{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T04:42:37Z","timestamp":1774672957941,"version":"3.50.1"},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,11,9]],"date-time":"2024-11-09T00:00:00Z","timestamp":1731110400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,11,9]],"date-time":"2024-11-09T00:00:00Z","timestamp":1731110400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"FCT","award":["UIDB\/04050\/2020"],"award-info":[{"award-number":["UIDB\/04050\/2020"]}]},{"name":"NORTE2020","award":["NORTE-01-0246-FEDER-000063"],"award-info":[{"award-number":["NORTE-01-0246-FEDER-000063"]}]},{"name":"NORTE2020","award":["NORTE-01-0246-FEDER-000063"],"award-info":[{"award-number":["NORTE-01-0246-FEDER-000063"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Environmental Microbiome"],"DOI":"10.1186\/s40793-024-00634-w","type":"journal-article","created":{"date-parts":[[2024,11,9]],"date-time":"2024-11-09T08:16:21Z","timestamp":1731140181000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification"],"prefix":"10.1186","volume":"19","author":[{"given":"M. Pilar","family":"Cabezas","sequence":"first","affiliation":[]},{"given":"Nuno A.","family":"Fonseca","sequence":"additional","affiliation":[]},{"given":"Antonio","family":"Mu\u00f1oz-M\u00e9rida","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,11,9]]},"reference":[{"issue":"Suppl 2","key":"634_CR1","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1186\/s12864-017-3501-4","volume":"18","author":"M Balvociute","year":"2017","unstructured":"Balvociute M, Huson DH. SILVA, RDP, greengenes, NCBI and OTT\u2014how do these taxonomies compare? BMC Genom. 2017;18(Suppl 2):114.","journal-title":"BMC Genom"},{"key":"634_CR2","doi-asserted-by":"publisher","first-page":"2454","DOI":"10.1002\/pmic.201600034","volume":"16","author":"J Bengtsson-Palme","year":"2016","unstructured":"Bengtsson-Palme J, et al. Strategies to improve usability and preserve accuracy in biological sequence databases. Proteomics. 2016;16:2454\u201360.","journal-title":"Proteomics"},{"key":"634_CR3","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1016\/j.tree.2017.03.001","volume":"32","author":"DA Bohan","year":"2017","unstructured":"Bohan DA, et al. Next-generation global biomonitoring: large-scale, automated reconstruction of ecological networks. Trends Ecol Evo. 2017;32:477\u201387.","journal-title":"Trends Ecol Evo"},{"key":"634_CR4","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen E, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852\u20137.","journal-title":"Nat Biotechnol"},{"key":"634_CR5","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1093\/bib\/bbx120","volume":"20","author":"FP Brietwieser","year":"2019","unstructured":"Brietwieser FP, Lu J, Salzber SL. A review of methods and databases for metagenomic classification and assembly. Brief Bioinf. 2019;20:1125\u201339.","journal-title":"Brief Bioinf"},{"key":"634_CR6","doi-asserted-by":"publisher","first-page":"3e17","DOI":"10.14304\/SURYA.JPR.V4N11.2","volume":"4","author":"LA Boughner","year":"2016","unstructured":"Boughner LA, Singh P. Microbial ecology: where are we now? Postdoc J. 2016;4:3e17.","journal-title":"Postdoc J"},{"issue":"7","key":"634_CR7","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581\u20133.","journal-title":"Nat Methods"},{"key":"634_CR8","first-page":"2","volume":"6","author":"K Cantrell","year":"2021","unstructured":"Cantrell K, et al. EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets. Microb Ecol. 2021;6:2.","journal-title":"Microb Ecol"},{"key":"634_CR9","doi-asserted-by":"publisher","first-page":"204","DOI":"10.3390\/pathogens9030204","volume":"9","author":"M Chalita","year":"2020","unstructured":"Chalita M, et al. Improved metagenomic taxonomic profiling using a curated core gene-based bacterial database reveals unrecognized species in the genus Streptococcus. Pathogens. 2020;9:204.","journal-title":"Pathogens"},{"key":"634_CR10","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/1471-2105-12-35","volume":"12","author":"H Chen","year":"2011","unstructured":"Chen H, Boutros PC. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinf. 2011;12:35.","journal-title":"BMC Bioinf"},{"key":"634_CR11","doi-asserted-by":"publisher","first-page":"D633","DOI":"10.1093\/nar\/gkt1244","volume":"42","author":"JR Cole","year":"2014","unstructured":"Cole JR, et al. Ribosomal database project: data and tools for highthroughput rRNA analysis. Nucleic Acids Res. 2014;42:D633\u201342.","journal-title":"Nucleic Acids Res"},{"key":"634_CR12","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","volume":"72","author":"TZ DeSantis","year":"2006","unstructured":"DeSantis TZ, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069\u201372.","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"634_CR13","doi-asserted-by":"publisher","first-page":"e01557","DOI":"10.1128\/mBio.01557-20","volume":"11","author":"MS Dueholm","year":"2020","unstructured":"Dueholm MS, et al. Generation of comprehensive ecosystems-specific reference databases with species-level resolution by high-throughput full-length 16S rRNA gene sequencing and automated taxonomy assignment (AutoTax). mBio. 2020;11(5):e01557-20.","journal-title":"mBio"},{"key":"634_CR14","doi-asserted-by":"publisher","first-page":"636","DOI":"10.1016\/j.mib.2013.08.003","volume":"16","author":"SS Epstein","year":"2013","unstructured":"Epstein SS. The phenomenon of microbial uncultivability. Curr Opin Microbiol. 