Respiratory and Gastrointestinal Mycobiome Profiles Identify Distinct Patient Clusters Associated with Asthma Control

The human microbiome contributes to asthma pathogenesis, yet most studies have focused on bacterial communities. This pilot study aimed to characterize fungal communities across multiple body sites in adults with asthma and evaluate whether integrated multisite mycobiome profiles are associated with asthma control.

We enrolled 24 adults with asthma evaluated at Mayo Clinic between 2020 and 2022. Oral wash, nasal swab, sputum, and stool samples were collected, and fungal communities were characterized using ITS2 sequencing. Multisite mycobiome data were integrated using an unsupervised clustering approach , with a two-cluster solution selected for exploratory clinical comparisons. Clusters were compared with respect to fungal composition, site-specific diversity metrics, and asthma control.

Two patient clusters with distinct multisite mycobiome profiles were identified. Cluster 1 demonstrated poorer asthma control, with lower Asthma Control Test scores than Cluster 2 (median [IQR], 15.0 [13.0-17.5] vs. 18.0 [17.0-19.0]; p = 0.040). Compared with Cluster 2, Cluster 1 exhibited a higher relative abundance of Cladosporium in nasal and sputum samples, and greater sputum fungal diversity (p = 0.016). In contrast, Cluster 2 exhibited a higher relative abundance of Candida in stool and sputum samples. No significant differences in fungal diversity were observed in oral, nasal, or stool samples.

Integrated multisite mycobiome profiling identified distinct fungal community patterns associated with asthma control, highlighting the need for larger, longitudinal studies to define their clinical relevance.