{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T20:51:21Z","timestamp":1765486281241},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T00:00:00Z","timestamp":1548028800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Conicyt Basal Centre Grant","award":["FB0001"],"award-info":[{"award-number":["FB0001"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12918-019-0683-1","type":"journal-article","created":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T15:02:34Z","timestamp":1548082954000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora"],"prefix":"10.1186","volume":"13","author":[{"given":"Carolina A.","family":"Contador","sequence":"first","affiliation":[]},{"given":"Vida","family":"Rodr\u00edguez","sequence":"additional","affiliation":[]},{"given":"Barbara A.","family":"Andrews","sequence":"additional","affiliation":[]},{"given":"Juan A.","family":"Asenjo","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,1,21]]},"reference":[{"key":"683_CR1","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1039\/C4NP00167B","volume":"32","author":"PR Jensen","year":"2015","unstructured":"Jensen PR, Moore BS, Fenical W. The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery. Nat Prod Rep. 2015;32:738\u201351.","journal-title":"Nat Prod Rep"},{"key":"683_CR2","doi-asserted-by":"crossref","unstructured":"Goodfellow M, Kampfer P, Busse H-J, Trujillo ME, Suzuki K, Ludwig W, et al., editors. Bergey\u2019s manual of systematic bacteriology: volume five. Second Edi: Springer; 2012.","DOI":"10.1007\/978-0-387-68233-4"},{"key":"683_CR3","doi-asserted-by":"publisher","first-page":"1525","DOI":"10.1007\/s00253-009-2424-7","volume":"86","author":"G Tsueng","year":"2010","unstructured":"Tsueng G, Lam KS. A preliminary investigation on the growth requirement for monovalent cations, divalent cations and medium ionic strength of marine actinomycete Salinispora. Appl Microbiol Biotechnol. 2010;86:1525\u201334.","journal-title":"Appl Microbiol Biotechnol"},{"key":"683_CR4","doi-asserted-by":"publisher","first-page":"1759","DOI":"10.1099\/ijs.0.63625-0","volume":"55","author":"LA Maldonado","year":"2005","unstructured":"Maldonado LA, Fenical W, Jensen PR, Kauffman CA, Mincer TJ, Ward AC, et al. Salinispora arenicola gen. Nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae. Int J Syst Evol Microbiol. 2005;55:1759\u201366.","journal-title":"Int J Syst Evol Microbiol"},{"key":"683_CR5","first-page":"1069","volume":"103","author":"L Ahmed","year":"2013","unstructured":"Ahmed L, Jensen PR, Freel KC, Brown R, Jones AL, Kim BY, et al. Salinispora pacifica sp. nov., an actinomycete from marine sediments. Antonie van Leeuwenhoek, Int. J. Gen. Mol Microbiol. 2013;103:1069\u201378.","journal-title":"Mol Microbiol"},{"key":"683_CR6","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1111\/j.1462-2920.2005.00716.x","volume":"7","author":"TK Kim","year":"2005","unstructured":"Kim TK, Garson MJ, Fuerst JA. Marine actinomycetes related to the \u201cSalinospora\u201d group from the great barrier reef sponge Pseudoceratina clavata. Environ Microbiol. 2005;7:509\u201318.","journal-title":"Environ Microbiol"},{"key":"683_CR7","first-page":"5005","volume":"68","author":"TJ Mincer","year":"2002","unstructured":"Mincer TJ, Jensen PR, Kauffman CA, Fenical W. Widespread and Persistent populations of a major new marine Actinomycete taxon in ocean sediments. Society. 2002;68:5005\u201311.","journal-title":"Society"},{"key":"683_CR8","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1111\/j.1462-2920.2011.02641.x","volume":"14","author":"KC Freel","year":"2012","unstructured":"Freel KC, Edlund A, Jensen PR. Microdiversity and evidence for high dispersal rates in the marine actinomycete \u201cSalinispora pacifica.\u201d. Environ Microbiol. 