UBC Faculty Research and Publications

Decreased microbiome diversity in the HIV small airway epithelium Xu, Stella; Tsai, Amy; Sze, Marc A; Vucic, Emily A; Shaipanich, Tawimas; Harris, Marianne; Guillemi, Silvia; Yang, Julia; Sinha, Sunita; Nislow, Corey; Montaner, Julio; Lam, Wan; Lam, Stephen; Sin, Don D; Paul Man, S. F; Leung, Janice M

Abstract

Background: Persons living with human immunodeficiency virus (PLWH) face an increased burden of chronic obstructive pulmonary disease (COPD). Repeated pulmonary infections, antibiotic exposures, and immunosuppression may contribute to an altered small airway epithelium (SAE) microbiome. Methods: SAE cells were collected from 28 PLWH and 48 HIV- controls through bronchoscopic cytologic brushings. DNA extracted from SAE cells was subjected to 16S rRNA amplification and sequencing. Comparisons of alpha and beta diversity between HIV+ and HIV- groups were performed and key operational taxonomic units (OTUs) distinguishing the two groups were identified using the Boruta feature selection after Random Forest Analysis. Results: PLWH demonstrated significantly reduced Shannon diversity compared with HIV- volunteers (1.82 ± 0.10 vs. 2.20 ± 0.073, p = 0.0024). This was primarily driven by a reduction in bacterial richness (23.29 ± 2.75 for PLWH and 46.04 ± 3.716 for HIV-, p 

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