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Microbial communities infiltrate the respiratory tract of cystic fibrosis patients, where chronic colonization and infection lead to clinical decline. This report aims to provide an overview of the diversity of bacterial and fungal species from the airway secretion of three young CF patients with severe pulmonary disease. The bacterial and fungal microbiomes were investigated by culture isolation, metataxonomics, and metagenomics shotgun. Virulence factors and antibiotic resistance genes were also explored.  A. fumigatus  was isolated from cultures and identified in high incidence from patient sputum samples.  Candida albicans, Penicillium  sp.,  Hanseniaspora  sp.,  Torulaspora delbrueckii , and  Talaromyces amestolkiae  were isolated sporadically. Metataxonomics and metagenomics detected fungal reads ( Saccharomyces cerevisiae ,  A. fumigatus , and  Schizophyllum  sp.) in one sputum sample. The main pathogenic bacteria identified were  Staphylococcus aureus ,  Pseudomonas aeruginosa ,  Burkholderia cepacia  complex, and  Achromobacter xylosoxidans . The canonical core CF microbiome is composed of species from the genera  Streptococcus, Neisseria, Rothia, Prevotella , and  Haemophilus . Thus, the airways of the three young CF patients presented dominant bacterial genera and interindividual variability in microbial community composition and diversity. Additionally, a wide diversity of virulence factors and antibiotic resistance genes were identified in the CF lung microbiomes, which may be linked to the clinical condition of the CF patients. Understanding the microbial community is crucial to improve therapy because it may have the opposite effect, restructuring the pathogenic microbiota. Future studies focusing on the influence of fungi on bacterial diversity and microbial interactions in CF microbiomes will be welcome to fulfill this huge gap of fungal influence on CF physiopathology.

The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi