{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T06:58:03Z","timestamp":1776063483842,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2022,6,17]],"date-time":"2022-06-17T00:00:00Z","timestamp":1655424000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"R&D project","award":["ANP 21005-4"],"award-info":[{"award-number":["ANP 21005-4"]}]},{"name":"PROBIO-DEEP\u2014Survey","award":["UFRJ\/Shell Brasil\/ANP"],"award-info":[{"award-number":["UFRJ\/Shell Brasil\/ANP"]}]},{"name":"Shell Brasil under the ANP R&D levy as \u2018Compromisso de Investimentos com Pesquisa e Desenvolvimento"},{"name":"Research Technology Services at UNSW Sydney"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Metagenome-assembled genomes (MAGs) have substantially extended our understanding of microbial functionality. However, 16S rRNA genes, which are commonly used in phylogenetic analysis and environmental surveys, are often missing from MAGs. Here, we developed MarkerMAG, a pipeline that links 16S rRNA genes to MAGs using paired-end sequencing reads.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Assessment of MarkerMAG on three benchmarking metagenomic datasets with various degrees of complexity shows substantial increases in the number of MAGs with 16S rRNA genes and a 100% assignment accuracy. MarkerMAG also estimates the copy number of 16S rRNA genes in MAGs with high accuracy. Assessments on three real metagenomic datasets demonstrate 1.1- to 14.2-fold increases in the number of MAGs with 16S rRNA genes. We also show that MarkerMAG-improved MAGs increase the accuracy of functional prediction from 16S rRNA gene amplicon data. MarkerMAG is helpful in connecting information in MAG databases with those in 16S rRNA databases and surveys and hence contributes to our increasing understanding of microbial diversity, function and phylogeny.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>MarkerMAG is implemented in Python3 and freely available at https:\/\/github.com\/songweizhi\/MarkerMAG.<\/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\/btac398","type":"journal-article","created":{"date-parts":[[2022,6,17]],"date-time":"2022-06-17T13:38:41Z","timestamp":1655473121000},"page":"3684-3688","source":"Crossref","is-referenced-by-count":27,"title":["MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads"],"prefix":"10.1093","volume":"38","author":[{"given":"Weizhi","family":"Song","sequence":"first","affiliation":[{"name":"Centre for Marine Science & Innovation, University of New South Wales , Sydney, NSW 2052, Australia"},{"name":"School of Biological, Earth and Environmental Sciences, University of New South Wales , Sydney, NSW 2052, Australia"}]},{"given":"Shan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Centre for Marine Science & Innovation, University of New South Wales , Sydney, NSW 2052, Australia"},{"name":"School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9557-3001","authenticated-orcid":false,"given":"Torsten","family":"Thomas","sequence":"additional","affiliation":[{"name":"Centre for Marine Science & Innovation, University of New South Wales , Sydney, NSW 2052, Australia"},{"name":"School of Biological, Earth and Environmental Sciences, University of New South Wales , Sydney, NSW 2052, Australia"}]}],"member":"286","published-online":{"date-parts":[[2022,6,17]]},"reference":[{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/nbt.2579","article-title":"Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes","volume":"31","author":"Albertsen","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. Biotechnol"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1038\/nature14486","article-title":"Unusual biology across a group comprising more than 15% of domain bacteria","volume":"523","author":"Brown","year":"2015","journal-title":"Nature"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1007\/978-1-4939-8728-3_11","volume-title":"Microbiome Analysis.","author":"Douglas","year":"2018"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","DOI":"10.1128\/MRA.00333-20","article-title":"Metagenome assembly and metagenome-assembled genome sequences from a historical oil field located in Wietze, Germany","volume":"9","author":"Eze","year":"2020","journal-title":"Microbiol. Resour. Announc"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"e129","DOI":"10.1093\/nar\/gkt371","article-title":"Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads\u2014a baiting and iterative mapping approach","volume":"41","author":"Hahn","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"e1165","DOI":"10.7717\/peerj.1165","article-title":"MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities","volume":"3","author":"Kang","year":"2015","journal-title":"PeerJ"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"24175","DOI":"10.1038\/srep24175","article-title":"Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes","volume":"6","author":"Lin","year":"2016","journal-title":"Sci. Rep"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2011-12-5-r44","article-title":"EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data","volume":"12","author":"Miller","year":"2011","journal-title":"Genome Biol"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"Parks","year":"2017","journal-title":"Nat. Microbiol"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/bioinformatics\/btx644","article-title":"MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes","volume":"34","author":"Pericard","year":"2018","journal-title":"Bioinformatics"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-016-0154-5","article-title":"Recovering complete and draft population genomes from metagenome datasets","volume":"4","author":"Sangwan","year":"2016","journal-title":"Microbiome"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1038\/nmeth.4458","article-title":"Critical Assessment of Metagenome Interpretation\u2014a benchmark of metagenomics software","volume":"14","author":"Sczyrba","year":"2017","journal-title":"Nat. Methods"},{"key":"2023041405353967100_","author":"Seemann","year":"2013"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/sdata.2016.81","article-title":"Next generation sequencing data of a defined microbial mock community","volume":"3","author":"Singer","year":"2016","journal-title":"Sci. Data"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.1093\/bioinformatics\/btx086","article-title":"Binning_refiner: improving genome bins through the combination of different binning programs","volume":"33","author":"Song","year":"2017","journal-title":"Bioinformatics"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1038\/s41396-020-00815-8","article-title":"Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae","volume":"15","author":"Song","year":"2021","journal-title":"ISME J"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms11870","article-title":"Diversity, structure and convergent evolution of the global sponge microbiome","volume":"7","author":"Thomas","year":"2016","journal-title":"Nat. Commun"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/nature24621","article-title":"A communal catalogue reveals earth\u2019s multiscale microbial diversity","volume":"551","author":"Thompson","year":"2017","journal-title":"Nature"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2010-11-4-r41","article-title":"Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps","volume":"11","author":"Tsai","year":"2010","journal-title":"Genome Biol"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The human microbiome project","volume":"449","author":"Turnbaugh","year":"2007","journal-title":"Nature"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"e57923","DOI":"10.1371\/journal.pone.0057923","article-title":"The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses","volume":"8","author":"V\u011btrovsk\u00fd","year":"2013","journal-title":"PLoS One"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"2019","DOI":"10.1093\/bioinformatics\/bty020","article-title":"BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach","volume":"34","author":"Wang","year":"2018","journal-title":"Bioinformatics"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s40793-020-00358-7","article-title":"Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences","volume":"15","author":"Wemheuer","year":"2020","journal-title":"Environ. Microbiome"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","first-page":"i35","DOI":"10.1093\/bioinformatics\/btv231","article-title":"Reconstructing 16S rRNA genes in metagenomic data","volume":"31","author":"Yuan","year":"2015","journal-title":"Bioinformatics"},{"key":"2023041405353967100_","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2020.595066","article-title":"Characterization of metagenome-assembled genomes and carbohydrate-degrading genes in the gut microbiota of Tibetan pig","volume":"11","author":"Zhou","year":"2020","journal-title":"Front. Microbiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac398\/44275904\/btac398.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/15\/3684\/49884276\/btac398.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/15\/3684\/49884276\/btac398.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,23]],"date-time":"2023-11-23T10:07:56Z","timestamp":1700734076000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/15\/3684\/6609767"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,6,17]]},"references-count":34,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2022,8,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac398","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,8,1]]},"published":{"date-parts":[[2022,6,17]]}}}