Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities

Yan Wei Lim, Robert Schmieder, Matthew Haynes, Dana Willner, Mike Furlan, Merry Youle, Katelynn Abbott, Robert Edwards, Jose Evangelista, Douglas Conrad, Forest Rohwer

Research output: Contribution to journalArticlepeer-review

96 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)154-164
Number of pages11
JournalJournal of Cystic Fibrosis
Volume12
Issue number2
DOIs
Publication statusPublished - Mar 2013
Externally publishedYes

Keywords

  • Cystic fibrosis
  • Metagenomics
  • Metatranscriptomics
  • Microbes
  • Viruses

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