2012;14:480\u201393.","journal-title":"Environ Microbiol"},{"key":"683_CR9","doi-asserted-by":"publisher","first-page":"1881","DOI":"10.1111\/j.1462-2920.2006.01093.x","volume":"8","author":"PR Jensen","year":"2006","unstructured":"Jensen PR, Mafnas C. Biogeography of the marine actinomycete Salinispora. Environ Microbiol. 2006;8:1881\u20138.","journal-title":"Environ Microbiol"},{"key":"683_CR10","first-page":"1193","volume":"3","author":"K Penn","year":"2009","unstructured":"Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, et al. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J Nature Publishing Group. 2009;3:1193\u2013203.","journal-title":"ISME J Nature Publishing Group"},{"key":"683_CR11","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.1128\/AEM.01891-06","volume":"73","author":"PR Jensen","year":"2007","unstructured":"Jensen PR, Williams PG, Oh DC, Zeigler L, Fenical W. Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Appl Environ Microbiol. 2007;73:1146\u201352.","journal-title":"Appl Environ Microbiol"},{"key":"683_CR12","doi-asserted-by":"crossref","unstructured":"Chaudhary AK, Dhakal D, Sohng JK. An insight into the \u201c-omics\u201d based engineering of streptomycetes for secondary metabolite overproduction. Biomed Res Int. 2013;2013:968518.","DOI":"10.1155\/2013\/968518"},{"key":"683_CR13","doi-asserted-by":"publisher","first-page":"3012","DOI":"10.1021\/cr900019j","volume":"109","author":"GM Cragg","year":"2009","unstructured":"Cragg GM, Grothaus PG, Newman DJ. Impact of natural products on developing new anti-cancer agents. Chem Rev. 2009;109:3012\u201343.","journal-title":"Chem Rev"},{"key":"683_CR14","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1016\/j.tim.2007.04.001","volume":"15","author":"KS Lam","year":"2007","unstructured":"Lam KS. New aspects of natural products in drug discovery. Trends Microbiol. 2007;15:279\u201389.","journal-title":"Trends Microbiol"},{"key":"683_CR15","doi-asserted-by":"crossref","unstructured":"Feling RH, Buchanan GO, Mincer TJ, Kauffman CA, Jensen PR, Fenical W. Salinosporamide A: A highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora. 2003;42:355\u20137.","DOI":"10.1002\/anie.200390115"},{"key":"683_CR16","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1039\/C1NP00052G","volume":"29","author":"SB Herzon","year":"2012","unstructured":"Herzon SB, Woo CM. The diazofluorene antitumor antibiotics: structural elucidation, biosynthetic, synthetic, and chemical biological studies. Nat Prod Rep. 2012;29:87\u2013118.","journal-title":"Nat Prod Rep"},{"key":"683_CR17","doi-asserted-by":"publisher","first-page":"2158","DOI":"10.1111\/1462-2920.12669","volume":"17","author":"TKS Richter","year":"2015","unstructured":"Richter TKS, Hughes CC, Moore BS. Sioxanthin, a novel glycosylated carotenoid, reveals an unusual subclustered biosynthetic pathway. Environ Microbiol. 2015;17:2158\u201371.","journal-title":"Environ Microbiol"},{"key":"683_CR18","doi-asserted-by":"publisher","first-page":"10376","DOI":"10.1073\/pnas.0700962104","volume":"104","author":"DW Udwary","year":"2007","unstructured":"Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, et al. Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci U S A. 2007;104:10376\u201381.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"683_CR19","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1351\/PAC-CON-08-08-08","volume":"81","author":"M Nett","year":"2009","unstructured":"Nett M, Moore BS. Exploration and engineering of biosynthetic pathways in the marine actinomycete Salinispora tropica. Pure Appl Chem. 2009;81:1075\u201384.","journal-title":"Pure Appl Chem"},{"key":"683_CR20","doi-asserted-by":"crossref","unstructured":"Duncan KR, Cr\u00fcsemann M, Lechner A, Sarkar A, Li J, Ziemert N, et al. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. Chem Biol. 2015:460\u201371.","DOI":"10.1016\/j.chembiol.2015.03.010"},{"key":"683_CR21","doi-asserted-by":"publisher","first-page":"2389","DOI":"10.1016\/j.febslet.2011.06.014","volume":"585","author":"MT Alam","year":"2011","unstructured":"Alam MT, Medema MH, Takano E, Breitling R. Comparative genome-scale metabolic modeling of actinomycetes: the topology of essential core metabolism. FEBS Lett. Fed Eur Biochem Soc. 2011;585:2389\u201394.","journal-title":"Fed Eur Biochem Soc"},{"key":"683_CR22","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1007\/s10482-015-0561-9","volume":"108","author":"CA Contador","year":"2015","unstructured":"Contador CA, Rodr\u00edguez V, Andrews BA, Asenjo JA. Genome-scale reconstruction of Salinispora tropica CNB-440 metabolism to study strain-specific adaptation. Antonie van Leeuwenhoek Int J Gen Mol Microbiol. 2015;108:1075\u201390.","journal-title":"Antonie van Leeuwenhoek Int J Gen Mol Microbiol"},{"key":"683_CR23","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1038\/nrmicro1949","volume":"7","author":"AM Feist","year":"2009","unstructured":"Feist AM, Herrg\u00e5rd MJ, Thiele I, Reed JL, Palsson B\u00d8. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol. 2009;7:129\u201343.","journal-title":"Nat Rev Microbiol"},{"key":"683_CR24","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1038\/msb.2009.77","volume":"5","author":"MA Oberhardt","year":"2009","unstructured":"Oberhardt MA, Palsson B\u00d8, Papin JA. Applications of genome-scale metabolic reconstructions. Mol Syst Biol. 2009;5:320.","journal-title":"Mol Syst Biol"},{"key":"683_CR25","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.ymben.2014.07.009","volume":"25","author":"MA Campodonico","year":"2014","unstructured":"Campodonico MA, Andrews BA, Asenjo JA, Palsson B\u00d8, Feist AM. Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm. GEM-Path Metab Eng Elsevier. 2014;25:140\u201358.","journal-title":"GEM-Path Metab Eng Elsevier"},{"key":"683_CR26","doi-asserted-by":"crossref","unstructured":"Aurich MK, Fleming RMT, Thiele I. MetaboTools: a comprehensive toolbox for analysis of genome-scale metabolic models. Front Physiol. 2016;7.","DOI":"10.3389\/fphys.2016.00327"},{"key":"683_CR27","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.meteno.2015.06.004","volume":"2","author":"CA Contador","year":"2015","unstructured":"Contador CA, Shene C, Yoshikuni Y, Buschmann A, Andrews BA, Asenjo JA. Analyzing redox balance in a synthetic yeast platform to improve utilization of brown macroalgae as feedstock. Metab Eng Commun. 2015;2:76\u201384.","journal-title":"Metab Eng Commun"},{"key":"683_CR28","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1104\/pp.17.00605","volume":"176","author":"C Zu\u00f1iga","year":"2018","unstructured":"Zu\u00f1iga C, Levering J, Antoniewicz MR, Guarnieri MT, Betenbaugh MJ, Zengler K. Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris. Plant Physiol. 2018;176:450\u201362.","journal-title":"Plant Physiol."},{"key":"683_CR29","doi-asserted-by":"publisher","first-page":"11548","DOI":"10.1073\/pnas.1705524114","volume":"114","author":"K Chen","year":"2017","unstructured":"Chen K, Gao Y, Mih N, O\u2019Brien EJ, Yang L, Palsson BO. Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proc Natl Acad Sci U S A. 2017;114:11548\u201353.","journal-title":"Proc Natl Acad Sci U S A."},{"key":"683_CR30","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/1752-0509-5-182","volume":"5","author":"DJ Baumler","year":"2011","unstructured":"Baumler DJ, Peplinski RG, Reed JL, Glasner JD, Perna NT. The evolution of metabolic networks of. E coli BMC Syst Biol BioMed Central Ltd. 2011;5:182.","journal-title":"E coli BMC Syst Biol BioMed Central Ltd"},{"key":"683_CR31","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/1752-0509-8-31","volume":"8","author":"W Ong","year":"2014","unstructured":"Ong W, Vu TT, Lovendahl KN, Llull JM, Serres MH, Romine MF, et al. Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. BMC Syst Biol. 2014;8:31.","journal-title":"BMC Syst Biol"},{"key":"683_CR32","doi-asserted-by":"publisher","first-page":"20338","DOI":"10.1073\/pnas.1307797110","volume":"110","author":"JM Monk","year":"2013","unstructured":"Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, et al. