Introduction: The respiratory tract is constantly exposed to various environmental and endogenous microbes; however, unlike other similar mucosal surfaces, there has been limited investigation of the microbiome of the respiratory tract.
Areas covered: In this review, we summarize the current state of knowledge of the bacterial, fungal, and viral respiratory microbiomes during HIV infection and how the microbiome might relate to HIV-associated lung disease. Expert commentary: HIV infection is associated with alterations in the respiratory microbiome. The clinical implications of lung microbial dysbiosis are however currently unknown. Mechanistic studies are needed to establish causality between shifts in the respiratory microbiome and pulmonary complications in HIV-infected individuals.
Keywords: HIV infection; bronchoalveolar lavage; lung microbiome; mycobiome; pulmonary disease; virome.