Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients
Abstract 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 consu...
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| Format: | Article |
| Language: | English |
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BMC
2017-08-01
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| Series: | Respiratory Research |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12931-017-0645-3 |
| _version_ | 1818028389375672320 |
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| author | Solveig Tangedal Marianne Aanerud Rune Grønseth Christine Drengenes Harald G. Wiker Per S. Bakke Tomas M. Eagan |
| author_facet | Solveig Tangedal Marianne Aanerud Rune Grønseth Christine Drengenes Harald G. Wiker Per S. Bakke Tomas M. Eagan |
| author_sort | Solveig Tangedal |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-10T05:03:01Z |
| format | Article |
| id | doaj.art-84431236ed424039a2fc49f98a92f03f |
| institution | Directory Open Access Journal |
| issn | 1465-993X |
| language | English |
| last_indexed | 2024-12-10T05:03:01Z |
| publishDate | 2017-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Respiratory Research |
| spelling | doaj.art-84431236ed424039a2fc49f98a92f03f2022-12-22T02:01:19ZengBMCRespiratory Research1465-993X2017-08-011811910.1186/s12931-017-0645-3Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patientsSolveig Tangedal0Marianne Aanerud1Rune Grønseth2Christine Drengenes3Harald G. Wiker4Per S. Bakke5Tomas M. Eagan6Department of Thoracic Medicine, Haukeland University HospitalDepartment of Thoracic Medicine, Haukeland University HospitalDepartment of Thoracic Medicine, Haukeland University HospitalDepartment of Thoracic Medicine, Haukeland University HospitalDepartment of Clinical Science, Faculty of Medicine and Dentistry, University of BergenDepartment of Clinical Science, Faculty of Medicine and Dentistry, University of BergenDepartment of Thoracic Medicine, Haukeland University HospitalAbstract 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.http://link.springer.com/article/10.1186/s12931-017-0645-3COPDSputumMicrobiotaHigh-throughput sequencing |
| spellingShingle | Solveig Tangedal Marianne Aanerud Rune Grønseth Christine Drengenes Harald G. Wiker Per S. Bakke Tomas M. Eagan Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients Respiratory Research COPD Sputum Microbiota High-throughput sequencing |
| title | Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients |
| title_full | Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients |
| title_fullStr | Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients |
| title_full_unstemmed | Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients |
| title_short | Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients |
| title_sort | comparing microbiota profiles in induced and spontaneous sputum samples in copd patients |
| topic | COPD Sputum Microbiota High-throughput sequencing |
| url | http://link.springer.com/article/10.1186/s12931-017-0645-3 |
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