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.