Comparative airway microbial metagenomics in health and chronic lung disease. metagenomisc_lung

To provide quantitative information about the composition of viral, bacterial and fungal communities in human airways in health and chronic lung disease, whole genome shotgun metagenome sequencing was performed of nasal lavage, throat swabs and sputum collected from healthy subjects, preschool wheezers and patients with inherited immunodeficiency (ID), cystic fibrosis (CF) or chronic pulmonary obstructive disease (COPD). Airway virome and mycobiome were dominated by phages, Candida and Aspergillus species, with Aspergillus fumigatus being the most prevelant fungus in health and disease. Only some wheezers carried a high load of herpes viruses in their respiratory tract. Healthy lungs were characterized by a diverse, but rather uniform repertoire of hundreds of species, mainly Actinobacteria, Firmicutes and Bacteroidetes. A similar, but less diverse spectrum of bacteria was found in COPD lungs irrespectively of whether the sample had been collected from a patient with mild or advanced disease. CF and ID airways showed the largest patient-to-patient variation ranging from highly diverse communities like in healthy airways to monocultures dominated by proteobacterial pathogens. The repertoire of Streptococcus species differed between COPD, CF and ID airways. Preschool wheezers carried a low-diversity airway microbiome of Actinobacteria, mainly Rothia mucilaginosa. Alpha-diversity was lower (Pcorr < 0.0001) and beta-diversity was higher (Pcorr < 0.0001) in all examined disease habitats indicating that dysbiosis in human chronic lung disease is characterized by depletion and individualization of the microbiome.