title: Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data.
abstract: The impaired mucociliary clearance in individuals with Cystic Fibrosis (CF) enables opportunistic pathogens to colonize CF lungs. Here we show that Rothia mucilaginosa is a common CF opportunist that was present in 83% of our patient cohort, almost as prevalent as Pseudomonas aeruginosa (89%). Sequencing of lung microbial metagenomes identified unique R. mucilaginosa strains in each patient, presumably due to evolution within the lung. The de novo assembly of a near-complete R. mucilaginosa (CF1E) genome illuminated a number of potential physiological adaptations to the CF lung, including antibiotic resistance, utilization of extracellular lactate, and modification of the type I restriction-modification system. Metabolic characteristics predicted from the metagenomes suggested R. mucilaginosa have adapted to live within the microaerophilic surface of the mucus layer in CF lungs. The results also highlight the remarkable evolutionary and ecological similarities of many CF pathogens; further examination of these similarities has the potential to guide patient care and treatment.
authors.affiliation: Department of Biology, San Diego State University, San Diego, California, USA. ylim@rohan.sdsu.edu
authors.forename: Yan Wei
authors.initials: YW
authors.lastname: Lim
authors.forename: Robert
authors.initials: R
authors.lastname: Schmieder
authors.forename: Matthew
authors.initials: M
authors.lastname: Haynes
authors.forename: Mike
authors.initials: M
authors.lastname: Furlan
authors.forename: T David
authors.initials: TD
authors.lastname: Matthews
authors.forename: Katrine
authors.initials: K
authors.lastname: Whiteson
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Poole
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Hayes
authors.forename: David A
authors.initials: DA
authors.lastname: Low
authors.forename: Heather
authors.initials: H
authors.lastname: Maughan
authors.forename: Robert
authors.initials: R
authors.lastname: Edwards
authors.forename: Douglas
authors.initials: D
authors.lastname: Conrad
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D003550:Cystic Fibrosis / Q000382:microbiology*; D006801:Humans; D008168:Lung / Q000382:microbiology*; D056186:Metagenomics; D008835:Micrococcaceae / Q000235:genetics* / Q000502:physiology*; D008954:Models, Biological; D058977:Molecular Sequence Annotation; D009876:Operon / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics
chemical_list: D012329:RNA, Bacterial; D012335:RNA, Ribosomal