ArticleBriefings in bioinformatics2024
Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Establishment of anmSystems · 2026Article
- OAPGC: a high-quality oral and airway prokaryotic genome catalog for enhanced ecological resolution and disease inference.NPJ biofilms and microbiomes · 2026Article
- Gingipain proteases from the bacteriumProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.Research square · 2026Article
- MDPD reveals specific microbial signatures in human pulmonary diseases.Briefings in bioinformatics · 2026Article
- MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.Nucleic acids research · 2026Article
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9 authors.
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Abstract
The human respiratory microbiome plays a crucial role in respiratory health, but there is no comprehensive respiratory genome catalogue (RGC) for studying the microbiome. In this study, we collected whole-metagenome shotgun sequencing data from 4067 samples and sequenced long reads of 124 samples, yielding 9.08 and 0.42 Tbp of short- and long-read data, respectively. By submitting these data with a novel assembly algorithm, we obtained a comprehensive human RGC. This high-quality RGC contains 190,443 contigs over 1 kbps and an N50 length exceeding 13 kbps; it comprises 159 high-quality and 393 medium-quality genomes, including 117 previously uncharacterized respiratory bacteria. Moreover, the RGC contains 209 respiratory-specific species not captured by the unified human gastrointestinal genome. Using the RGC, we revisited a study on a pediatric pneumonia dataset and identified 17 pneumonia-specific respiratory pathogens, reversing an inaccurate etiological conclusion due to the previous incomplete reference. Furthermore, we applied the RGC to the data of 62 participants with a clinical diagnosis of infection. Compared to the Nucleotide database, the RGC yielded greater specificity (0 versus 0.444, respectively) and sensitivity (0.852 versus 0.881, respectively), suggesting that the RGC provides superior sensitivity and specificity for the clinical diagnosis of respiratory diseases.
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