{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T17:56:25Z","timestamp":1784742985476,"version":"3.55.0"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2018,8,28]],"date-time":"2018-08-28T00:00:00Z","timestamp":1535414400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31700427"],"award-info":[{"award-number":["31700427"]}],"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":["41606154"],"award-info":[{"award-number":["41606154"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["LQ17D060002"],"award-info":[{"award-number":["LQ17D060002"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Qilu Young Scholarship of Shandong University"},{"DOI":"10.13039\/501100011491","name":"Bureau of Science and Technology of Zhoushan","doi-asserted-by":"publisher","award":["2017C82218"],"award-info":[{"award-number":["2017C82218"]}],"id":[{"id":"10.13039\/501100011491","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Open Funding of State Key Laboratory of Applied Microbiology Southern China","award":["SKYAM002-2016"],"award-info":[{"award-number":["SKYAM002-2016"]}]},{"name":"Open Project of Key Laboratory of Environmental Biotechnology, CAS","award":["kf2016002"],"award-info":[{"award-number":["kf2016002"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>The nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups and low coverage of N cycle genes and\/or gene (sub)families.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>To solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84 759 and 219 146 representative sequences at 95 and 100% identity cutoffs, respectively. We also identified 1958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to \u2018small database\u2019 issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analysis showed that the structure and composition of N cycle gene families were most strongly correlated with latitude and temperature. NCycDB is expected to facilitate N cycle studies via shotgun metagenome sequencing approaches in various environments. The framework developed in this study can be served as a good reference to build similar knowledge-based functional gene databases in various processes and pathways.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>NCycDB database files are available at https:\/\/github.com\/qichao1984\/NCyc.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty741","type":"journal-article","created":{"date-parts":[[2018,8,23]],"date-time":"2018-08-23T07:26:53Z","timestamp":1535009213000},"page":"1040-1048","source":"Crossref","is-referenced-by-count":443,"title":["NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3245-7545","authenticated-orcid":false,"given":"Qichao","family":"Tu","sequence":"first","affiliation":[{"name":"Institute of Marine Science and Technology, Shandong University, Qingdao, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Lin","sequence":"additional","affiliation":[{"name":"Institute of Marine Science and Technology, Shandong University, Qingdao, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Ecology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ye","family":"Deng","sequence":"additional","affiliation":[{"name":"Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, China"},{"name":"College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhili","family":"He","sequence":"additional","affiliation":[{"name":"Department of Environmental Science, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, Guangdong, China"},{"name":"Department of Agriculture, College of Agriculture, Hunan Agricultural University, Changsha, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,8,28]]},"reference":[{"key":"2023013107262026700_bty741-B1","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1890\/03-9000","article-title":"Toward a metabolic theory of ecology","volume":"85","author":"Brown","year":"2004","journal-title":"Ecology"},{"key":"2023013107262026700_bty741-B2","doi-asserted-by":"crossref","first-page":"595.","DOI":"10.1038\/msb.2012.28","article-title":"Global biogeography of SAR11 marine bacteria","volume":"8","author":"Brown","year":"2012","journal-title":"Mol. 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