{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T02:50:16Z","timestamp":1789095016866,"version":"build-2803163510"},"reference-count":29,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2023,2,20]],"date-time":"2023-02-20T00:00:00Z","timestamp":1676851200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":["enviromicro-journals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Environmental Microbiology"],"published-print":{"date-parts":[[2023,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Resolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earth's biomes yet producing high\u2010quality genomes from assembled fragments has been an ever\u2010standing problem. While automated binning software and their combination produce prokaryotic bins in high throughput, their manual refinement has been slow, sometimes difficult or missing entirely facilitating error propagation in public databases. Here, we present uBin, a GUI\u2010based, standalone bin refiner that runs on all major operating platforms and was additionally designed for educational purposes. When applied to the public CAMI dataset, refinement of bins using GC content, coverage and taxonomy was able to improve 78.9% of bins by decreasing their contamination. We also applied the bin refiner as a standalone binner to public metagenomes from the International Space Station and demonstrate the recovery of near\u2010complete genomes, whose replication indices indicate the active proliferation of microbes in Earth's lower orbit. uBin is an easy to instal software for bin refinement, binning of simple metagenomes and communication of metagenomic results to other scientists and in classrooms. The software and its helper scripts are open source and available under\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/ProbstLab\/uBin\">https:\/\/github.com\/ProbstLab\/uBin<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1111\/1462-2920.16351","type":"journal-article","created":{"date-parts":[[2023,2,10]],"date-time":"2023-02-10T19:29:22Z","timestamp":1676057362000},"page":"1077-1083","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["<scp>uBin:<\/scp>\n                    A manual refining tool for genomes from metagenomes"],"prefix":"10.1111","volume":"25","author":[{"given":"Till L. V.","family":"Bornemann","sequence":"first","affiliation":[{"name":"Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg\u2010Essen  Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah P.","family":"Esser","sequence":"additional","affiliation":[{"name":"Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg\u2010Essen  Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom L.","family":"Stach","sequence":"additional","affiliation":[{"name":"Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg\u2010Essen  Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Burg","sequence":"additional","affiliation":[{"name":"Independent Researcher, Im Acker 59  Koblenz Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9392-6544","authenticated-orcid":false,"given":"Alexander J.","family":"Probst","sequence":"additional","affiliation":[{"name":"Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg\u2010Essen  Germany"},{"name":"Centre of Water and Environmental Research (ZWU) University of Duisburg\u2010Essen  Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,2,20]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2579"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3103"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-017-0366-6"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3893"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3704"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-015-0116-3"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.258640.119"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-8-r85"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1319"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00756"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-8-460"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiy152"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3711"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7359"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0422-6"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02393-0"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp077"},{"key":"e_1_2_7_20_1","volume-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2008"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00039-18"},{"key":"e_1_2_7_22_1","first-page":"10","article-title":"Composite metagenome\u2010assembled genomes reduce the quality of public genome repositories","author":"Shaiber A.","year":"2019","journal-title":"mBio"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0171-1"},{"key":"e_1_2_7_24_1","article-title":"Connecting structure to function with the recovery of over 1000 high\u2010quality activated sludge metagenome\u2010assembled genomes encoding full\u2010length rRNA genes using long\u2010read sequencing","volume":"12","author":"Singleton C.M.","year":"2020","journal-title":"Nature Communications"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2004.00624.x"},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0541-1"},{"key":"e_1_2_7_27_1","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bap021","article-title":"MicroScope: a platform for microbial genome annotation and comparative genomics","volume":"2009","author":"Vallenet D.","year":"2009","journal-title":"Database: The Journal of Biological Databases and Curation"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-98141-3"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1224041"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv638"}],"container-title":["Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1462-2920.16351","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/1462-2920.16351","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1462-2920.16351","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T00:54:57Z","timestamp":1761872097000},"score":1,"resource":{"primary":{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/10.1111\/1462-2920.16351"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,20]]},"references-count":29,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,6]]}},"alternative-id":["10.1111\/1462-2920.16351"],"URL":"https:\/\/doi.org\/10.1111\/1462-2920.16351","archive":["Portico"],"relation":{},"ISSN":["1462-2912","1462-2920"],"issn-type":[{"value":"1462-2912","type":"print"},{"value":"1462-2920","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,20]]},"assertion":[{"value":"2023-01-10","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-02-03","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-02-20","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}