title: MediaDB: a database of microbial growth conditions in defined media.
abstract: Isolating pure microbial cultures and cultivating them in the laboratory on defined media is used to more fully characterize the metabolism and physiology of organisms. However, identifying an appropriate growth medium for a novel isolate remains a challenging task. Even organisms with sequenced and annotated genomes can be difficult to grow, despite our ability to build genome-scale metabolic networks that connect genomic data with metabolic function. The scientific literature is scattered with information about defined growth media used successfully for cultivating a wide variety of organisms, but to date there exists no centralized repository to inform efforts to cultivate less characterized organisms by bridging the gap between genomic data and compound composition for growth media. Here we present MediaDB, a manually curated database of defined media that have been used for cultivating organisms with sequenced genomes, with an emphasis on organisms with metabolic network models. The database is accessible online, can be queried by keyword searches or downloaded in its entirety, and can generate exportable individual media formulation files. The data assembled in MediaDB facilitate comparative studies of organism growth media, serve as a starting point for formulating novel growth media, and contribute to formulating media for in silico investigation of metabolic networks. MediaDB is freely available for public use at https://mediadb.systemsbiology.net.
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America; Institute for Systems Biology, Seattle, Washington, United States of America.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Richards
authors.affiliation: Institute for Systems Biology, Seattle, Washington, United States of America.
authors.forename: Victor
authors.initials: V
authors.lastname: Cassen
authors.affiliation: Institute for Systems Biology, Seattle, Washington, United States of America.
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Heavner
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Nassim E
authors.initials: NE
authors.lastname: Ajami
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Andrea
authors.initials: A
authors.lastname: Herrmann
authors.affiliation: Institute for Systems Biology, Seattle, Washington, United States of America; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
authors.forename: Evangelos
authors.initials: E
authors.lastname: Simeonidis
authors.affiliation: Institute for Systems Biology, Seattle, Washington, United States of America.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Price
mesh_terms: D001105:Archaea / Q000235:genetics / Q000254:growth & development*; D001419:Bacteria / Q000235:genetics / Q000254:growth & development*; D001483:Base Sequence; D003470:Culture Media / Q000737:chemistry*; D016208:Databases, Factual; D005057:Eukaryotic Cells / Q000502:physiology; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data
chemical_list: D003470:Culture Media
references.citation: Mar Biotechnol (NY). 2006 May-Jun;8(3):227-37
references.pmid: 16763938
references.citation: Appl Environ Microbiol. 2005 Feb;71(2):826-34
references.pmid: 15691937
references.citation: Appl Microbiol Biotechnol. 2013 Jan;97(1):51-62
references.pmid: 23138712
references.citation: Science. 2002 May 10;296(5570):1127-9
references.pmid: 12004133
references.citation: FEMS Microbiol Lett. 2010 Aug 1;309(1):1-7
references.pmid: 20487025
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D456-63
references.pmid: 23180789
references.citation: Microb Biotechnol. 2010 Sep;3(5):564-75
references.pmid: 21255353
references.citation: Environ Microbiol. 2002 Nov;4(11):654-66
references.pmid: 12460273
references.citation: Appl Environ Microbiol. 2007 Oct;73(20):6386-90
references.pmid: 17720826
references.citation: Nucleic Acids Res. 1999 Jan 1;27(1):29-34
references.pmid: 9847135
references.citation: Biotechnol Bioeng. 2003 Dec 30;84(7):763-72
references.pmid: 14708117
references.citation: Appl Environ Microbiol. 2005 Dec;71(12):8714-20
references.pmid: 16332866
references.citation: Nucleic Acids Res. 2005 Oct 07;33(17):5691-702
references.pmid: 16214803
references.citation: Appl Environ Microbiol. 1997 Apr;63(4):1382-8
references.pmid: 9097435
references.citation: Nat Rev Microbiol. 2009 Feb;7(2):129-43
references.pmid: 19116616
references.citation: Methods Enzymol. 2005;397:124-30
references.pmid: 16260288
references.citation: Appl Environ Microbiol. 2003 Apr;69(4):1980-9
references.pmid: 12676673
references.citation: Nat Rev Microbiol. 2004 Nov;2(11):886-97
references.pmid: 15494745
references.citation: Nat Protoc. 2010 Jan;5(1):93-121
references.pmid: 20057383
references.citation: Appl Environ Microbiol. 2002 May;68(5):2391-6
references.pmid: 11976113
references.citation: ISME J. 2013 Mar;7(3):592-602
references.pmid: 23096402
references.citation: Extremophiles. 2009 Jul;13(4):583-94
references.pmid: 19548063
references.citation: Appl Environ Microbiol. 1993 Mar;59(3):881-91
references.pmid: 16348896
references.citation: Appl Environ Microbiol. 2002 Aug;68(8):3878-85
references.pmid: 12147485
references.citation: Chem Biol. 2010 Mar 26;17(3):254-64
references.pmid: 20338517
references.citation: Environ Microbiol. 2008 Aug;10(8):2030-41
references.pmid: 18422642
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
references.pmid: 23193283
references.citation: Appl Environ Microbiol. 2005 Dec;71(12):8402-10
references.pmid: 16332828
references.citation: Appl Environ Microbiol. 2004 Aug;70(8):4748-55
references.pmid: 15294811
references.citation: Syst Appl Microbiol. 2000 Apr;23(1):1-8
references.pmid: 10879972
references.citation: Trends Biotechnol. 2012 Sep;30(9):475-84
references.pmid: 22770837
references.citation: Appl Microbiol Biotechnol. 2008 May;79(2):263-72
references.pmid: 18379780
references.citation: Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15681-6
references.pmid: 12438682
references.citation: Proteins. 1998 Jul 1;32(1):1-2
references.pmid: 9672036
references.citation: Appl Environ Microbiol. 2008 Aug;74(15):4889-97
references.pmid: 18515474
references.citation: Nat Biotechnol. 2010 Sep;28(9):977-82
references.pmid: 20802497
references.citation: Nat Rev Microbiol. 2004 Feb;2(2):141-50
references.pmid: 15040261
references.citation: Curr Opin Biotechnol. 2003 Oct;14(5):491-6
references.pmid: 14580578
references.citation: Nature. 2002 Aug 8;418(6898):630-3
references.pmid: 12167859
references.citation: Genome Biol. 2003;4(9):R54
references.pmid: 12952533
references.citation: BMC Bioinformatics. 2010 Apr 29;11:213
references.pmid: 20426874
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: Appl Environ Microbiol. 2002 Aug;68(8):3978-87
references.pmid: 12147499
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W17-22
references.pmid: 19454601
references.citation: Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18217-22
references.pmid: 17989237
references.citation: J Bacteriol. 2012 Feb;194(4):855-65
references.pmid: 22139506