**Background:** The human lung, once considered sterile, is now known to harbor a diverse microbiome including both bacteria and fungi. While bacterial lung microbiome research has advanced significantly, the fungal component (mycobiome) remains understudied due to technical challenges including limited fungal databases, difficulties in nucleic acid isolation from fungal cells, and primer selection biases. Fungi account for a significant proportion of airborne microorganisms, reaching 82% in some studies. Aspergillus spp., comprising hundreds of species, are particularly relevant due to their environmental ubiquity, resilience, and immune evasion strategies. The co-existence of Aspergillus with pulmonary diseases such as asthma, cystic fibrosis (CF), and chronic obstructive pulmonary disease (COPD) poses increased risk of worsened clinical outcomes, contributing to conditions like chronic pulmonary aspergillosis (CPA) and allergic bronchopulmonary aspergillosis (ABPA).
**Methods:** This is a narrative review synthesizing existing literature on the fungal and bacterial interface in the respiratory mycobiome. The review draws on studies employing culture-independent techniques including 16S rRNA gene sequencing for bacterial identification and targeted amplicon sequencing for fungal identification. Studies examining bacterial-fungal interactions in vitro, in animal models (murine aspergillosis models), and in clinical samples from patients with COPD, CF, and CPA are included. The review also incorporates literature on the gut-lung microbiome axis and its immunological implications.
**Key Results:** The review identifies that Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria dominate healthy lungs, with approximately 2000 bacterial genomes per cm². The lung mycobiome is predominantly composed of Basidiomycota and Ascomycota, with common species including Cladosporium, Eurotium, and Aspergillus. In COPD patients hospitalized for severe exacerbation, Aspergillus was identified from 17% of patients' sputum. More than 50% of cystic fibrosis patients have A. fumigatus colonization. The review details multiple mechanisms of bacterial-fungal interaction: Pseudomonas aeruginosa inhibits A. fumigatus through phenazine production (inducing ROS and NOS), pyoverdine-mediated iron competition, dirhamnolipid secretion, and alkylhydroxyquinolones that disrupt fungal biofilm integrity. Conversely, A. fumigatus counteracts P. aeruginosa through gliotoxin production, hydroxamate siderophore release for iron acquisition, and biotransformation of phenazine into beneficial forms. Cooperative interactions also exist, with P. aeruginosa volatile organic chemicals potentially encouraging fungal growth, and A. fumigatus potentially enhancing P. aeruginosa virulence through phenotypic and genetic changes. In a study of 119 patients with fungal and bacterial coinfection, Aspergillus was the most common fungi detected (43.8% in coinfection, 36.6% in fungal infection alone). The gut-lung axis is highlighted, with intestinal Candida albicans influencing pulmonary immune responses to A. fumigatus through prostaglandin E2 pathways and Th17 modulation. Antibiotic-induced gut dysbiosis in mice increased susceptibility to A. fumigatus allergic airway disease, characterized by increased eosinophils, mast cells, IL-5, IgE, and mucus production.
**Clinical Implications:** Understanding the fungal-bacterial interface has direct clinical relevance. In COPD, a 'high-risk' mycobiome dominated by Penicillium, Aspergillus, and Curvularia is associated with more exacerbations, greater symptoms, and higher two-year mortality compared to Saccharomyces-dominated mycobiomes. In CF, the complex interaction between P. aeruginosa and A. fumigatus affects disease prognosis, with co-colonization linked to worse outcomes than single-pathogen infection. The use of antibiotics against Pseudomonas spp. in CF patients was followed by reduced aspergillosis in sputum, emphasizing the clinical importance of bacterial-fungal interactions. For CPA diagnosis, metagenomic approaches and real-time multiplex PCR show high Aspergillus prevalence in at-risk populations, and HIV-positive patients are frequently misdiagnosed with pulmonary tuberculosis when they may actually have CPA. The review identifies pulmonary cavity and immunocompromised status as risk factors for fungal and bacterial co-infections. Challenges remain in standardizing lung microbiome detection methods, avoiding upper airway contamination, and improving fungal DNA extraction from biological samples. Future research should focus on comparing healthy and diseased lung models, optimizing sampling methods, and combining metagenomics with sequencing to better understand the respiratory microbiome's role in chronic lung disease pathogenesis.