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Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. To achieve these goals, we performed manual curation on the meta-data and organized the datasets in a phenotype-centric manner. GMrepo v2 contains 353 projects and 71,642 runs\/samples, which are significantly increased from the previous version. Among these runs\/samples, 45,111 and 26,531 were obtained by 16S rRNA amplicon and whole-genome metagenomics sequencing, respectively. We also increased the number of phenotypes from 92 to 133. In addition, we introduced disease-marker identification and cross-project\/phenotype comparison. We first identified disease markers between two phenotypes (e.g.\u00a0health versus diseases) on a per-project basis for selected projects. We then compared the identified markers for each phenotype pair across datasets to facilitate the identification of consistent microbial markers across datasets. Finally, we provided a marker-centric view to allow users to check if a marker has different trends in different diseases. So far, GMrepo includes 592 marker taxa (350 species and 242 genera) for 47 phenotype pairs, identified from 83 selected projects. GMrepo v2 is freely available at: https:\/\/gmrepo.humangut.info.<\/jats:p>","DOI":"10.1093\/nar\/gkab1019","type":"journal-article","created":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T19:25:40Z","timestamp":1634153140000},"page":"D777-D784","source":"Crossref","is-referenced-by-count":162,"title":["GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison"],"prefix":"10.1093","volume":"50","author":[{"given":"Die","family":"Dai","sequence":"first","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, China"}]},{"given":"Jiaying","family":"Zhu","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, China"}]},{"given":"Chuqing","family":"Sun","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, China"}]},{"given":"Min","family":"Li","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, China"}]},{"given":"Jinxin","family":"Liu","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai\u00a0200433, China"}]},{"given":"Sicheng","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, China"}]},{"given":"Kang","family":"Ning","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, China"}]},{"given":"Li-jie","family":"He","sequence":"additional","affiliation":[{"name":"Department of Oncology, The People's Hospital of Liaoning Province, People's Hospital of China Medical University\u00a0110016Shenyang, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4531-3970","authenticated-orcid":false,"given":"Xing-Ming","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai\u00a0200433, China"},{"name":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China"},{"name":"Research Institute of Intelligent Complex System, Fudan University, Shanghai\u00a0200433, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5160-4398","authenticated-orcid":false,"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, China"},{"name":"Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai\u00a0264003, China"}]}],"member":"286","published-online":{"date-parts":[[2021,11,12]]},"reference":[{"key":"2022010507330844200_B1","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/s41579-020-0433-9","article-title":"Gut microbiota in human metabolic health and disease","volume":"19","author":"Fan","year":"2021","journal-title":"Nat. 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