步注释为106个分类单元。对分类组成与β多样性分别进行组间比较后发现，1/3的样本对在至少一项参数上存在显著差异。α多样性则无明显组间差异。按疾病状态分层后，对各注释分类单元的相对丰度进行比较，结果显示15个分类单元的诱导痰与自发性咳痰样本平均丰度存在统计学显著差异，其中包括嗜血杆菌属（Haemophilus）与莫拉菌属（Moraxella）等潜在致病菌。

结论：在开展痰液样本的微生物群研究时，应充分考虑样本的采集方式，避免在同一研究中混合使用诱导痰与自发性咳痰样本。