Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?

Abstract Objective Little is known concerning the stability of the lower airway microbiome. We have compared the microbiota identified by repeated bronchoscopy in healthy subjects and patients with ostructive lung diseaseases (OLD). Methods 21 healthy controls and 41 patients with OLD completed two...

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Autores principales:	Rune Nielsen, Yaxin Xue, Inge Jonassen, Ingvild Haaland, Øyvind Kommedal, Harald G. Wiker, Christine Drengenes, Per S. Bakke, Tomas M. L. Eagan
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Microbiota Microbiome COPD Repeatability Reliability Bronchoscopy Diseases of the respiratory system RC705-779
Acceso en línea:	https://doaj.org/article/8ddbf77337724a52aed4ff24f7d0d198
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spelling	oai:doaj.org-article:8ddbf77337724a52aed4ff24f7d0d1982021-11-08T11:13:29ZRepeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?10.1186/s12890-021-01687-01471-2466https://doaj.org/article/8ddbf77337724a52aed4ff24f7d0d1982021-11-01T00:00:00Zhttps://doi.org/10.1186/s12890-021-01687-0https://doaj.org/toc/1471-2466Abstract Objective Little is known concerning the stability of the lower airway microbiome. We have compared the microbiota identified by repeated bronchoscopy in healthy subjects and patients with ostructive lung diseaseases (OLD). Methods 21 healthy controls and 41 patients with OLD completed two bronchoscopies. In addition to negative controls (NCS) and oral wash (OW) samples, we gathered protected bronchoalveolar lavage in two fractions (PBAL1 and PBAL2) and protected specimen brushes (PSB). After DNA extraction, we amplified the V3V4 region of the 16S rRNA gene, and performed paired-end sequencing (Illumina MiSeq). Initial bioinformatic processing was carried out in the QIIME-2 pipeline, identifying amplicon sequence variants (ASVs) with the DADA2 algorithm. Potentially contaminating ASVs were identified and removed using the decontam package in R and the sequenced NCS. Results A final table of 551 ASVs consisted of 19 × 106 sequences. Alpha diversity was lower in the second exam for OW samples, and borderline lower for PBAL1, with larger differences in subjects not having received intercurrent antibiotics. Permutational tests of beta diversity indicated that within-individual changes were significantly lower than between-individual changes. A non-parametric trend test showed that differences in composition between the two exams (beta diversity) were largest in the PSBs, and that these differences followed a pattern of PSB > PBAL2 > PBAL1 > OW. Time between procedures was not associated with increased diversity. Conclusion The airways microbiota varied between examinations. However, there is compositional microbiota stability within a person, beyond that of chance, supporting the notion of a transient airways microbiota with a possibly more stable individual core microbiome.Rune NielsenYaxin XueInge JonassenIngvild HaalandØyvind KommedalHarald G. WikerChristine DrengenesPer S. BakkeTomas M. L. EaganBMCarticleMicrobiotaMicrobiomeCOPDRepeatabilityReliabilityBronchoscopyDiseases of the respiratory systemRC705-779ENBMC Pulmonary Medicine, Vol 21, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiota Microbiome COPD Repeatability Reliability Bronchoscopy Diseases of the respiratory system RC705-779
spellingShingle	Microbiota Microbiome COPD Repeatability Reliability Bronchoscopy Diseases of the respiratory system RC705-779 Rune Nielsen Yaxin Xue Inge Jonassen Ingvild Haaland Øyvind Kommedal Harald G. Wiker Christine Drengenes Per S. Bakke Tomas M. L. Eagan Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?
description	Abstract Objective Little is known concerning the stability of the lower airway microbiome. We have compared the microbiota identified by repeated bronchoscopy in healthy subjects and patients with ostructive lung diseaseases (OLD). Methods 21 healthy controls and 41 patients with OLD completed two bronchoscopies. In addition to negative controls (NCS) and oral wash (OW) samples, we gathered protected bronchoalveolar lavage in two fractions (PBAL1 and PBAL2) and protected specimen brushes (PSB). After DNA extraction, we amplified the V3V4 region of the 16S rRNA gene, and performed paired-end sequencing (Illumina MiSeq). Initial bioinformatic processing was carried out in the QIIME-2 pipeline, identifying amplicon sequence variants (ASVs) with the DADA2 algorithm. Potentially contaminating ASVs were identified and removed using the decontam package in R and the sequenced NCS. Results A final table of 551 ASVs consisted of 19 × 106 sequences. Alpha diversity was lower in the second exam for OW samples, and borderline lower for PBAL1, with larger differences in subjects not having received intercurrent antibiotics. Permutational tests of beta diversity indicated that within-individual changes were significantly lower than between-individual changes. A non-parametric trend test showed that differences in composition between the two exams (beta diversity) were largest in the PSBs, and that these differences followed a pattern of PSB > PBAL2 > PBAL1 > OW. Time between procedures was not associated with increased diversity. Conclusion The airways microbiota varied between examinations. However, there is compositional microbiota stability within a person, beyond that of chance, supporting the notion of a transient airways microbiota with a possibly more stable individual core microbiome.
format	article
author	Rune Nielsen Yaxin Xue Inge Jonassen Ingvild Haaland Øyvind Kommedal Harald G. Wiker Christine Drengenes Per S. Bakke Tomas M. L. Eagan
author_facet	Rune Nielsen Yaxin Xue Inge Jonassen Ingvild Haaland Øyvind Kommedal Harald G. Wiker Christine Drengenes Per S. Bakke Tomas M. L. Eagan
author_sort	Rune Nielsen
title	Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?
title_short	Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?
title_full	Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?
title_fullStr	Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?
title_full_unstemmed	Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?
title_sort	repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?
publisher	BMC
publishDate	2021
url	https://doaj.org/article/8ddbf77337724a52aed4ff24f7d0d198
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Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?

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