ArticleJournal of cystic fibrosis : official journal of the European Cystic Fibrosis Society2013
Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities.
Article in Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
What it found
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Who cites it
101 citing papers in PubMed.
- A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease.International journal of molecular sciences · 2017Trial
- Bridging bench and bedside: translational omics ofEuropean respiratory review : an official journal of the European Respiratory Society · 2026Review
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- An ode to the 16S rRNA gene: its history, importance, caveats and future in microbiome research.Microbial genomics · 2026Review
- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.medRxiv : the preprint server for health sciences · 2026Article
- The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.European respiratory review : an official journal of the European Respiratory Society · 2025Review
- The Lung Microbiome and Its Impact on Obstructive Sleep Apnea: A Diagnostic Frontier.Diagnostics (Basel, Switzerland) · 2025Review
- Relationship between pediatric asthma and respiratory microbiota, intestinal microbiota: a narrative review.Frontiers in microbiology · 2025Review
- Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.Communications biology · 2024Article
- Integrated multi-omics identifies pathways governing interspecies interaction between A. fumigatus and K. pneumoniae.Communications biology · 2024Article
- Article
- Genome-scale model ofMicrobiology spectrum · 2024Article
- The Impact of Antimicrobial Resistance in Cystic Fibrosis.Journal of clinical medicine · 2024Review
- Lung microbiome: new insights into the pathogenesis of respiratory diseases.Signal transduction and targeted therapy · 2024Review
- Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.Nature microbiology · 2022Article
- Dynamic impact of virome on colitis and colorectal cancer: Immunity, inflammation, prevention and treatment.Seminars in cancer biology · 2022Review
- A restructuring of microbiome niche space is associated with Elexacaftor-Tezacaftor-Ivacaftor therapy in the cystic fibrosis lung.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2022Article
- Article
- Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome.Microbiology spectrum · 2022Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
backgroundSamples 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.
methodsMicrobial and viral metagenomes, and microbial metatranscriptomes, were successfully prepared from sputum samples from five adult CF patients.
resultsContaminating 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.
conclusionsMicrobial 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.
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