Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing.
Determination of the precise composition and variation of microbiota in cystic fibrosis lungs is crucial since chronic inflammation due to microorganisms leads to lung damage and ultimately, death. However, this constitutes a major technical challenge. Culturing of microorganisms does not provide a...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3944733?pdf=render |
| _version_ | 1818951587854286848 |
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| author | Philippe M Hauser Thomas Bernard Gilbert Greub Katia Jaton Marco Pagni Gaudenz M Hafen |
| author_facet | Philippe M Hauser Thomas Bernard Gilbert Greub Katia Jaton Marco Pagni Gaudenz M Hafen |
| author_sort | Philippe M Hauser |
| collection | DOAJ |
| description | Determination of the precise composition and variation of microbiota in cystic fibrosis lungs is crucial since chronic inflammation due to microorganisms leads to lung damage and ultimately, death. However, this constitutes a major technical challenge. Culturing of microorganisms does not provide a complete representation of a microbiota, even when using culturomics (high-throughput culture). So far, only PCR-based metagenomics have been investigated. However, these methods are biased towards certain microbial groups, and suffer from uncertain quantification of the different microbial domains. We have explored whole genome sequencing (WGS) using the Illumina high-throughput technology applied directly to DNA extracted from sputa obtained from two cystic fibrosis patients. To detect all microorganism groups, we used four procedures for DNA extraction, each with a different lysis protocol. We avoided biases due to whole DNA amplification thanks to the high efficiency of current Illumina technology. Phylogenomic classification of the reads by three different methods produced similar results. Our results suggest that WGS provides, in a single analysis, a better qualitative and quantitative assessment of microbiota compositions than cultures and PCRs. WGS identified a high quantity of Haemophilus spp. (patient 1) or Staphylococcus spp. plus Streptococcus spp. (patient 2) together with low amounts of anaerobic (Veillonella, Prevotella, Fusobacterium) and aerobic bacteria (Gemella, Moraxella, Granulicatella). WGS suggested that fungal members represented very low proportions of the microbiota, which were detected by cultures and PCRs because of their selectivity. The future increase of reads' sizes and decrease in cost should ensure the usefulness of WGS for the characterisation of microbiota. |
| first_indexed | 2024-12-20T09:36:52Z |
| format | Article |
| id | doaj.art-42947bd093504a01a07a06975b1fdee5 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T09:36:52Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-42947bd093504a01a07a06975b1fdee52022-12-21T19:44:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0193e9093410.1371/journal.pone.0090934Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing.Philippe M HauserThomas BernardGilbert GreubKatia JatonMarco PagniGaudenz M HafenDetermination of the precise composition and variation of microbiota in cystic fibrosis lungs is crucial since chronic inflammation due to microorganisms leads to lung damage and ultimately, death. However, this constitutes a major technical challenge. Culturing of microorganisms does not provide a complete representation of a microbiota, even when using culturomics (high-throughput culture). So far, only PCR-based metagenomics have been investigated. However, these methods are biased towards certain microbial groups, and suffer from uncertain quantification of the different microbial domains. We have explored whole genome sequencing (WGS) using the Illumina high-throughput technology applied directly to DNA extracted from sputa obtained from two cystic fibrosis patients. To detect all microorganism groups, we used four procedures for DNA extraction, each with a different lysis protocol. We avoided biases due to whole DNA amplification thanks to the high efficiency of current Illumina technology. Phylogenomic classification of the reads by three different methods produced similar results. Our results suggest that WGS provides, in a single analysis, a better qualitative and quantitative assessment of microbiota compositions than cultures and PCRs. WGS identified a high quantity of Haemophilus spp. (patient 1) or Staphylococcus spp. plus Streptococcus spp. (patient 2) together with low amounts of anaerobic (Veillonella, Prevotella, Fusobacterium) and aerobic bacteria (Gemella, Moraxella, Granulicatella). WGS suggested that fungal members represented very low proportions of the microbiota, which were detected by cultures and PCRs because of their selectivity. The future increase of reads' sizes and decrease in cost should ensure the usefulness of WGS for the characterisation of microbiota.http://europepmc.org/articles/PMC3944733?pdf=render |
| spellingShingle | Philippe M Hauser Thomas Bernard Gilbert Greub Katia Jaton Marco Pagni Gaudenz M Hafen Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. PLoS ONE |
| title | Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. |
| title_full | Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. |
| title_fullStr | Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. |
| title_full_unstemmed | Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. |
| title_short | Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. |
| title_sort | microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing |
| url | http://europepmc.org/articles/PMC3944733?pdf=render |
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