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Sputum microbiome profiling in COPD: beyond singular pathogen detection
Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. The contribution of the microbiome to chronic obstructive pulmonary disease (COPD) pathobiology and the potential for microbiom...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BMJ Publishing Group
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7231454/ https://www.ncbi.nlm.nih.gov/pubmed/31996401 http://dx.doi.org/10.1136/thoraxjnl-2019-214168 |
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author | Ditz, Benedikt Christenson, Stephanie Rossen, John Brightling, Chris Kerstjens, Huib A M van den Berge, Maarten Faiz, Alen |
author_facet | Ditz, Benedikt Christenson, Stephanie Rossen, John Brightling, Chris Kerstjens, Huib A M van den Berge, Maarten Faiz, Alen |
author_sort | Ditz, Benedikt |
collection | PubMed |
description | Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. The contribution of the microbiome to chronic obstructive pulmonary disease (COPD) pathobiology and the potential for microbiome-based clinical biomarkers in COPD are still in the early phases of investigation. Sputum is an easily obtainable sample and has provided a wealth of information on COPD pathobiology, and thus has been a preferred sample type for microbiome studies. Although the sputum microbiome likely reflects the respiratory microbiome only in part, there is increasing evidence that microbial community structure and diversity are associated with disease severity and clinical outcomes, both in stable COPD and during the exacerbations. Current evidence has been limited to mainly cross-sectional studies using 16S rRNA gene sequencing, attempting to answer the question ‘who is there?’ Longitudinal studies using standardised protocols are needed to answer outstanding questions including differences between sputum sampling techniques. Further, with advancing technologies, microbiome studies are shifting beyond the examination of the 16S rRNA gene, to include whole metagenome and metatranscriptome sequencing, as well as metabolome characterisation. Despite being technically more challenging, whole-genome profiling and metabolomics can address the questions ‘what can they do?’ and ‘what are they doing?’ This review provides an overview of the basic principles of high-throughput microbiome sequencing techniques, current literature on sputum microbiome profiling in COPD, and a discussion of the associated limitations and future perspectives. |
format | Online Article Text |
id | pubmed-7231454 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BMJ Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-72314542020-05-18 Sputum microbiome profiling in COPD: beyond singular pathogen detection Ditz, Benedikt Christenson, Stephanie Rossen, John Brightling, Chris Kerstjens, Huib A M van den Berge, Maarten Faiz, Alen Thorax State of the Art Review Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. The contribution of the microbiome to chronic obstructive pulmonary disease (COPD) pathobiology and the potential for microbiome-based clinical biomarkers in COPD are still in the early phases of investigation. Sputum is an easily obtainable sample and has provided a wealth of information on COPD pathobiology, and thus has been a preferred sample type for microbiome studies. Although the sputum microbiome likely reflects the respiratory microbiome only in part, there is increasing evidence that microbial community structure and diversity are associated with disease severity and clinical outcomes, both in stable COPD and during the exacerbations. Current evidence has been limited to mainly cross-sectional studies using 16S rRNA gene sequencing, attempting to answer the question ‘who is there?’ Longitudinal studies using standardised protocols are needed to answer outstanding questions including differences between sputum sampling techniques. Further, with advancing technologies, microbiome studies are shifting beyond the examination of the 16S rRNA gene, to include whole metagenome and metatranscriptome sequencing, as well as metabolome characterisation. Despite being technically more challenging, whole-genome profiling and metabolomics can address the questions ‘what can they do?’ and ‘what are they doing?’ This review provides an overview of the basic principles of high-throughput microbiome sequencing techniques, current literature on sputum microbiome profiling in COPD, and a discussion of the associated limitations and future perspectives. BMJ Publishing Group 2020-04 2020-01-29 /pmc/articles/PMC7231454/ /pubmed/31996401 http://dx.doi.org/10.1136/thoraxjnl-2019-214168 Text en © Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY. Published by BMJ. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See: https://creativecommons.org/licenses/by/4.0/. |
spellingShingle | State of the Art Review Ditz, Benedikt Christenson, Stephanie Rossen, John Brightling, Chris Kerstjens, Huib A M van den Berge, Maarten Faiz, Alen Sputum microbiome profiling in COPD: beyond singular pathogen detection |
title | Sputum microbiome profiling in COPD: beyond singular pathogen detection |
title_full | Sputum microbiome profiling in COPD: beyond singular pathogen detection |
title_fullStr | Sputum microbiome profiling in COPD: beyond singular pathogen detection |
title_full_unstemmed | Sputum microbiome profiling in COPD: beyond singular pathogen detection |
title_short | Sputum microbiome profiling in COPD: beyond singular pathogen detection |
title_sort | sputum microbiome profiling in copd: beyond singular pathogen detection |
topic | State of the Art Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7231454/ https://www.ncbi.nlm.nih.gov/pubmed/31996401 http://dx.doi.org/10.1136/thoraxjnl-2019-214168 |
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