{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T03:27:33Z","timestamp":1762918053026,"version":"3.37.3"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,12,3]],"date-time":"2019-12-03T00:00:00Z","timestamp":1575331200000},"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":["[KFZD-SW-219-5]","[31771463]"],"award-info":[{"award-number":["[KFZD-SW-219-5]","[31771463]"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["ZR2017ZB0421","ZR201807060158"],"award-info":[{"award-number":["ZR2017ZB0421","ZR201807060158"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shandong Provincial Natural Science Foundation of China","award":["2018M630807"],"award-info":[{"award-number":["2018M630807"]}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>An accurate and reliable distance (or dissimilarity) among shotgun metagenomes is fundamental to deducing the beta-diversity of microbiomes. To compute the distance at the species level, current methods either ignore the evolutionary relationship among species or fail to account for unclassified organisms that cannot be mapped to definite tip nodes in the phylogenic tree, thus can produce erroneous beta-diversity pattern.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To solve these problems, we propose the Dynamic Meta-Storms (DMS) algorithm to enable the comprehensive comparison of metagenomes on the species level with both taxonomy and phylogeny profiles. It compares the identified species of metagenomes with phylogeny, and then dynamically places the unclassified species to the virtual nodes of the phylogeny tree via their higher-level taxonomy information. Its high speed and low memory consumption enable pairwise comparison of 100 000 metagenomes (synthesized from 3688 bacteria) within 6.4 h on a single computing node.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>An optimized implementation of DMS is available on GitHub (https:\/\/github.com\/qibebt-bioinfo\/dynamic-meta-storms) under a GNU GPL license. It takes the species-level profiles of metagenomes as input, and generates their pairwise distance matrix. The bacterial species-level phylogeny tree and taxonomy information of MetaPhlAn2 have been integrated into this implementation, while customized tree and taxonomy are also supported.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz910","type":"journal-article","created":{"date-parts":[[2019,12,2]],"date-time":"2019-12-02T16:58:29Z","timestamp":1575305909000},"page":"2308-2310","source":"Crossref","is-referenced-by-count":9,"title":["<i>Dynamic Meta-Storms<\/i> enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level"],"prefix":"10.1093","volume":"36","author":[{"given":"Gongchao","family":"Jing","sequence":"first","affiliation":[{"name":"Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, Shandong 266101, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yufeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, Shandong 266101, China"},{"name":"School of Data Science and Software Engineering, Qingdao University , Qingdao, Shandong 266071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Yang","sequence":"additional","affiliation":[{"name":"Office of General Affairs, Chinese Academy of Sciences , Beijing 100864, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lu","family":"Liu","sequence":"additional","affiliation":[{"name":"Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, Shandong 266101, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Xu","sequence":"additional","affiliation":[{"name":"Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, Shandong 266101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoquan","family":"Su","sequence":"additional","affiliation":[{"name":"Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, Shandong 266101, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,12,3]]},"reference":[{"key":"2023062300073722100_btz910-B1","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1093\/bib\/bbx120","article-title":"A review of methods and databases for metagenomic classification and assembly","volume":"20","author":"Breitwieser","year":"2019","journal-title":"Brief Bioinform"},{"key":"2023062300073722100_btz910-B2","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":"2023062300073722100_btz910-B3","doi-asserted-by":"crossref","first-page":"e00018-16","DOI":"10.1128\/mSystems.00018-16","article-title":"Urban transit system microbial communities differ by surface type and interaction with humans and the environment","volume":"1","author":"Hsu","year":"2016","journal-title":"mSystems"},{"key":"2023062300073722100_btz910-B4","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1038\/s41586-019-1238-8","article-title":"The Integrative Human Microbiome Project","volume":"569","year":"2019","journal-title":"Nature"},{"key":"2023062300073722100_btz910-B5","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. 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