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Precise understanding of its metabolism is essential for designing engineering strategies to further optimize <jats:italic>B<\/jats:italic>. <jats:italic>megaterium<\/jats:italic> for biotechnology applications. Here, we present a genome-scale metabolic model for <jats:italic>B<\/jats:italic>. <jats:italic>megaterium<\/jats:italic> DSM319, <jats:italic>i<\/jats:italic>JA1121, which is a result of a metabolic network reconciliation process. The model includes 1709 reactions, 1349 metabolites, and 1121 genes. Based on multiple-genome alignments and available genome-scale metabolic models for other <jats:italic>Bacillus<\/jats:italic> species, we constructed a draft network using an automated approach followed by manual curation. The refinements were performed using a gap-filling process. Constraint-based modeling was used to scrutinize network features. Phenotyping assays were performed in order to validate the growth behavior of the model using different substrates. To verify the model accuracy, experimental data reported in the literature (growth behavior patterns, metabolite production capabilities, metabolic flux analysis using <jats:sup>13<\/jats:sup>C glucose and formaldehyde inhibitory effect) were confronted with model predictions. This indicated a very good agreement between <jats:italic>in silico<\/jats:italic> results and experimental data. For example, our <jats:italic>in silico<\/jats:italic> study of fatty acid biosynthesis and lipid accumulation in <jats:italic>B<\/jats:italic>. <jats:italic>megaterium<\/jats:italic> highlighted the importance of adopting appropriate carbon sources for fermentation purposes. We conclude that the genome-scale metabolic model <jats:italic>i<\/jats:italic>JA1121 represents a useful tool for systems analysis and furthers our understanding of the metabolism of <jats:italic>B<\/jats:italic>. <jats:italic>megaterium<\/jats:italic>.<\/jats:p>","DOI":"10.1038\/s41598-019-55041-w","type":"journal-article","created":{"date-parts":[[2019,12,10]],"date-time":"2019-12-10T11:03:32Z","timestamp":1575975812000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4936-6535","authenticated-orcid":false,"given":"Javad","family":"Aminian-Dehkordi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seyyed Mohammad","family":"Mousavi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arezou","family":"Jafari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Mijakovic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9801-7449","authenticated-orcid":false,"given":"Sayed-Amir","family":"Marashi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,10]]},"reference":[{"key":"55041_CR1","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1016\/0006-291X(71)90380-9","volume":"42","author":"C Elmerich","year":"1971","unstructured":"Elmerich, C. & Aubert, J. 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