The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach.

Ditz, B; Boekhoudt, J; Couto, N; Brandsma, CA; Hiemstra, PS; Tew, GW; Neighbors, M; Grimbaldeston, MA; Timens, W; Kerstjens, HAM; Rossen, JWA; Guryev, V; van den Berge, M; Faiz, A

The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach.

Ditz, B Boekhoudt, J Couto, N Brandsma, CA Hiemstra, PS Tew, GW Neighbors, M Grimbaldeston, MA Timens, W Kerstjens, HAM Rossen, JWA Guryev, V van den Berge, M Faiz, A

Permalink

Publisher:: TAYLOR & FRANCIS INC
Publication Type:: Journal Article
Citation:: COPD, 2022, 19, (1), pp. 81-87
Issue Date:: 2022

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Download full textAdobe PDF (1.34 MB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Ditz, B
dc.contributor.author	Boekhoudt, J
dc.contributor.author	Couto, N
dc.contributor.author	Brandsma, CA
dc.contributor.author	Hiemstra, PS
dc.contributor.author	Tew, GW
dc.contributor.author	Neighbors, M
dc.contributor.author	Grimbaldeston, MA
dc.contributor.author	Timens, W
dc.contributor.author	Kerstjens, HAM
dc.contributor.author	Rossen, JWA
dc.contributor.author	Guryev, V
dc.contributor.author	van den Berge, M
dc.contributor.author	Faiz, A https://orcid.org/0000-0003-1740-3538
dc.date.accessioned	2023-02-03T00:49:33Z
dc.date.available	2023-02-03T00:49:33Z
dc.date.issued	2022
dc.identifier.citation	COPD, 2022, 19, (1), pp. 81-87
dc.identifier.issn	1541-2555
dc.identifier.issn	1541-2563
dc.identifier.uri	http://hdl.handle.net/10453/165874
dc.description.abstract	Current knowledge about the respiratory microbiome is mainly based on 16S ribosomal RNA gene sequencing. Newer sequencing approaches, such as metatranscriptomics, offer the technical ability to measure the viable microbiome response to environmental conditions such as smoking as well as to explore its functional role by investigating host-microbiome interactions. However, knowledge about its feasibility in respiratory microbiome research, especially in lung biopsies, is still very limited. RNA sequencing was performed in bronchial biopsies from clinically stable smokers (n = 5) and ex-smokers (n = 6) with COPD not using (inhaled) steroids. The Trinity assembler was used to assemble non-human reads in order to allow unbiased taxonomical and microbial transcriptional analyses. Subsequently, host-microbiome interactions were analyzed based on associations with host transcriptomic data. Ultra-low levels of microbial mass (0.009%) were identified in the RNA-seq data. Overall, no differences were identified in microbiome diversity or transcriptional profiles of microbial communities or individual microbes between COPD smokers and ex-smokers in the initial test dataset as well as a larger replication dataset. We identified an upregulated host gene set, related to the simultaneous presence of Bradyrhizobium, Roseomonas, Brevibacterium.spp., which were related to PERK-mediated unfolded protein response (UPR) and expression of the microRNA-155-5p. Our results show that metatranscriptomic profiling in bronchial biopsy samples from stable COPD patients yields ultra-low levels of microbial mass. Further, this study illustrates the potential of using transcriptional profiling of the host and microbiome to gain more insight into their interaction in the airways.
dc.format	Print-Electronic
dc.language	eng
dc.publisher	TAYLOR & FRANCIS INC
dc.relation.ispartof	COPD
dc.relation.isbasedon	10.1080/15412555.2022.2033193
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	1115 Pharmacology and Pharmaceutical Sciences, 1116 Medical Physiology, 1117 Public Health and Health Services
dc.subject.classification	Respiratory System
dc.subject.mesh	Biopsy
dc.subject.mesh	Ex-Smokers
dc.subject.mesh	Humans
dc.subject.mesh	MicroRNAs
dc.subject.mesh	Microbiota
dc.subject.mesh	Pulmonary Disease, Chronic Obstructive
dc.subject.mesh	Smokers
dc.subject.mesh	Humans
dc.subject.mesh	Pulmonary Disease, Chronic Obstructive
dc.subject.mesh	MicroRNAs
dc.subject.mesh	Biopsy
dc.subject.mesh	Microbiota
dc.subject.mesh	Smokers
dc.subject.mesh	Ex-Smokers
dc.title	The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach.
dc.type	Journal Article
utslib.citation.volume	19
utslib.location.activity	England
utslib.for	1115 Pharmacology and Pharmaceutical Sciences
utslib.for	1116 Medical Physiology
utslib.for	1117 Public Health and Health Services
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
pubs.organisational-group	/University of Technology Sydney/Centre for Health Technologies (CHT)
pubs.organisational-group	/University of Technology Sydney/Strength - CFI - Centre for Inflammation
utslib.copyright.status	open_access	*
dc.date.updated	2023-02-03T00:49:31Z
pubs.issue	1
pubs.publication-status	Published
pubs.volume	19
utslib.citation.issue	1

Abstract:

Current knowledge about the respiratory microbiome is mainly based on 16S ribosomal RNA gene sequencing. Newer sequencing approaches, such as metatranscriptomics, offer the technical ability to measure the viable microbiome response to environmental conditions such as smoking as well as to explore its functional role by investigating host-microbiome interactions. However, knowledge about its feasibility in respiratory microbiome research, especially in lung biopsies, is still very limited. RNA sequencing was performed in bronchial biopsies from clinically stable smokers (n = 5) and ex-smokers (n = 6) with COPD not using (inhaled) steroids. The Trinity assembler was used to assemble non-human reads in order to allow unbiased taxonomical and microbial transcriptional analyses. Subsequently, host-microbiome interactions were analyzed based on associations with host transcriptomic data. Ultra-low levels of microbial mass (0.009%) were identified in the RNA-seq data. Overall, no differences were identified in microbiome diversity or transcriptional profiles of microbial communities or individual microbes between COPD smokers and ex-smokers in the initial test dataset as well as a larger replication dataset. We identified an upregulated host gene set, related to the simultaneous presence of Bradyrhizobium, Roseomonas, Brevibacterium.spp., which were related to PERK-mediated unfolded protein response (UPR) and expression of the microRNA-155-5p. Our results show that metatranscriptomic profiling in bronchial biopsy samples from stable COPD patients yields ultra-low levels of microbial mass. Further, this study illustrates the potential of using transcriptional profiling of the host and microbiome to gain more insight into their interaction in the airways.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/165874