{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T17:59:55Z","timestamp":1791568795340,"version":"4.3.4"},"reference-count":97,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T00:00:00Z","timestamp":1762560000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32470699"],"award-info":[{"award-number":["32470699"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004374","name":"Chongqing Medical University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004374","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http:\/\/www.inbirg.com\/hlrmdb\/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed &amp;gt;98 Gb of contigs and yielded 18\u2009721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.<\/jats:p>","DOI":"10.1093\/nar\/gkaf1152","type":"journal-article","created":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T23:26:33Z","timestamp":1762730793000},"page":"D763-D775","source":"Crossref","is-referenced-by-count":3,"title":["HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2983-6149","authenticated-orcid":false,"given":"Zhaoyu","family":"Zhai","sequence":"first","affiliation":[{"name":"Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), College of Pharmacy, and Precision Medicine Center, the Second Affiliated Hospital, and Reproductive Medicine Center, the First Affiliated Hospital, Chongqing Medical University , Chongqing 400016 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohui","family":"Che","sequence":"additional","affiliation":[{"name":"Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), College of Pharmacy, and Precision Medicine Center, the Second Affiliated Hospital, and Reproductive Medicine Center, the First Affiliated Hospital, Chongqing Medical University , Chongqing 400016 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, the Second Affiliated Hospital, Chongqing Medical University , Chongqing 400010 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zishun","family":"Zhang","sequence":"additional","affiliation":[{"name":"Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), College of Pharmacy, and Precision Medicine Center, the Second Affiliated Hospital, and Reproductive Medicine Center, the First Affiliated Hospital, Chongqing Medical University , Chongqing 400016 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yapeng","family":"Li","sequence":"additional","affiliation":[{"name":"Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), College of Pharmacy, and Precision Medicine Center, the Second Affiliated Hospital, and Reproductive Medicine Center, the First Affiliated Hospital, Chongqing Medical University , Chongqing 400016 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6014-8160","authenticated-orcid":false,"given":"Jianbo","family":"Pan","sequence":"additional","affiliation":[{"name":"Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), College of Pharmacy, and Precision Medicine Center, the Second Affiliated Hospital, and Reproductive Medicine Center, the First Affiliated Hospital, Chongqing Medical University , Chongqing 400016 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,11,8]]},"reference":[{"key":"2026012005361205300_B1","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1038\/s41392-022-00974-4","article-title":"Microbiota in health and diseases","volume":"7","author":"Hou","year":"2022","journal-title":"Sig Transduct Target 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