2013;16:636\u201342.","journal-title":"Curr Opin Microbiol"},{"key":"634_CR15","doi-asserted-by":"publisher","DOI":"10.1016\/j.biortech.2020.123557","volume":"313","author":"MJ Estrella-Gonz\u00e1lez","year":"2020","unstructured":"Estrella-Gonz\u00e1lez MJ, et al. Uncovering new indicators to predict stability, maturity and biodiversity of compost on an industrial scale. Bioresour Technol. 2020;313: 123557.","journal-title":"Bioresour Technol"},{"key":"634_CR16","doi-asserted-by":"publisher","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","volume":"40","author":"S Federhen","year":"2012","unstructured":"Federhen S. The NCBI taxonomy database. Nucleic Acids Res. 2012;40:D136\u201343.","journal-title":"Nucleic Acids Res"},{"key":"634_CR17","first-page":"184","volume":"3","author":"A Ghosh","year":"2019","unstructured":"Ghosh A, Mehta A, Khan AM. Metagenomic analysis and its applications. J Bioinf Comput Biol. 2019;3:184\u201393.","journal-title":"J Bioinf Comput Biol"},{"key":"634_CR18","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1128\/MMBR.68.4.669-685.2004","volume":"68","author":"J Handelsman","year":"2004","unstructured":"Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68:669\u201385.","journal-title":"Microbiol Mol Biol Rev"},{"key":"634_CR19","doi-asserted-by":"publisher","first-page":"2761","DOI":"10.1128\/JCM.01228-07","volume":"45","author":"JM Janda","year":"2007","unstructured":"Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol. 2007;45:2761\u20134.","journal-title":"J Clin Microbiol"},{"key":"634_CR20","doi-asserted-by":"publisher","first-page":"3100","DOI":"10.1093\/nar\/gkm160","volume":"35","author":"K Lagesen","year":"2007","unstructured":"Lagesen K, et al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"634_CR21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0237108","volume":"15","author":"SJ Lee","year":"2020","unstructured":"Lee SJ, et al. Comparison of microbiota in the cloaca, colon, and magnum of layer chicken. PLoS ONE. 2020;15(8): e0237108.","journal-title":"PLoS ONE"},{"key":"634_CR22","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1093\/nar\/29.1.173","volume":"29","author":"BL Maidak","year":"2001","unstructured":"Maidak BL, et al. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 2001;29:173\u20134.","journal-title":"Nucleic Acids Res"},{"key":"634_CR23","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1038\/ismej.2011.139","volume":"6","author":"D McDonald","year":"2012","unstructured":"McDonald D, et al. An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610\u20138.","journal-title":"ISME J"},{"key":"634_CR24","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1038\/s41587-023-01845-1","volume":"42","author":"D McDonald","year":"2024","unstructured":"McDonald D, et al. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol. 2024;42:715\u20138.","journal-title":"Nat Biotechnol"},{"key":"634_CR25","doi-asserted-by":"publisher","DOI":"10.5808\/GI.2018.16.4.e24","volume":"16","author":"SC Park","year":"2018","unstructured":"Park SC, Won S. Evaluation of 16S rRNA databases for taxonomic assignments using mock community. Genomics Inf. 2018;16: e24.","journal-title":"Genomics Inf"},{"key":"634_CR26","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nbt.4229","volume":"36","author":"DH Parks","year":"2018","unstructured":"Parks DH, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996\u20131004.","journal-title":"Nat Biotechnol"},{"issue":"D1","key":"634_CR27","doi-asserted-by":"publisher","first-page":"D785","DOI":"10.1093\/nar\/gkab776","volume":"50","author":"DH Parks","year":"2021","unstructured":"Parks DH, et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 2021;50(D1):D785-94.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"634_CR28","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1093\/nar\/gkt1111","volume":"42","author":"AC Parte","year":"2014","unstructured":"Parte AC. LPSN\u2014list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 2014;42(D1):613\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"634_CR29","doi-asserted-by":"publisher","first-page":"25","DOI":"10.3390\/microorganisms5020025","volume":"5","author":"A Poli","year":"2017","unstructured":"Poli A, et al. Microbial diversity in extreme marine habitats and their biomolecules. Microorganisms. 