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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\u00a0kbps and an N50 length exceeding 13\u00a0kbps; 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.<\/jats:p>","DOI":"10.1093\/bib\/bbae620","type":"journal-article","created":{"date-parts":[[2024,11,14]],"date-time":"2024-11-14T12:48:18Z","timestamp":1731588498000},"source":"Crossref","is-referenced-by-count":4,"title":["Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6378-6571","authenticated-orcid":false,"given":"Yinhu","family":"Li","sequence":"first","affiliation":[{"name":"Institutes for Systems Genetics , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, , No. 2222 Xinchuan Road, Gaoxin District, Chengdu 610212 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1068 Xueyuan Avenue, Nanshan District, Shenzhen 518055 ,","place":["China"]},{"name":"The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen\u2013Hong Kong Institute of Brain Science\u2013Shenzhen Fundamental Research Institutions , Shenzhen Key Laboratory of Translational Research for Brain Diseases, , No. 1068 Xueyuan Avenue, Nanshan District, Shenzhen 518055 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6246-6349","authenticated-orcid":false,"given":"Shuai Cheng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , 83 Tat Chee Avenue, Kowloon Tong, Hong Kong 999077 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