ArticlemBio2021
Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis.
Article in mBio, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 22 citations in OpenAlex.
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 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
- PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes.Bioinformatics advances · 2026Article
- Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.Mycopathologia · 2024Review
- Article
- Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis.Nature communications · 2024Observational
- Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.International journal of molecular sciences · 2024Article
- Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis.Research square · 2024Article
- Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies.Cell reports. Medicine · 2024Review
- From bench to bedside: an interdisciplinary journey through the gut-lung axis with insights into lung cancer and immunotherapy.Frontiers in immunology · 2024Review
- Airway environment drives the selection of quorum sensing mutants and promote Staphylococcus aureus chronic lifestyle.Nature communications · 2023Article
- Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome.Nature communications · 2023Article
- Article
- Exploring the Cystic Fibrosis Lung Microbiome: Making the Most of a Sticky Situation.Journal of the Pediatric Infectious Diseases Society · 2022Review
- Article
- Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives.Genes · 2021Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In cystic fibrosis, dynamic and complex communities of microbial pathogens and commensals can colonize the lung. Cultured isolates from lung sputum reveal high inter- and intraindividual variability in pathogen strains, sequence variants, and phenotypes; disease progression likely depends on the precise combination of infecting lineages. Routine clinical protocols, however, provide a limited overview of the colonizer populations. Therefore, a more comprehensive and precise identification and characterization of infecting lineages could assist in making corresponding decisions on treatment. Here, we describe longitudinal tracking for four cystic fibrosis patients who exhibited extreme clinical phenotypes and, thus, were selected from a pilot cohort of 11 patients with repeated sampling for more than a year. Following metagenomics sequencing of lung sputum, we find that the taxonomic identity of individual colonizer lineages can be easily established. Crucially, even superficially clonal pathogens can be subdivided into multiple sublineages at the sequence level. By tracking individual allelic differences over time, an assembly-free clustering approach allows us to reconstruct multiple lineage-specific genomes with clear structural differences. Our study showcases a culture-independent shotgun metagenomics approach for longitudinal tracking of sublineage pathogen dynamics, opening up the possibility of using such methods to assist in monitoring disease progression through providing high-resolution routine characterization of the cystic fibrosis lung microbiome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.