The Cystic Fibrosis Upper and Lower Airway Metagenome

• DOI: 10.1128/spectrum.03633-22
• Publication Date: 2023-03-09T14:02:26Z
• Authors: Katarzyna Pienkowska; Marie-Madlen Pust; Margaux Gessner; Svenja Gaedcke; Ajith Thavarasa; Ilona Rosenboom; Patricia Morán Lo...; Rebecca Minso; Christin Arnold; Silke Hedtfeld; Marie Dorda; Lutz Wiehlmann; Jochen G. Mainz; Jens Klockgether; Burkhard Tümmler
• Keywords: Stenotrophomonas maltophilia; Stenotrophomonas

The microbial metagenome in cystic fibrosis (CF) airways was investigated by whole-genome shotgun sequencing of total DNA isolated from nasal lavage samples, oropharyngeal swabs, and induced sputum samples collected 65 individuals with CF aged 7 to 50 years. Each patient harbored a personalized unique load composition, the exception being monocultures most common pathogens Staphylococcus aureus Pseudomonas aeruginosa patients advanced lung disease. sampling upper uncovered fungus Malassezia restricta bacterium epidermidis as prominent species. Healthy donors qualitatively quantitatively different spectra commensal bacteria their sputa, even absence any typical pathogen. If P. aeruginosa, S. aureus, or Stenotrophomonas maltophilia belonged trio abundant species metagenome, inhabitants respiratory tract healthy subjects, i.e., Eubacterium sulci, Fusobacterium periodonticum, Neisseria subflava, were present only low numbers not detectable. Random forest analysis identified numerical ecological parameters bacterial community, such Shannon Simpson diversity, key that globally distinguish donors.