Shotgun metagenomic data from bronchoalveolar lavage fluid (BALF) samples of infants with CF

Cystic fibrosis (CF) is a genetic disease characterized by persistent infection and inflammation that drive irreversible lung damage. Airway microbial diversity is higher in children with CF, evolving into pathogen-dominated communities as individuals age and lung function declines. Understanding the microbiome associated with infections is crucial due to their significant impact on population dynamics and antibiotic resistance. However, low biomass of clinical samples, particularly from the lower airways, precludes capture of microbes genomes in the lungs of infants with CF.