{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T11:31:36Z","timestamp":1768476696458,"version":"3.49.0"},"posted":{"date-parts":[[2018,1,12]]},"group-title":"Bioinformatics","reference-count":48,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2018,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Genome-scale metabolic models are instrumental in uncovering operating principles of cellular metabolism and model-guided re-engineering. Recent applications of metabolic models have also demonstrated their usefulness in unraveling cross-feeding within microbial communities. Yet, the application of genome-scale models, especially to microbial communities, is lagging far behind the availability of sequenced genomes. This is largely due to the time-consuming steps of manual cura-tion required to obtain good quality models and thus physiologically meaningful simulation results. Here, we present an automated tool \u2013 CarveMe \u2013 for reconstruction of species and community level metabolic models. We introduce the concept of a universal model, which is manually curated and simulation-ready. Starting with this universal model and annotated genome sequences, CarveMe uses a top-down approach to build single-species and community models in a fast and scalable manner. We build reconstructions for two model organisms,\n                  <jats:italic>Escherichia coli<\/jats:italic>\n                  and\n                  <jats:italic>Bacillus subtillis<\/jats:italic>\n                  , as well as a collection of human gut bacteria, and show that CarveMe models perform similarly to manually curated models in reproducing experimental phenotypes. Finally, we demonstrate the scalability of CarveMe through reconstructing 5587 bacterial models. Overall, CarveMe provides an open-source and user-friendly tool towards broadening the use of metabolic modeling in studying microbial species and communities.\n                <\/jats:p>","DOI":"10.1101\/223198","type":"posted-content","created":{"date-parts":[[2018,1,13]],"date-time":"2018-01-13T01:10:21Z","timestamp":1515805821000},"source":"Crossref","is-referenced-by-count":5,"title":["Fast automated reconstruction of genome-scale metabolic models for microbial species and communities"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2063-5383","authenticated-orcid":false,"given":"Daniel","family":"Machado","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7875-0261","authenticated-orcid":false,"given":"Sergej","family":"Andrejev","sequence":"additional","affiliation":[]},{"given":"Melanie","family":"Tramontano","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6166-8640","authenticated-orcid":false,"given":"Kiran Raosaheb","family":"Patil","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2019071809460748000_223198v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2009.77"},{"key":"2019071809460748000_223198v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3643"},{"key":"2019071809460748000_223198v1.3","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.meteno.2015.04.001","article-title":"Co-evolution of strain design methods based on flux balance and elementary mode analysis","volume":"2","year":"2015","journal-title":"Metabolic Engineering Communications"},{"issue":"1","key":"2019071809460748000_223198v1.4","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/1475-2859-9-84","article-title":"Improved vanillin production in bakers yeast through in silico design","volume":"9","year":"2010","journal-title":"Microbial Cell Factories"},{"key":"2019071809460748000_223198v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymben.2009.05.004"},{"issue":"3","key":"2019071809460748000_223198v1.6","doi-asserted-by":"crossref","first-page":"e1002018","DOI":"10.1371\/journal.pcbi.1002018","article-title":"Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect","volume":"7","year":"2011","journal-title":"PLoS Computational Biology"},{"key":"2019071809460748000_223198v1.7","first-page":"92","article-title":"Novel insights into obesity and diabetes through genome-scale metabolic modeling","volume":"4","year":"2013","journal-title":"Frontiers in Physiology"},{"issue":"4","key":"2019071809460748000_223198v1.8","doi-asserted-by":"crossref","first-page":"e1000729","DOI":"10.1371\/journal.pcbi.1000729","article-title":"Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes","volume":"6","year":"2010","journal-title":"PLoS Computational Biology"},{"key":"2019071809460748000_223198v1.9","doi-asserted-by":"publisher","DOI":"10.1172\/JCI89914"},{"issue":"2","key":"2019071809460748000_223198v1.10","doi-asserted-by":"crossref","first-page":"e1002363","DOI":"10.1371\/journal.pcbi.1002363","article-title":"OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities","volume":"8","year":"2012","journal-title":"PLoS Computational Biology"},{"key":"2019071809460748000_223198v1.11","doi-asserted-by":"crossref","unstructured":"A. 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