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The bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus Sze, Marc A.; Xu, Stella; Leung, Janice M.; Vucic, Emily A.; Shaipanich, Tawimas; Moghadam, Aida; Harris, Marianne; Guillemi, Silvia; Sinha, Sunita; Nislow, Corey; et al.

Abstract

Background: Chronic Obstructive Pulmonary Disease (COPD) is an important comorbidity in patients living with human immunodeficiency virus (HIV). Previous bacterial microbiome studies have shown increased abundance of specific bacterium, like Tropheryma whipplei, and no overall community differences. However, the host response to the lung microbiome is unknown in patients infected with HIV. Methods: Two bronchial brush samples were obtained from 21 HIV-infected patients. One brush was used for bacterial microbiome analysis using the Illumina MiSeqTM platform, while the other was used to evaluate gene expression patterns of the host using the Affymetrix Human Gene ST 2.0 array. Weighted gene co-expression network analysis was used to determine the relationship between the bacterial microbiome and host gene expression response. Results: The Shannon Diversity was inversely related to only one gene expression module (p = 0.02); whereas evenness correlated with five different modules (p ≤ 0.05). After FDR correction only the Firmicutes phylum was significantly correlated with any modules (FDR < 0.05). These modules were enriched for cilia, transcription regulation, and immune response. Specific operational taxonomic units (OTUs), such as OTU4 (Pasteurellaceae), were able to distinguish HIV patients with and without COPD and severe emphysema. Conclusion: These data support the hypothesis that the bacterial microbiome in HIV lungs is associated with specific host immune responses. Whether or not these responses are also seen in non-HIV infected individuals needs to be addressed in future studies.

Item Metadata

Title
The bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus
Creator
Sze, Marc A.; Xu, Stella; Leung, Janice M.; Vucic, Emily A.; Shaipanich, Tawimas; Moghadam, Aida; Harris, Marianne; Guillemi, Silvia; Sinha, Sunita; Nislow, Corey; Murphy, Darra; Hague, Cameron; Leipsic, Jonathon; Lam, Stephen; Lam, Wan; Montaner, Julio; Sin, Don D.; Man, S. F. P.
Contributor
University of British Columbia. Centre for Heart Lung Innovation; St. Paul's Hospital (Vancouver, B.C.); British Columbia Centre for Excellence in HIV/AIDS
Publisher
BioMed Central
Date Issued
2016-11-09
Description
Background: Chronic Obstructive Pulmonary Disease (COPD) is an important comorbidity in patients living with human immunodeficiency virus (HIV). Previous bacterial microbiome studies have shown increased abundance of specific bacterium, like Tropheryma whipplei, and no overall community differences. However, the host response to the lung microbiome is unknown in patients infected with HIV. Methods: Two bronchial brush samples were obtained from 21 HIV-infected patients. One brush was used for bacterial microbiome analysis using the Illumina MiSeqTM platform, while the other was used to evaluate gene expression patterns of the host using the Affymetrix Human Gene ST 2.0 array. Weighted gene co-expression network analysis was used to determine the relationship between the bacterial microbiome and host gene expression response. Results: The Shannon Diversity was inversely related to only one gene expression module (p = 0.02); whereas evenness correlated with five different modules (p ≤ 0.05). After FDR correction only the Firmicutes phylum was significantly correlated with any modules (FDR < 0.05). These modules were enriched for cilia, transcription regulation, and immune response. Specific operational taxonomic units (OTUs), such as OTU4 (Pasteurellaceae), were able to distinguish HIV patients with and without COPD and severe emphysema. Conclusion: These data support the hypothesis that the bacterial microbiome in HIV lungs is associated with specific host immune responses. Whether or not these responses are also seen in non-HIV infected individuals needs to be addressed in future studies.
Subject
Bronchial brushing; Bacterial microbiome; HIV; Lungs; Gene expression
Genre
Article
Type
Text
Language
eng
Date Available
2017-12-14
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0362016
URI
http://hdl.handle.net/2429/64000
Affiliation
Medicine, Faculty of; Pharmaceutical Sciences, Faculty of; Other UBC; Family Practice, Department of; Medicine, Department of
Citation
BMC Pulmonary Medicine. 2016 Nov 09;16(1):142
Publisher DOI
10.1186/s12890-016-0303-4
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
The Author(s).
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Attribution 4.0 International (CC BY 4.0)