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

Lim, Yan Wei, Schmieder, Robert, Haynes, Matthew, Willner, Dana, Furlan, Mike, Youle, Merry, Abbott, Katelynn, Edwards, Robert, Evangelista, Jose, Conrad, Douglas and Rohwer, Forest (2013) Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. Journal of Cystic Fibrosis, 12 2: 154-164. doi:10.1016/j.jcf.2012.07.009


Author Lim, Yan Wei
Schmieder, Robert
Haynes, Matthew
Willner, Dana
Furlan, Mike
Youle, Merry
Abbott, Katelynn
Edwards, Robert
Evangelista, Jose
Conrad, Douglas
Rohwer, Forest
Title Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities
Journal name Journal of Cystic Fibrosis   Check publisher's open access policy
ISSN 1569-1993
1873-5010
Publication date 2013-03-01
Year available 2012
Sub-type Article (original research)
DOI 10.1016/j.jcf.2012.07.009
Volume 12
Issue 2
Start page 154
End page 164
Total pages 11
Place of publication Amsterdam, Netherlands
Publisher Elsevier
Collection year 2013
Language eng
Formatted 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.
Keyword Cystic fibrosis
Viruses
Microbes
Metagenomics
Metatranscriptomics
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Available online: 28 August 2012.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2013 Collection
School of Chemistry and Molecular Biosciences
 
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