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. PNAS. 2013;110:20338\u201343.","journal-title":"PNAS"},{"key":"683_CR33","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1007\/s00253-008-1357-x","volume":"78","author":"G Tsueng","year":"2008","unstructured":"Tsueng G, Lam KS. A low-sodium-salt formulation for the fermentation of salinosporamides by Salinispora tropica strain NPS21184. Appl Microbiol Biotechnol. 2008;78:821\u20136.","journal-title":"Appl Microbiol Biotechnol"},{"key":"683_CR34","doi-asserted-by":"publisher","first-page":"1527","DOI":"10.1016\/j.chembiol.2011.10.014","volume":"18","author":"A Lechner","year":"2011","unstructured":"Lechner A, Eust\u00e1quio AS, Gulder TAM, Hafner M, Moore BS. Selective overproduction of the proteasome inhibitor salinosporamide a via precursor pathway regulation. Chem Biol. 2011;18:1527\u201336.","journal-title":"Chem Biol"},{"key":"683_CR35","doi-asserted-by":"publisher","first-page":"D234","DOI":"10.1093\/nar\/gku1203","volume":"43","author":"ELL Sonnhammer","year":"2015","unstructured":"Sonnhammer ELL, \u00d6stlund G. InParanoid 8: Orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res. 2015;43:D234\u20139.","journal-title":"Nucleic Acids Res"},{"key":"683_CR36","unstructured":"NCBI. Basic Local Alignment Search Tool. Available from: https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi ."},{"key":"683_CR37","doi-asserted-by":"crossref","unstructured":"Arkin AP, Stevens RL, Cottingham RW, Maslov S, Henry CS, Dehal P, et al. The DOE systems biology knowledgebase (KBase). bioRxiv. 2016;","DOI":"10.1145\/2808719.2811433"},{"key":"683_CR38","doi-asserted-by":"publisher","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","volume":"45","author":"M Kanehisa","year":"2017","unstructured":"Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45:D353\u201361.","journal-title":"Nucleic Acids Res"},{"key":"683_CR39","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1089\/1066527041410319","volume":"11","author":"M Kellis","year":"2004","unstructured":"Kellis M, Patterson N, Birren B, Berger B, Lander ES. Methods in comparative Genomics\u00a0: genome correspondence, gene identification and regulatory motif discovery. J Comput Biol. 2004;11:319\u201355.","journal-title":"J Comput Biol"},{"key":"683_CR40","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/nprot.2009.203","volume":"5","author":"I Thiele","year":"2010","unstructured":"Thiele I, Palsson B\u00d8. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc Nat Publ Group. 2010;5:93\u2013121.","journal-title":"Nat Protoc Nat Publ Group"},{"key":"683_CR41","doi-asserted-by":"publisher","first-page":"D30","DOI":"10.1093\/nar\/gku1216","volume":"43","author":"DA Benson","year":"2015","unstructured":"Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2015;43:D30\u20135.","journal-title":"Nucleic Acids Res"},{"key":"683_CR42","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"R Edgar","year":"2004","unstructured":"Edgar R. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792\u20137.","journal-title":"Nucleic Acids Res"},{"key":"683_CR43","doi-asserted-by":"publisher","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","volume":"28","author":"M Kearse","year":"2012","unstructured":"Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28:1647\u20139.","journal-title":"Bioinformatics"},{"key":"683_CR44","doi-asserted-by":"crossref","unstructured":"Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870\u20134.","DOI":"10.1093\/molbev\/msw054"},{"key":"683_CR45","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1007\/BF01734359","volume":"17","author":"J Felsenstein","year":"1981","unstructured":"Felsenstein J. Evolutionary trees from DNA sequences: maximum-likelihood approach. Mol Evol. 1981;17:368\u201376.","journal-title":"Mol Evol"},{"key":"683_CR46","doi-asserted-by":"crossref","unstructured":"Orth JD, Fleming RMT, Palsson B\u00d8. Reconstruction and use of microbial metabolic Netwroks: the Core Escherichia coli metabolic model as an educational guide. EcoSal Plus. 2010;4.","DOI":"10.1128\/ecosalplus.10.2.1"},{"key":"683_CR47","doi-asserted-by":"publisher","first-page":"3603","DOI":"10.1093\/bioinformatics\/btx453","volume":"33","author":"SHJ Chan","year":"2017","unstructured":"Chan SHJ, Cai J, Wang L, Simons-Senftle MN, Maranas CD. Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models. Bioinformatics. 2017;33:3603\u20139.","journal-title":"Bioinformatics"},{"key":"683_CR48","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/nbt.1614","volume":"28","author":"JD Orth","year":"2010","unstructured":"Orth JD, Thiele I, Palsson B\u00d8. What is flux balance analysis? Nat Biotechnol Nature Publishing Group. 2010;28:245\u20138.","journal-title":"Nat Biotechnol Nature Publishing Group"},{"key":"683_CR49","first-page":"1710.04038","volume":"arXiv","author":"L Heirendt","year":"2017","unstructured":"Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, et al. Creation and analysis of biochemical constraint-based models: the COBRA toolbox v3.0. Quant. Methods. 2017;arXiv:1710.04038.","journal-title":"Methods"},{"key":"683_CR50","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.ymben.2009.10.003","volume":"12","author":"AM Feist","year":"2010","unstructured":"Feist AM, Zielinski DC, Orth JD, Schellenberger J, Markus J, Palsson B\u00d8. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng. 2010;12:173\u201386.","journal-title":"Metab Eng"},{"key":"683_CR51","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1093\/bioinformatics\/btp704","volume":"26","author":"N Tepper","year":"2010","unstructured":"Tepper N, Shlomi T. Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics. 2010;26:536\u201343.","journal-title":"Bioinformatics"},{"key":"683_CR52","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1038\/nprot.2007.99","volume":"2","author":"SA Becker","year":"2007","unstructured":"Becker SA, Feist AM, Mo ML, Hannum G, Palsson B\u00d8, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox. Nat Protoc. 2007;2:727\u201338.","journal-title":"Nat Protoc"},{"key":"683_CR53","doi-asserted-by":"crossref","unstructured":"Conway JR, Lex A, Gehlenborg N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics. 2017:2\u20135.","DOI":"10.1101\/120600"},{"key":"683_CR54","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","volume":"32","author":"Z Gu","year":"2016","unstructured":"Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847\u20139.","journal-title":"Bioinformatics"},{"key":"683_CR55","doi-asserted-by":"publisher","first-page":"1290","DOI":"10.1038\/nprot.2011.308","volume":"6","author":"J Schellenberger","year":"2011","unstructured":"Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox v2. 0. Nat Protoc. 2011;6:1290\u2013307.","journal-title":"Nat Protoc"},{"key":"683_CR56","volume-title":"Discovery, biosynthesis and evolutionary history of sioxanthin, a novel glycosylated carotenoid from marine bacteria Salinispora","author":"TKS Richter","year":"2014","unstructured":"Richter TKS. Discovery, biosynthesis and evolutionary history of sioxanthin, a novel glycosylated carotenoid from marine bacteria Salinispora. San Diego: University of California; 2014."},{"key":"683_CR57","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1007\/s00253-008-1614-z","volume":"80","author":"G Tsueng","year":"2008","unstructured":"Tsueng G, Lam KS. Growth of Salinispora tropica strains CNB440, CNB476, and NPS21184 in nonsaline, low-sodium media. Appl Microbiol Biotechnol. 2008;80:873\u201380.","journal-title":"Appl Microbiol Biotechnol"},{"key":"683_CR58","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1101\/gr.3364705","volume":"15","author":"I Borodina","year":"2005","unstructured":"Borodina I, Krabben P, Nielsen J. Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res. 2005;15:820\u20139.","journal-title":"Genome Res"},{"key":"683_CR59","doi-asserted-by":"publisher","first-page":"4156","DOI":"10.1016\/j.tet.2014.03.009","volume":"70","author":"JE Janso","year":"2014","unstructured":"Janso JE, Haltli BA, Eust\u00e1quio AS, Kulowski K, Waldman AJ, Zha L, et al. Discovery of the lomaiviticin biosynthetic gene cluster in Salinispora pacifica. Tetrahedron. 2014;70:4156\u201364.","journal-title":"Tetrahedron"},{"key":"683_CR60","doi-asserted-by":"publisher","first-page":"7674","DOI":"10.1038\/ncomms8674","volume":"6","author":"B Wang","year":"2015","unstructured":"Wang B, Guo F, Ren J, Ai G, Aigle B, Fan K, et al. Identification of Alp1U and Lom6 as epoxy hydrolases and implications for kinamycin and lomaiviticin biosynthesis. Nat Commun. 2015;6:7674.","journal-title":"Nat Commun"},{"key":"683_CR61","doi-asserted-by":"publisher","unstructured":"Mill\u00e1n-Agui\u00f1aga N, Chavarria KL, Ugalde JA, Letzel A-C, Rouse GW, Jensen PR. Phylogenomic insight into Salinispora (Bacteria, Actinobacteria) species designations. Sci Rep. 2017;7:3564. Available from: https:\/\/doi.org\/10.1038\/s41598-017-02845-3","DOI":"10.1038\/s41598-017-02845-3"},{"key":"683_CR62","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1016\/j.ymben.2003.09.002","volume":"5","author":"R Mahadevan","year":"2003","unstructured":"Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng. 2003;5:264\u201376.","journal-title":"Metab Eng"},{"key":"683_CR63","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1007\/s11306-014-0721-3","volume":"11","author":"MK Aurich","year":"2015","unstructured":"Aurich MK, Paglia G, Rolfsson O, Hrafnsd\u00f3ttir S, Magn\u00fasd\u00f3ttir M, Stefaniak MM, et al. Prediction of intracellular metabolic states from extracellular metabolomic data. Metabolomics. 2015;11:603\u201319.","journal-title":"Metabolomics"},{"key":"683_CR64","doi-asserted-by":"publisher","first-page":"11273","DOI":"10.1021\/ja992482o","volume":"121","author":"MK Renner","year":"1999","unstructured":"Renner MK, Shen Y-C, Cheng X-C, Jensen PR, Frankmoelle W, Kauffman CA, et al. Cyclomarins A-C, New Antiinflammatory Cyclic Peptides Produced by a Marine Bacterium ( Streptomyces sp.). J Am Chem Soc. 1999;121:11273\u20136.","journal-title":"J Am Chem Soc"},{"key":"683_CR65","doi-asserted-by":"publisher","first-page":"1246","DOI":"10.1101\/gr.186501","volume":"11","author":"BR Bochner","year":"2001","unstructured":"Bochner BR. Phenotype MicroArrays for high-throughput phenotypic testing and assay of gene function. Genome Res. 2001;11:1246\u201355.","journal-title":"Genome Res"},{"key":"683_CR66","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1111\/j.1574-6976.2008.00149.x","volume":"33","author":"BR Bochner","year":"2009","unstructured":"Bochner BR. Global phenotypic characterization of bacteria. FEMS Microbiol Rev. 2009;33:191\u2013205.","journal-title":"FEMS Microbiol Rev"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-019-0683-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12918-019-0683-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-019-0683-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,13]],"date-time":"2023-09-13T02:36:58Z","timestamp":1694572618000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-019-0683-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,21]]},"references-count":66,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["683"],"URL":"https:\/\/doi.org\/10.1186\/s12918-019-0683-1","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,1,21]]},"assertion":[{"value":"22 December 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 January 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 January 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"11"}}