{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T08:02:55Z","timestamp":1776326575991,"version":"3.50.1"},"reference-count":96,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,4,27]],"date-time":"2023-04-27T00:00:00Z","timestamp":1682553600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFA0712403"],"award-info":[{"award-number":["2020YFA0712403"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["T2225015"],"award-info":[{"award-number":["T2225015"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61932008"],"award-info":[{"award-number":["61932008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2018SHZDZX01"],"award-info":[{"award-number":["2018SHZDZX01"]}]},{"name":"Greater Bay Area Institute of Precision Medicine","award":["IPM21C008"],"award-info":[{"award-number":["IPM21C008"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe\u2013phenotype associations. However, multiple sequencing platforms and computational tools for this purpose may confuse researchers and thus call for extensive evaluation. Here, we systematically evaluated a total of 40 combinations of popular computational tools and sequencing platforms (i.e. strategies), involving eight assemblers, eight metagenomic binners and four sequencing technologies, including short-, long-read and metaHiC sequencing. We identified the best tools for the individual tasks (e.g. the assembly and binning) and combinations (e.g. generating more HQ-MAGs) depending on the availability of the sequencing data. We found that the combination of the hybrid assemblies and metaHiC-based binning performed best, followed by the hybrid and long-read assemblies. More importantly, both long-read and metaHiC sequencings link more mobile elements and antibiotic resistance genes to bacterial hosts and improve the quality of public human gut reference genomes with 32% (34\/105) HQ-MAGs that were either of better quality than those in the Unified Human Gastrointestinal Genome catalog version 2 or novel.<\/jats:p>","DOI":"10.1093\/bib\/bbad162","type":"journal-article","created":{"date-parts":[[2023,4,28]],"date-time":"2023-04-28T10:16:30Z","timestamp":1682676990000},"source":"Crossref","is-referenced-by-count":12,"title":["A survey on computational strategies for genome-resolved gut metagenomics"],"prefix":"10.1093","volume":"24","author":[{"given":"Longhao","family":"Jia","sequence":"first","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China"}]},{"given":"Yingjian","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China"}]},{"given":"Yanqi","family":"Dong","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China"}]},{"given":"Jingchao","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China"}]},{"given":"Wei-Hua","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei, China"},{"name":"Institution of Medical Artificial Intelligence, Binzhou Medical University , Yantai 264003, China"}]},{"given":"Xing-Ming","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China"},{"name":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Ministry of Education , Shanghai 200433, China"},{"name":"MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433, China"},{"name":"State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University , Shanghai, China"}]}],"member":"286","published-online":{"date-parts":[[2023,4,27]]},"reference":[{"key":"2023052022331194400_ref1","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1016\/j.chom.2015.04.004","article-title":"Dynamics and stabilization of the human gut microbiome during the first year of life","volume":"17","author":"Backhed","year":"2015","journal-title":"Cell Host Microbe"},{"key":"2023052022331194400_ref2","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-018-0617-x","article-title":"Temporal development of the gut microbiome in early childhood from the TEDDY study","volume":"562","author":"Stewart","year":"2018","journal-title":"Nature"},{"key":"2023052022331194400_ref3","doi-asserted-by":"crossref","first-page":"1766","DOI":"10.1038\/s41591-020-1095-x","article-title":"Maturation of the gut microbiome during the first year of 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