title: The cystic fibrosis lower airways microbial metagenome.
abstract: Chronic airway infections determine most morbidity in people with cystic fibrosis (CF). Herein, we present unbiased quantitative data about the frequency and abundance of DNA viruses, archaea, bacteria, moulds and fungi in CF lower airways. Induced sputa were collected on several occasions from children, adolescents and adults with CF. Deep sputum metagenome sequencing identified, on average, approximately 10 DNA viruses or fungi and several hundred bacterial taxa. The metagenome of a CF patient was typically found to be made up of an individual signature of multiple, lowly abundant species superimposed by few disease-associated pathogens, such asPseudomonas aeruginosaandStaphylococcus aureus, as major components. The host-associated signatures ranged from inconspicuous polymicrobial communities in healthy subjects to low-complexity microbiomes dominated by the typical CF pathogens in patients with advanced lung disease. The DNA virus community in CF lungs mainly consisted of phages and occasionally of human pathogens, such as adeno- and herpesviruses. TheS. aureusandP. aeruginosapopulations were composed of one major and numerous minor clone types. The rare clones constitute a low copy genetic resource that could rapidly expand as a response to habitat alterations, such as antimicrobial chemotherapy or invasion of novel microbes.
authors.affiliation: Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
authors.forename: Patricia
authors.initials: P
authors.lastname: Moran Losada
authors.affiliation: Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
authors.forename: Philippe
authors.initials: P
authors.lastname: Chouvarine
authors.affiliation: Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
authors.forename: Marie
authors.initials: M
authors.lastname: Dorda
authors.affiliation: Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
authors.forename: Silke
authors.initials: S
authors.lastname: Hedtfeld
authors.affiliation: Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany.
authors.forename: Samira
authors.initials: S
authors.lastname: Mielke
authors.affiliation: Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research, Hannover, Germany.
authors.forename: Angela
authors.initials: A
authors.lastname: Schulz
authors.affiliation: Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research, Hannover, Germany.
authors.forename: Lutz
authors.initials: L
authors.lastname: Wiehlmann
authors.affiliation: Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research, Hannover, Germany.
authors.forename: Burkhard
authors.initials: B
authors.lastname: Tümmler