Sputum metagenomics of people with bronchiectasis

Ilona Rosenboom; Ajith Thavarasa; Hollian Richardson; Merete B. Long; Lutz Wiehlmann; Colin F. Davenport; Amelia Shoemark; James D. Chalmers; Burkhard Tümmler

doi:10.1183/23120541.01008-2023

Sputum metagenomics of people with bronchiectasis

Ilona Rosenboom (Lead / Corresponding author), Ajith Thavarasa, Hollian Richardson, Merete B. Long, Lutz Wiehlmann, Colin F. Davenport, Amelia Shoemark, James D. Chalmers, Burkhard Tümmler

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Abstract

BACKGROUND: The microbiota in the sputum of people with bronchiectasis has repeatedly been investigated in cohorts of different geographic origin, but so far has not been studied to the species level in comparison to control populations including healthy adults and smokers without lung disease.

METHODS: The microbial metagenome from sputa of 101 European Bronchiectasis Registry (EMBARC) study participants was examined by using whole-genome shotgun sequencing.

RESULTS: Our analysis of the metagenome of people with bronchiectasis revealed four clusters characterised by a predominance of Haemophilus influenzae, Pseudomonas aeruginosa or polymicrobial communities with varying compositions of nonpathogenic commensals and opportunistic pathogens. The metagenomes of the severely affected patients showed individual profiles characterised by low alpha diversity. Importantly, nearly 50% of patients with severe disease were grouped in a cluster characterised by commensals. Comparisons with the sputum metagenomes of healthy smokers and healthy nonsmokers revealed a gradient of depletion of taxa in bronchiectasis, most often Neisseria subflava, Fusobacterium periodonticum and Eubacterium sulci.

CONCLUSION: The gradient of depletion of commensal taxa found in healthy airways is a key feature of bronchiectasis associated with disease severity.

Original language	English
Number of pages	13
Journal	ERJ Open Research
Volume	10
Issue number	2
DOIs	https://doi.org/10.1183/23120541.01008-2023
Publication status	Published - 4 Mar 2024

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Final published versionFinal published version, 1.45 MBLicence: CC BY-NC

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title = "Sputum metagenomics of people with bronchiectasis",

abstract = "BACKGROUND: The microbiota in the sputum of people with bronchiectasis has repeatedly been investigated in cohorts of different geographic origin, but so far has not been studied to the species level in comparison to control populations including healthy adults and smokers without lung disease.METHODS: The microbial metagenome from sputa of 101 European Bronchiectasis Registry (EMBARC) study participants was examined by using whole-genome shotgun sequencing.RESULTS: Our analysis of the metagenome of people with bronchiectasis revealed four clusters characterised by a predominance of Haemophilus influenzae, Pseudomonas aeruginosa or polymicrobial communities with varying compositions of nonpathogenic commensals and opportunistic pathogens. The metagenomes of the severely affected patients showed individual profiles characterised by low alpha diversity. Importantly, nearly 50% of patients with severe disease were grouped in a cluster characterised by commensals. Comparisons with the sputum metagenomes of healthy smokers and healthy nonsmokers revealed a gradient of depletion of taxa in bronchiectasis, most often Neisseria subflava, Fusobacterium periodonticum and Eubacterium sulci.CONCLUSION: The gradient of depletion of commensal taxa found in healthy airways is a key feature of bronchiectasis associated with disease severity.",

author = "Ilona Rosenboom and Ajith Thavarasa and Hollian Richardson and Long, {Merete B.} and Lutz Wiehlmann and Davenport, {Colin F.} and Amelia Shoemark and Chalmers, {James D.} and Burkhard T{\"u}mmler",

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year = "2024",

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doi = "10.1183/23120541.01008-2023",

language = "English",

volume = "10",

journal = "ERJ Open Research",

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T1 - Sputum metagenomics of people with bronchiectasis

AU - Rosenboom, Ilona

AU - Thavarasa, Ajith

AU - Richardson, Hollian

AU - Long, Merete B.

AU - Wiehlmann, Lutz

AU - Davenport, Colin F.

AU - Shoemark, Amelia

AU - Chalmers, James D.

AU - Tümmler, Burkhard

PY - 2024/3/4

Y1 - 2024/3/4

N2 - BACKGROUND: The microbiota in the sputum of people with bronchiectasis has repeatedly been investigated in cohorts of different geographic origin, but so far has not been studied to the species level in comparison to control populations including healthy adults and smokers without lung disease.METHODS: The microbial metagenome from sputa of 101 European Bronchiectasis Registry (EMBARC) study participants was examined by using whole-genome shotgun sequencing.RESULTS: Our analysis of the metagenome of people with bronchiectasis revealed four clusters characterised by a predominance of Haemophilus influenzae, Pseudomonas aeruginosa or polymicrobial communities with varying compositions of nonpathogenic commensals and opportunistic pathogens. The metagenomes of the severely affected patients showed individual profiles characterised by low alpha diversity. Importantly, nearly 50% of patients with severe disease were grouped in a cluster characterised by commensals. Comparisons with the sputum metagenomes of healthy smokers and healthy nonsmokers revealed a gradient of depletion of taxa in bronchiectasis, most often Neisseria subflava, Fusobacterium periodonticum and Eubacterium sulci.CONCLUSION: The gradient of depletion of commensal taxa found in healthy airways is a key feature of bronchiectasis associated with disease severity.

AB - BACKGROUND: The microbiota in the sputum of people with bronchiectasis has repeatedly been investigated in cohorts of different geographic origin, but so far has not been studied to the species level in comparison to control populations including healthy adults and smokers without lung disease.METHODS: The microbial metagenome from sputa of 101 European Bronchiectasis Registry (EMBARC) study participants was examined by using whole-genome shotgun sequencing.RESULTS: Our analysis of the metagenome of people with bronchiectasis revealed four clusters characterised by a predominance of Haemophilus influenzae, Pseudomonas aeruginosa or polymicrobial communities with varying compositions of nonpathogenic commensals and opportunistic pathogens. The metagenomes of the severely affected patients showed individual profiles characterised by low alpha diversity. Importantly, nearly 50% of patients with severe disease were grouped in a cluster characterised by commensals. Comparisons with the sputum metagenomes of healthy smokers and healthy nonsmokers revealed a gradient of depletion of taxa in bronchiectasis, most often Neisseria subflava, Fusobacterium periodonticum and Eubacterium sulci.CONCLUSION: The gradient of depletion of commensal taxa found in healthy airways is a key feature of bronchiectasis associated with disease severity.

U2 - 10.1183/23120541.01008-2023

DO - 10.1183/23120541.01008-2023

M3 - Article

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SN - 2312-0541

VL - 10

JO - ERJ Open Research

JF - ERJ Open Research

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Sputum metagenomics of people with bronchiectasis

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