Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Author(s)
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Detail(s)
Original language | English |
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Article number | bbae620 |
Journal / Publication | Briefings in Bioinformatics |
Volume | 26 |
Issue number | 1 |
Online published | 24 Nov 2024 |
Publication status | Published - Jan 2025 |
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DOI | DOI |
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Publisher's Copyright Statement
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Link to Scopus | https://www.scopus.com/record/display.uri?eid=2-s2.0-85210549464&origin=recordpage |
Permanent Link | https://scholars.cityu.edu.hk/en/publications/publication(3db1972a-3ca2-4743-b45a-26032c2371c9).html |
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. © The Author(s) 2024. Published by Oxford University Press.
Research Area(s)
- human respiratory genome catalogue, metagenomic assembly, microbial etiology, respiratory microbiome
Citation Format(s)
Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome. / Li, Yinhu; Pan, Guangze; Wang, Shuai et al.
In: Briefings in Bioinformatics, Vol. 26, No. 1, bbae620, 01.2025.
In: Briefings in Bioinformatics, Vol. 26, No. 1, bbae620, 01.2025.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review