title: Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities.
abstract: BACKGROUND
  Samples collected from CF patient airways often contain large amounts of host-derived nucleic acids that interfere with recovery and purification of microbial and viral nucleic acids. This study describes metagenomic and metatranscriptomic methods that address these issues.
  
  
  METHODS
  Microbial and viral metagenomes, and microbial metatranscriptomes, were successfully prepared from sputum samples from five adult CF patients.
  
  
  RESULTS
  Contaminating host DNA was dramatically reduced in the metagenomes. Each CF patient presented a unique microbiome; in some Pseudomonas aeruginosa was replaced by other opportunistic bacteria. Even though the taxonomic composition of the microbiomes is very different, the metabolic potentials encoded by the community are very similar. The viral communities were dominated by phages that infect major CF pathogens. The metatranscriptomes reveal differential expression of encoded metabolic potential with changing health status.
  
  
  CONCLUSIONS
  Microbial and viral metagenomics combined with microbial transcriptomics characterize the dynamic polymicrobial communities found in CF airways, revealing both the taxa present and their current metabolic activities. These approaches can facilitate the development of individualized treatment plans and novel therapeutic approaches.
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, 92182, USA. Electronic address: ylim@rohan.sdsu.edu.
authors.forename: Yan Wei
authors.initials: YW
authors.lastname: Lim
authors.affiliation: Computational Science Research Center, San Diego State University, San Diego, CA, 92182, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Schmieder
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, 92182, USA; DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Haynes
authors.affiliation: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia.
authors.forename: Dana
authors.initials: D
authors.lastname: Willner
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
authors.forename: Mike
authors.initials: M
authors.lastname: Furlan
authors.affiliation: Rainbow Rock, Ocean View, HI 96737, USA.
authors.forename: Merry
authors.initials: M
authors.lastname: Youle
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
authors.forename: Katelynn
authors.initials: K
authors.lastname: Abbott
authors.affiliation: Computational Science Research Center, San Diego State University, San Diego, CA, 92182, USA; Mathematics and Computer Science Division, Argonne National, Laboratory, Argonne, IL 60439, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Edwards
authors.affiliation: Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
authors.forename: Jose
authors.initials: J
authors.lastname: Evangelista
authors.affiliation: Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
authors.forename: Douglas
authors.initials: D
authors.lastname: Conrad
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D000328:Adult; D001424:Bacterial Infections / Q000235:genetics / Q000382:microbiology*; D058448:Biota; D003550:Cystic Fibrosis / Q000235:genetics / Q000382:microbiology* / Q000821:virology*; D006801:Humans; D008168:Lung / Q000382:microbiology*; D053858:Metabolic Networks and Pathways / Q000502:physiology*; D054892:Metagenome; D013183:Sputum / Q000382:microbiology; D059467:Transcriptome; D014777:Virus Diseases / Q000235:genetics / Q000821:virology*