Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients
<p>Abstract</p> <p>Chronic bronchopulmonary bacterial infections remain the most common cause of morbidity and mortality among patients with cystic fibrosis (CF). Recent community sequencing work has now shown that the bacterial community in the CF lung is polymicrobial. Identifyin...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-02-01
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| Series: | Human Genomics |
| Subjects: | |
| Online Access: | http://www.humgenomics.com/content/4/2/147 |
| _version_ | 1817993774025932800 |
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| author | Doud Melissa S Light Michael Gonzalez Gisela Narasimhan Giri Mathee Kalai |
| author_facet | Doud Melissa S Light Michael Gonzalez Gisela Narasimhan Giri Mathee Kalai |
| author_sort | Doud Melissa S |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Chronic bronchopulmonary bacterial infections remain the most common cause of morbidity and mortality among patients with cystic fibrosis (CF). Recent community sequencing work has now shown that the bacterial community in the CF lung is polymicrobial. Identifying bacteria in the CF lung through sequencing can be costly and is not practical for many laboratories. Molecular techniques such as terminal restriction fragment length polymorphism or amplicon length heterogeneity-polymerase chain reaction (LH-PCR) can provide many laboratories with the ability to study CF bacterial communities without costly sequencing. The aim of this study was to determine if the use of LH-PCR with multiple hypervariable regions of the 16S rRNA gene could be used to identify organisms found in sputum DNA. This work also determined if LH-PCR could be used to observe the dynamics of lung infections over a period of time. Nineteen samples were analysed with the V1 and the V1_V2 region of the 16S rRNA gene. Based on the amplicon size present in the V1_V2 region, <it>Pseudomonas aeruginosa </it>was confirmed to be in all 19 samples obtained from the patients. The V1 region provided a higher power of discrimination between bacterial profiles of patients. Both regions were able to identify trends in the bacterial population over a period of time. LH profiles showed that the CF lung community is dynamic and that changes in the community may in part be driven by the patient's antibiotic treatment. LH-PCR is a tool that is well suited for studying bacterial communities and their dynamics.</p> |
| first_indexed | 2024-04-14T01:43:29Z |
| format | Article |
| id | doaj.art-b9df4c723b5345409e2af1afbe291fb8 |
| institution | Directory Open Access Journal |
| issn | 1479-7364 |
| language | English |
| last_indexed | 2024-04-14T01:43:29Z |
| publishDate | 2010-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Human Genomics |
| spelling | doaj.art-b9df4c723b5345409e2af1afbe291fb82022-12-22T02:19:38ZengBMCHuman Genomics1479-73642010-02-014314716910.1186/1479-7364-4-3-147Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patientsDoud Melissa SLight MichaelGonzalez GiselaNarasimhan GiriMathee Kalai<p>Abstract</p> <p>Chronic bronchopulmonary bacterial infections remain the most common cause of morbidity and mortality among patients with cystic fibrosis (CF). Recent community sequencing work has now shown that the bacterial community in the CF lung is polymicrobial. Identifying bacteria in the CF lung through sequencing can be costly and is not practical for many laboratories. Molecular techniques such as terminal restriction fragment length polymorphism or amplicon length heterogeneity-polymerase chain reaction (LH-PCR) can provide many laboratories with the ability to study CF bacterial communities without costly sequencing. The aim of this study was to determine if the use of LH-PCR with multiple hypervariable regions of the 16S rRNA gene could be used to identify organisms found in sputum DNA. This work also determined if LH-PCR could be used to observe the dynamics of lung infections over a period of time. Nineteen samples were analysed with the V1 and the V1_V2 region of the 16S rRNA gene. Based on the amplicon size present in the V1_V2 region, <it>Pseudomonas aeruginosa </it>was confirmed to be in all 19 samples obtained from the patients. The V1 region provided a higher power of discrimination between bacterial profiles of patients. Both regions were able to identify trends in the bacterial population over a period of time. LH profiles showed that the CF lung community is dynamic and that changes in the community may in part be driven by the patient's antibiotic treatment. LH-PCR is a tool that is well suited for studying bacterial communities and their dynamics.</p>http://www.humgenomics.com/content/4/2/147LH-PCR16S rRNAV1V1_V2cystic fibrosisAmpliQuécystic fibrosis microbiomemetagenome |
| spellingShingle | Doud Melissa S Light Michael Gonzalez Gisela Narasimhan Giri Mathee Kalai Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients Human Genomics LH-PCR 16S rRNA V1 V1_V2 cystic fibrosis AmpliQué cystic fibrosis microbiome metagenome |
| title | Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients |
| title_full | Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients |
| title_fullStr | Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients |
| title_full_unstemmed | Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients |
| title_short | Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients |
| title_sort | combination of 16s rrna variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients |
| topic | LH-PCR 16S rRNA V1 V1_V2 cystic fibrosis AmpliQué cystic fibrosis microbiome metagenome |
| url | http://www.humgenomics.com/content/4/2/147 |
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