Metagenomic analysis of fungal balls from chronic pulmonary aspergillosis patients to characterize microbial interactions and metabolic adaptations.

Fungal balls are a debilitating pulmonary complication, yet their functional biology as multi-kingdom ecosystems is poorly understood. Through a multi-omics analysis of 61 patient-derived fungal balls, we reveal their complex ecology. While Aspergillus fumigatus was the dominant fungus (57%), bacterial co-colonization was ubiquitous, with a community prevalence of Pseudomonas aeruginosa and Haemophilus influenzae. Metabolomics unveiled a structured division of labor: P. aeruginosa degraded host tissues, while H. influenzae contributed essential vitamins, indicating metabolic cross-feeding. The ecosystem is also defined by active warfare, including competition for iron assimilation, bacterial antifungal agents, and A. fumigatus secondary metabolites, such as fumigaclavine C and fumagillin, indicating bidirectional antagonism and impact on the host. Host transcriptomics revealed a potent but dysregulated human immune response, characterized by neutrophil activation and failed resolution. Our findings redefine the fungal ball as a resilient, cross-kingdom battlefield where synergistic and antagonistic interactions drive pathogenesis and persistence.