2017;5(2):25.","journal-title":"Microorganisms"},{"key":"634_CR30","doi-asserted-by":"publisher","first-page":"7188","DOI":"10.1093\/nar\/gkm864","volume":"35","author":"E Pruesse","year":"2007","unstructured":"Pruesse E, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188\u201396.","journal-title":"Nucleic Acids Res"},{"key":"634_CR31","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast C, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590\u20136.","journal-title":"Nucleic Acids Res"},{"key":"634_CR32","doi-asserted-by":"publisher","first-page":"xtad011","DOI":"10.1093\/femsmc\/xtad011","volume":"4","author":"D Rosado","year":"2023","unstructured":"Rosado D, et al. Disruption of the skin, gill, and gut mucosae microbiome of gilthead seabream fingerlings after bacterial infection and antibiotic treatment. FEMS Microbes. 2023;4:xtad011.","journal-title":"FEMS Microbes"},{"key":"634_CR33","unstructured":"RStudio Team. RStudio: Integrated Development for R. RStudio, PBC, Boston, MA. http:\/\/www.rstudio.com\/ (2020)."},{"key":"634_CR34","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1093\/bib\/bbs036","volume":"13","author":"M Santamaria","year":"2012","unstructured":"Santamaria M, et al. Reference databases for taxonomic assignment in metagenomics. Brief Bioinf. 2012;13:682\u201395.","journal-title":"Brief Bioinf"},{"key":"634_CR35","doi-asserted-by":"crossref","unstructured":"Sattley WM, Madigan MT. Microbiology. eLS 2015; 1\u201310.","DOI":"10.1002\/9780470015902.a0000459.pub2"},{"key":"634_CR36","doi-asserted-by":"publisher","first-page":"7537","DOI":"10.1128\/AEM.01541-09","volume":"75","author":"PD Schloss","year":"2009","unstructured":"Schloss PD, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537\u201341.","journal-title":"Appl Environ Microbiol"},{"key":"634_CR37","doi-asserted-by":"crossref","unstructured":"Schoch CL et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database 2020; baaa062.","DOI":"10.1093\/database\/baaa062"},{"issue":"1","key":"634_CR38","doi-asserted-by":"publisher","DOI":"10.1038\/sdata.2016.81","volume":"3","author":"E Singer","year":"2016","unstructured":"Singer E, et al. Next generation sequencing data of a defined microbial mock community. Sci Data. 2016;3(1): 160081.","journal-title":"Sci Data"},{"key":"634_CR39","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1128\/AEM.01127-09","volume":"76","author":"M Vaitilingom","year":"2010","unstructured":"Vaitilingom M, et al. Contribution of microbial activity to carbon chemistry in clouds. Appl Environ Microbiol. 2010;76:23\u20139.","journal-title":"Appl Environ Microbiol"},{"issue":"2","key":"634_CR40","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0057923","volume":"8","author":"T V\u011btrovsk\u00fd","year":"2013","unstructured":"V\u011btrovsk\u00fd T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE. 2013;8(2): e57923.","journal-title":"PLoS ONE"},{"key":"634_CR41","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/J.ENG.2017.01.008","volume":"3","author":"B Wang","year":"2017","unstructured":"Wang B, et al. The human microbiota in health and disease. Engineering. 2017;3:71\u201382.","journal-title":"Engineering"},{"key":"634_CR42","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1128\/AEM.00062-07","volume":"73","author":"QG Wang","year":"2007","unstructured":"Wang QG, et al. Na\u00efve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261\u20137.","journal-title":"Appl Environ Microbiol"},{"key":"634_CR43","unstructured":"Whitman WB. Bergey\u2019s Manual of Systematic of Archaea and Bacteria. New Jersey, EUA: Wiley Online Library, 2015."},{"key":"634_CR44","doi-asserted-by":"publisher","first-page":"D643","DOI":"10.1093\/nar\/gkt1209","volume":"42","author":"P Yilmaz","year":"2014","unstructured":"Yilmaz P, et al. The SILVA and \u201cAll-species living tree project (LTP)\u201d taxonomic frameworks. Nucleic Acids Res. 2014;42:D643\u20138.","journal-title":"Nucleic Acids Res"}],"container-title":["Environmental Microbiome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40793-024-00634-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40793-024-00634-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40793-024-00634-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,12]],"date-time":"2024-11-12T13:04:52Z","timestamp":1731416692000},"score":1,"resource":{"primary":{"URL":"https:\/\/environmentalmicrobiome.biomedcentral.com\/articles\/10.1186\/s40793-024-00634-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,9]]},"references-count":44,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["634"],"URL":"https:\/\/doi.org\/10.1186\/s40793-024-00634-w","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.12.15.571851","asserted-by":"object"}]},"ISSN":["2524-6372"],"issn-type":[{"value":"2524-6372","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,9]]},"assertion":[{"value":"7 March 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 October 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 November 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All authors are aware of the work developed in this manuscript and consent to participate.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"All authors give their consent to publish all the information that appears in this manuscript.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"88"}}