Article (Scientific journals)
MediaDB: A Database of Microbial Growth Conditions in Defined Media
Richards, Matthew A.; Cassen, Victor; Heavner, Benjamin D. et al.
2014In PLoS ONE, 9 (8), p. 103548
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Abstract :
[en] 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.
Research center :
Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group)
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Richards, Matthew A.
Cassen, Victor
Heavner, Benjamin D.
Ajami, Nassim E.
HerrMann, Andrea
Simeonidis, Vangelis ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Price, Nathan D.
External co-authors :
yes
Language :
English
Title :
MediaDB: A Database of Microbial Growth Conditions in Defined Media
Publication date :
06 August 2014
Journal title :
PLoS ONE
ISSN :
1932-6203
Publisher :
Public Library of Science, San Franscisco, United States - California
Volume :
9
Issue :
8
Pages :
e103548
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 07 August 2014

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