ArticleGenome biology2014
Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
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Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives.Drugs · 2021Pooled it
- Blood mNGS: an effective non-invasive diagnostic tool for Pneumocystis jirovecii pneumonia.BMC microbiology · 2026Article
- The diagnostic and prognostic utility of blood metagenomic next-generation sequencing for invasive pulmonary aspergillosis.Microbiology spectrum · 2026Article
- From Sampling to Identification of Arbuscular Mycorrhizal Fungi Through Next Generation Sequencing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing.bioRxiv : the preprint server for biology · 2025Article
- Clinical Value of Metagenomic Next-Generation Sequencing From Blood Samples to IdentifyOpen forum infectious diseases · 2025Article
- Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis ofFrontiers in cellular and infection microbiology · 2025Article
- Affinity of Malassezia and Other Yeasts for Pulmonary Lipids.Mycopathologia · 2024Article
- The clinical application of metagenomic next-generation sequencing in immunocompromised patients with severe respiratory infections in the ICU.Respiratory research · 2024Article
- Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs.BMC medical genomics · 2024Article
- Metagenomic next-generation sequencing for the diagnosis of invasive pulmonary aspergillosis in type 2 diabetes mellitus patients.Scientific reports · 2024Article
- The Metabolic Potential of the Human Lung Microbiome.Microorganisms · 2024Article
- Alterations of lung microbiota in lung transplant recipients with pneumocystis jirovecii pneumonia.Respiratory research · 2024Observational
- Clinical application of bronchoalveolar lavage fluid metagenomics next-generation sequencing in cancer patients with severe pneumonia.Respiratory research · 2024Article
- Methanogenic symbionts of anaerobic ciliates are host and habitat specific.The ISME journal · 2024Article
- DNA metabarcoding analysis of fungal community on surface of four root herbs.Chinese herbal medicines · 2024Article
- Diagnostic values of BALF metagenomic next-generation sequencing, BALF real-time PCR and serum BDG forFrontiers in microbiology · 2024Article
- Clinical performance of metagenomic next-generation sequencing for diagnosis of invasive fungal disease after hematopoietic cell transplant.Frontiers in cellular and infection microbiology · 2024Article
- Exploring the Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Unexplained Pulmonary Infection.International journal of general medicine · 2024Article
- Clinical performance of metagenomic next-generation sequencing for diagnosis of pulmonaryFrontiers in cellular and infection microbiology · 2024Article
30 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors.
Funding
Abstract
backgroundFungi are important pathogens but challenging to enumerate using next-generation sequencing because of low absolute abundance in many samples and high levels of fungal DNA from contaminating sources.
resultsHere, we analyze fungal lineages present in the human airway using an improved method for contamination filtering. We use DNA quantification data, which are routinely acquired during DNA library preparation, to annotate output sequence data, and improve the identification and filtering of contaminants. We compare fungal communities and bacterial communities from healthy subjects, HIV+ subjects, and lung transplant recipients, providing a gradient of increasing lung impairment for comparison. We use deep sequencing to characterize ribosomal rRNA gene segments from fungi and bacteria in DNA extracted from bronchiolar lavage samples and oropharyngeal wash. Comparison to clinical culture data documents improved detection after applying the filtering procedure.
conclusionsWe find increased representation of medically relevant organisms, including Candida, Cryptococcus, and Aspergillus, in subjects with increasingly severe pulmonary and immunologic deficits. We analyze covariation of fungal and bacterial taxa, and find that oropharyngeal communities rich in Candida are also rich in mitis group Streptococci,a community pattern associated with pathogenic polymicrobial biofilms. Thus, using this approach, it is possible to characterize fungal communities in the human respiratory tract more accurately and explore their interactions with bacterial communities in health and disease.
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