{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T05:14:57Z","timestamp":1768454097895,"version":"3.49.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Background: It has long been intriguing scientists to effectively compare different microbial communities (also referred as \u2018metagenomic samples\u2019 here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database.<\/jats:p>\n               <jats:p>Results: In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods.<\/jats:p>\n               <jats:p>Conclusion: Meta-Storms method would serve as a suitable database management and search system to quickly identify similar metagenomic samples from a large pool of samples.<\/jats:p>\n               <jats:p>Contact: \u00a0ningkang@qibebt.ac.cn<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts470","type":"journal-article","created":{"date-parts":[[2012,7,28]],"date-time":"2012-07-28T10:52:46Z","timestamp":1343472766000},"page":"2493-2501","source":"Crossref","is-referenced-by-count":49,"title":["Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data"],"prefix":"10.1093","volume":"28","author":[{"given":"Xiaoquan","family":"Su","sequence":"first","affiliation":[{"name":"Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and BioEnergy Genome Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong Province, People\u2019s Republic of China"}]},{"given":"Jian","family":"Xu","sequence":"additional","affiliation":[{"name":"Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and BioEnergy Genome Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong Province, People\u2019s Republic of China"}]},{"given":"Kang","family":"Ning","sequence":"additional","affiliation":[{"name":"Shandong Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels and BioEnergy Genome Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong Province, People\u2019s Republic of China"}]}],"member":"286","published-online":{"date-parts":[[2012,7,26]]},"reference":[{"key":"2023012513143777300_bts470-B1","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving pictures of the human microbiome","volume":"12","author":"Caporaso","year":"2011","journal-title":"Genome Biol."},{"key":"2023012513143777300_bts470-B2","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1159\/000262383","article-title":"The influence of audit on the diagnosis of occlusal caries","volume":"31","author":"Cayley","year":"1997","journal-title":"Caries Res."},{"key":"2023012513143777300_bts470-B3","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1093\/ejo\/22.5.463","article-title":"Electropalatographic and cephalometric assessment of tongue function in open bite and non-open bite subjects","volume":"22","author":"Cayley","year":"2000","journal-title":"Eur. J. Orthod."},{"key":"2023012513143777300_bts470-B4","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1126\/science.1206025","article-title":"Predicting a human gut microbiota's response to diet in gnotobiotic mice","volume":"333","author":"Faith","year":"2011","journal-title":"Science"},{"key":"2023012513143777300_bts470-B5","doi-asserted-by":"crossref","first-page":"17994","DOI":"10.1073\/pnas.0807920105","article-title":"The influence of sex, handedness, and washing on the diversity of hand surface bacteria","volume":"105","author":"Fierer","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012513143777300_bts470-B6","doi-asserted-by":"crossref","first-page":"2631","DOI":"10.1093\/bioinformatics\/btq455","article-title":"METAREP: JCVI metagenomics reports\u2013an open source tool for high-performance comparative metagenomics","volume":"26","author":"Goll","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012513143777300_bts470-B7","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1111\/j.1461-0248.2008.01256.x","article-title":"Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time","volume":"11","author":"Graham","year":"2008","journal-title":"Ecol. Lett."},{"key":"2023012513143777300_bts470-B8","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1101\/gr.085464.108","article-title":"Microbial community profiling for human microbiome projects: Tools, techniques, and challenges","volume":"19","author":"Hamady","year":"2009","journal-title":"Genome Res."},{"key":"2023012513143777300_bts470-B9","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1038\/ismej.2009.97","article-title":"Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data","volume":"4","author":"Hamady","year":"2010","journal-title":"ISME J."},{"key":"2023012513143777300_bts470-B10","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1126\/science.1146689","article-title":"Microbial population structures in the deep marine biosphere","volume":"318","author":"Huber","year":"2007","journal-title":"Science"},{"key":"2023012513143777300_bts470-B11","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/455481a","article-title":"Microbiology - Metagenomics","volume":"455","author":"Hugenholtz","year":"2008","journal-title":"Nature"},{"key":"2023012513143777300_bts470-B12","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1101\/gr.5969107","article-title":"MEGAN analysis of metagenomic data","volume":"17","author":"Huson","year":"2007","journal-title":"Genome Res."},{"key":"2023012513143777300_bts470-B13","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1187\/cbe.07-09-0075","article-title":"Metagenomics: a call for bringing a new science into the classroom (while it's still new)","volume":"6","author":"Jurkowski","year":"2007","journal-title":"CBE Life Sci. Educ."},{"key":"2023012513143777300_bts470-B14","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.molmed.2011.01.013","article-title":"Skin microbiome: genomics-based insights into the diversity and role of skin microbes","volume":"17","author":"Kong","year":"2011","journal-title":"Trends Mol. Med."