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.COPDindspon_mapping_DRYADMetadatafile for Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients, allowing rerun of analysis.COPDindspon_commands_DRYADCommand file for correct sample selection and creation of sub populations as in article: Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients.uc_fast_paramsParameter file necessary for OTU-picking.COPD_BERGEN_Fastq175Resulting Illumina fastq files from 175 sputum samples collected as part of the Bergen COPD Cohort Study (BCCS) and its adjunct Bergen COPD Exacerbation Study (BCES)