The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients

Although the taxonomical composition of the cystic fibrosis (CF) lung microbiome has been largely inspected, little is still known about the overall gene content and functional profiles of the resident microbiome. To understand the dynamics of the lung microbiome in relation with patient9s disease status, a large cohort of CF subjects with moderate-severe lung disease was followed over a 15-month period. Longitudinal assessment of sputum microbiome by shotgun metagenomics revealed a patient-specific colonization of the primary and emerging CF pathogens. Even if patient genotype and exacerbation events impacted the microbiome diversity, CF microbiota rebounds to pre-treatment state. A core set of antibiotic resistance genes was found although their presence was not affected by antibiotic intake. The microbial resilience and persistence of antibiotic resistant genes support the growing consensus that the management of chronic CF infection may be improved by a more patient-specific personalization of clinical care and treatment.