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.

Figure 1. Simplified database schema.

This graph shows the connections between the 6 main tables, Organisms, Compounds, Media_Names, Biomass, Sources, and Growth_Data. Also shown are Media_Compounds and Biomass_Compounds, linking tables that connect the Compounds table to the Media_Names and Biomass tables, respectively. Arrows indicate foreign key relationships, in which the head of the arrow points to the primary key being referenced. A full map of the MediaDB schema containing all tables and their connections can be found in Figure S1.

Figure 2. The MediaDB website.

The database can be found at https://mediadb.systemsbiology.net. This page shows the composition of a media formulation and displays links to the organism, source, and growth record that use this medium. The “Site Navigation” panel lists the different tables that can be browsed manually and also the “Downloads” tab, where the user can export a copy of the entire MediaDB schema. The search field is at the top right of the page.

Figure 3. Heat map and dendrogram showing hierarchical clustering of species based on media compositions.

Red bars indicate compounds that occur in at least one medium for that species. Black bars indicate compounds that do not appear in any media for that species. This figure was generated using the Statistics Toolbox in Matlab.

Figure 4. Phylogenetic tree of 16S rRNA sequences for species in MediaDB.

Phylogeny was inferred from a CLUSTAL W alignment generated in the Biology Workbench using 16S rRNA sequences from the SILVA database.