{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:43Z","timestamp":1740185143743,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Mobilno\u015b\u0107 Plus V from the Polish Ministry of Science and Higher Education","award":["1639\/MOB\/V\/2017\/0"],"award-info":[{"award-number":["1639\/MOB\/V\/2017\/0"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n The gut microbiota is the human body\u2019s largest population of microorganisms that interact with human intestinal cells. They use ingested nutrients for fundamental biological processes and have important impacts on human physiology, immunity and metabolome in the gastrointestinal tract.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Here, we present M2R, a Python add-on to cobrapy that allows incorporating information about the gut microbiota metabolism models to human genome-scale metabolic models (GEMs) like RECON3D. The idea behind the software is to modify the lower bounds of the exchange reactions in the model using aggregated in- and out-fluxes from selected microbes. M2R enables users to quickly and easily modify the pool of the metabolites that enter and leave the GEM, which is particularly important for those looking into an analysis of the metabolic interaction between the gut microbiota and human cells and its dysregulation.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n M2R is freely available under an MIT License at https:\/\/github.com\/e-weglarz-tomczak\/m2r.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab060","type":"journal-article","created":{"date-parts":[[2021,1,27]],"date-time":"2021-01-27T04:13:32Z","timestamp":1611720812000},"page":"2785-2786","source":"Crossref","is-referenced-by-count":0,"title":["M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models"],"prefix":"10.1093","volume":"37","author":[{"given":"Ewelina","family":"Weglarz-Tomczak","sequence":"first","affiliation":[{"name":"Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam , Amsterdam, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8634-694X","authenticated-orcid":false,"given":"Jakub M.","family":"Tomczak","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Faculty of Science, Vrije Universiteit Amsterdam , Amsterdam, The Netherlands"}]},{"given":"Stanley","family":"Brul","sequence":"additional","affiliation":[{"name":"Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam , Amsterdam, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2021,2,1]]},"reference":[{"key":"2023051609163802900_btab060-B1","doi-asserted-by":"crossref","first-page":"2332","DOI":"10.1093\/bioinformatics\/bty941","article-title":"The microbiome modeling toolbox: from microbial interactions to personalized microbial communities","volume":"35","author":"Baldini","year":"2019","journal-title":"Bioinformatics"},{"key":"2023051609163802900_btab060-B2","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nbt.4072","article-title":"Recon3d enables a three-dimensional view of gene variation in human metabolism","volume":"36","author":"Brunk","year":"2018","journal-title":"Nat. Biotechnol"},{"key":"2023051609163802900_btab060-B3","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/1752-0509-7-74","article-title":"COBRApy: constraints-based reconstruction and analysis for Python","volume":"7","author":"Ebrahim","year":"2013","journal-title":"BMC Syst. Biol"},{"key":"2023051609163802900_btab060-B4","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1126\/science.aau5812","article-title":"The gut microbiota at the intersection of diet and human health","volume":"362","author":"Gentile","year":"2018","journal-title":"Science"},{"key":"2023051609163802900_btab060-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1769-1","article-title":"A systematic assessment of current genome-scale metabolic reconstruction tools","volume":"20","author":"Mendoza","year":"2019","journal-title":"Genome Biol"},{"key":"2023051609163802900_btab060-B6","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nbt.1614","article-title":"What is flux balance analysis?","volume":"28","author":"Orth","year":"2010","journal-title":"Nat. Biotechnol"},{"key":"2023051609163802900_btab060-B7","doi-asserted-by":"crossref","first-page":"e1007036","DOI":"10.1371\/journal.pcbi.1007036","article-title":"Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models","volume":"15","author":"Pandey","year":"2019","journal-title":"PLoS Comput. Biol"},{"key":"2023051609163802900_btab060-B8","doi-asserted-by":"crossref","first-page":"e8982","DOI":"10.15252\/msb.20198982","article-title":"Personalized whole-body models integrate metabolism, physiology, and the gut microbiome","volume":"16","author":"Thiele","year":"2020","journal-title":"Mol. Syst. Biol"},{"key":"2023051609163802900_btab060-B9","first-page":"674150","article-title":"Simultaneous integration of gene expression and nutrient availability for studying metabolism of hepatocellular carcinoma","author":"W\u0119glarz-Tomczak","year":"2020","journal-title":"BioRxiv"},{"key":"2023051609163802900_btab060-B10","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1038\/s41575-019-0209-8","article-title":"Gut microbiota in colorectal cancer: mechanisms of action and clinical applications","volume":"16","author":"Wong","year":"2019","journal-title":"Nat. Rev. Gastroenterol. Hepatol"},{"key":"2023051609163802900_btab060-B11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-019-11331-5","article-title":"Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli","volume":"10","author":"Zampieri","year":"2019","journal-title":"Nat. Commun"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab060\/36256422\/btab060.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/17\/2785\/50339046\/btab060.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/17\/2785\/50339046\/btab060.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T09:20:09Z","timestamp":1684228809000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/17\/2785\/6125380"}},"subtitle":[],"editor":[{"given":"Teresa","family":"Przytycka","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,2,1]]},"references-count":11,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2021,9,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab060","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,9,1]]},"published":{"date-parts":[[2021,2,1]]}}}