The airway fungal microbiome in asthma.

Background: Fungal involvement in asthma is associated with severe disease. The full spectrum of fungal species in asthma is not well described and is derived largely from insensitive culture techniques. Objectives: To use high-throughput sequencing to describe the airway mycobiome in asthmatics with and without fungal-sensitisation and healthy controls; to compare samples representing different airway compartments; to determine if the mycobiome was influenced by the fungal composition of outdoor air, and to compare findings with clinically relevant outcomes.Methods: We amplified the internal transcribed spacer region 2 of the nuclear ribosomal operon to identify the fungal species present. Ninety-seven subjects were recruited (83 asthmatics; 14 healthy subjects), with 29 undergoing a bronchoscopy. Airway samples were compared with matched environmental and mouthwash samples. Results: Two hundred and six taxa at the species level were identified in sputum, most at low abundance. Aspergillus fumigatus, Candida albicans and Mycosphaerella tassiana were the most abundant and prevalent species across all subjects. The airway mycobiome consisted of a network of overlapping, but distinct communities with a distinct profile in the epithelial compartment where Aspergillus tubingensis and Cryptococcus pseudolongus were more prevalent in asthma than health and significantly associated with sputum neutrophilia.Conclusions: The airway mycobiome was dominated by a relatively small number of species but was distinct from the oropharyngeal mycobiome and air samples. A. tubingensis and C. pseudolongus may play unexpected roles in the pathogenesis of asthma.