The bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus.
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.



Two bronchial brush samples were obtained from 21 HIV-infected patients. One brush was used for bacterial microbiome analysis using the Illumina MiSeqTMplatform, 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.



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.



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.
Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada. marcsze@med.umich.edu.
Marc A
MA
Sze
Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada.
Stella
S
Xu
Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada.
Janice M
JM
Leung
Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada.
Emily A
EA
Vucic
Division of Respiratory Medicine, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
Tawimas
T
Shaipanich
AIDS Research Program, St. Paul's Hospital, Vancouver, BC, Canada.
Aida
A
Moghadam
AIDS Research Program, St. Paul's Hospital, Vancouver, BC, Canada.|Department of Family Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.|Division of HIV/AIDS, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
Marianne
M
Harris
AIDS Research Program, St. Paul's Hospital, Vancouver, BC, Canada.|Department of Family Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.|Division of HIV/AIDS, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
Silvia
S
Guillemi
Faculty of Pharmaceutical Sciences, Pharmaceutical Sciences Building, University of British Columbia, Vancouver, BC, Canada.
Sunita
S
Sinha
Faculty of Pharmaceutical Sciences, Pharmaceutical Sciences Building, University of British Columbia, Vancouver, BC, Canada.
Corey
C
Nislow
Department of Radiology and Diagnostic Imaging, St. Paul's Hospital, Vancouver, BC, Canada.
Darra
D
Murphy
Department of Radiology and Diagnostic Imaging, St. Paul's Hospital, Vancouver, BC, Canada.
Cameron
C
Hague
Department of Radiology and Diagnostic Imaging, St. Paul's Hospital, Vancouver, BC, Canada.
Jonathon
J
Leipsic
Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada.
Stephen
S
Lam
Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada.
Wan
W
Lam
Division of HIV/AIDS, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.|British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, Vancouver, BC, Canada.
Julio S
JS
Montaner
Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada.|Division of Respiratory Medicine, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
Don D
DD
Sin
Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada.|Division of Respiratory Medicine, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
S F Paul
SF
Man
D000328:Adult; D000368:Aged; D001419:Bacteria / Q000145:classification; D004847:Epithelial Cells / Q000166:cytology; D005260:Female; D015870:Gene Expression; D015658:HIV Infections / Q000150:complications* / Q000382:microbiology; D006801:Humans; D008168:Lung / Q000166:cytology / Q000382:microbiology*; D008297:Male; D046228:Microarray Analysis; D064307:Microbiota; D008875:Middle Aged; D029424:Pulmonary Disease, Chronic Obstructive / Q000276:immunology / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D014057:Tomography, X-Ray Computed
D012336:RNA, Ribosomal, 16S
Bacterial microbiome; Bronchial brushing; Gene expression; HIV; Lungs