},{"key":"2023012513143777300_bts470-B15","doi-asserted-by":"crossref","first-page":"2737","DOI":"10.1093\/bioinformatics\/btp508","article-title":"ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes","volume":"25","author":"Kristiansson","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012513143777300_bts470-B16","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"Lozupone","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012513143777300_bts470-B17","doi-asserted-by":"crossref","first-page":"15076","DOI":"10.1073\/pnas.0807339105","article-title":"The convergence of carbohydrate active gene repertoires in human gut microbes","volume":"105","author":"Lozupone","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012513143777300_bts470-B18","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1093\/bioinformatics\/17.7.664","article-title":"T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks","volume":"17","author":"Makarenkov","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012513143777300_bts470-B19","doi-asserted-by":"crossref","first-page":"3673","DOI":"10.1128\/AEM.68.8.3673-3682.2002","article-title":"Phylogenetic approaches for describing and comparing the diversity of microbial communities","volume":"68","author":"Martin","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012513143777300_bts470-B20","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1186\/1471-2105-9-386","article-title":"The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes","volume":"9","author":"Meyer","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012513143777300_bts470-B21","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1038\/ismej.2010.51","article-title":"Comparison of multiple metagenomes using phylogenetic networks based on ecological indices","volume":"4","author":"Mitra","year":"2010","journal-title":"ISME J."},{"key":"2023012513143777300_bts470-B22","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1093\/bioinformatics\/btp341","article-title":"Visual and statistical comparison of metagenomes","volume":"25","author":"Mitra","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012513143777300_bts470-B23","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1126\/science.1198719","article-title":"Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans","volume":"332","author":"Muegge","year":"2011","journal-title":"Science"},{"key":"2023012513143777300_bts470-B24","volume-title":"The New Science of Metagenomics: Revealing the Secrets of our Microbial Planet","author":"National Research Council (U.S.); Committee on Metagenomics: Challenges and Functional Applications. and National Academies Press (U.S.)","year":"2007"},{"key":"2023012513143777300_bts470-B25","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1093\/bioinformatics\/btq041","article-title":"Identifying biologically relevant differences between metagenomic communities","volume":"26","author":"Parks","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012513143777300_bts470-B26","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1006\/plas.1994.1051","article-title":"Mathematics of microbial plasmid instability and subsequent differential growth of plasmid-free and plasmid-containing cells, relevant to the analysis of experimental colony number data","volume":"32","author":"Proctor","year":"1994","journal-title":"Plasmid"},{"key":"2023012513143777300_bts470-B27","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/ismej.2007.53","article-title":"Pyrosequencing enumerates and contrasts soil microbial diversity","volume":"1","author":"Roesch","year":"2007","journal-title":"ISME J."},{"key":"2023012513143777300_bts470-B28","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012513143777300_bts470-B29","doi-asserted-by":"crossref","first-page":"12115","DOI":"10.1073\/pnas.0605127103","article-title":"Microbial diversity in the deep sea and the underexplored \u201crare biosphere\u201d","volume":"103","author":"Sogin","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012513143777300_bts470-B30","doi-asserted-by":"crossref","first-page":"S16","DOI":"10.1186\/1752-0509-6-S1-S16","article-title":"Parallel-META: efficient metagenomic data analysis based on high-performance computation","volume":"6","author":"Su","year":"2012","journal-title":"BMC Systems Biology"},{"key":"2023012513143777300_bts470-B31","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins","volume":"457","author":"Turnbaugh","year":"2009","journal-title":"Nature"},{"key":"2023012513143777300_bts470-B32","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1038\/nature05414","article-title":"An obesity-associated gut microbiome with increased capacity for energy harvest","volume":"444","author":"Turnbaugh","year":"2006","journal-title":"Nature"},{"key":"2023012513143777300_bts470-B33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ismej.2011.71","article-title":"Saliva microbiomes distinguish caries-active from healthy human populations","volume":"6","author":"Yang","year":"2012","journal-title":"ISME J."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/19\/2493\/48880116\/bioinformatics_28_19_2493.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/19\/2493\/48880116\/bioinformatics_28_19_2493.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T19:16:40Z","timestamp":1674674200000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/19\/2493\/289148"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,7,26]]},"references-count":33,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2012,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts470","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,10,1]]},"published":{"date-parts":[[2012,7,26]]}}}