ArticlePloS one2014
Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 2 syntheses or guidelines pooled it, 46 citations in OpenAlex.
- The under reporting of recruitment strategies in research with children with life-threatening illnesses: A systematic review.Palliative medicine · 2017Pooled it
- Systematic review of mutations in pyrazinamidase associated with pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates.Antimicrobial agents and chemotherapy · 2015Pooled it
- Assessing anaerobe detection in routine sputum analyses from cystic fibrosis patients.Scientific reports · 2026Article
- Whole genome sequencing of the pulmonary microbiome in interstitial lung disease subtypes.Respiratory research · 2025Article
- Emerging liver infection ofAnnals of medicine and surgery (2012) · 2024Article
- Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.International journal of molecular sciences · 2024Article
- Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome.Microbiology spectrum · 2022Article
- Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives.Genes · 2021Review
- Article
- Review
- Detection of Bacteriophage Particles Containing Antibiotic Resistance Genes in the Sputum of Cystic Fibrosis Patients.Frontiers in microbiology · 2018Article
- Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2017Review
- Comparison of sputum microbiome of legionellosis-associated patients and other pneumonia patients: indications for polybacterial infections.Scientific reports · 2017Article
- A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer.PloS one · 2017Article
- Cystic Fibrosis Mice Develop Spontaneous ChronicJournal of infectious pulmonary diseases · 2017Article
- Article
- The Role of Short-Chain Fatty Acids, Produced by Anaerobic Bacteria, in the Cystic Fibrosis Airway.American journal of respiratory and critical care medicine · 2015Article
- Identification of low abundance microbiome in clinical samples using whole genome sequencing.Genome biology · 2015Article
- CoMeta: classification of metagenomes using k-mers.PloS one · 2015Article
- Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa.Genome biology and evolution · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Determination of the precise composition and variation of microbiota in cystic fibrosis lungs is crucial since chronic inflammation due to microorganisms leads to lung damage and ultimately, death. However, this constitutes a major technical challenge. Culturing of microorganisms does not provide a complete representation of a microbiota, even when using culturomics (high-throughput culture). So far, only PCR-based metagenomics have been investigated. However, these methods are biased towards certain microbial groups, and suffer from uncertain quantification of the different microbial domains. We have explored whole genome sequencing (WGS) using the Illumina high-throughput technology applied directly to DNA extracted from sputa obtained from two cystic fibrosis patients. To detect all microorganism groups, we used four procedures for DNA extraction, each with a different lysis protocol. We avoided biases due to whole DNA amplification thanks to the high efficiency of current Illumina technology. Phylogenomic classification of the reads by three different methods produced similar results. Our results suggest that WGS provides, in a single analysis, a better qualitative and quantitative assessment of microbiota compositions than cultures and PCRs. WGS identified a high quantity of Haemophilus spp. (patient 1) or Staphylococcus spp. plus Streptococcus spp. (patient 2) together with low amounts of anaerobic (Veillonella, Prevotella, Fusobacterium) and aerobic bacteria (Gemella, Moraxella, Granulicatella). WGS suggested that fungal members represented very low proportions of the microbiota, which were detected by cultures and PCRs because of their selectivity. The future increase of reads' sizes and decrease in cost should ensure the usefulness of WGS for the characterisation of microbiota.
Indexed as
Identifiers
What OpenQuestion holds
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.