The diversity of fungal species comprising the lung mycobiome is a reflection of exposure to environmental and endogenous filamentous fungi and yeasts. Most lung mycobiome studies have been culture-based. A few have utilized next generation sequencing (NGS). Despite the low number of published NGS studies, several themes emerge from the literature: (1) moulds and yeasts are present in the human respiratory tract, even during health; (2) the fungi present in the respiratory tract are highly variable between individuals; and (3) many diseases are accompanied by decreased diversity of fungi in the lungs. Even in patients with the same disease, different patients have been shown to harbor distinct fungal communities. Those fungal species present in any one individual may represent a patient’s unique environmental exposure(s), either to species restricted to the indoor environment, for example, Penicillium, or species found in the outdoor environment such as Aspergillus, wood and vegetation colonizing fungi and plant pathogens. In addition to causing clinical fungal infections, the lung mycobiome may have inflammatory effects that can cause or worsen lung disease. Most respiratory diseases that have been studied, have been associated with decreases in fungal diversity. However, none of these diversity studies distinguish between accidental, transient fungal colonizers and true residents of the respiratory tract.

Medical Mycology, Volume 57, Issue Supplement_2, April 2019, Pages S145–S154,