MediaDive: the expert-curated cultivation media database

Abstract

We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instructions and molecular compositions of >3200 standardized cultivation media for >40 000 microbial strains from all domains of life. MediaDive is designed to enable broad range applications from every-day-use in research and diagnostic laboratories to knowledge-driven support of new media design and artificial intelligence-driven data mining. It offers a number of intuitive search functions and comparison tools, for example to identify media for related taxonomic groups and to integrate strain-specific modifications. Besides classical PDF archiving and printing, the state-of-the-art website allows paperless use of media recipes on mobile devices for convenient wet-lab use. In addition, data can be retrieved using a RESTful web service for large-scale data analyses. An internal editor interface ensures continuous extension and curation of media by cultivation experts from the Leibniz Institute DSMZ, which is interlinked with the growing microbial collections at DSMZ. External user engagement is covered by a dedicated media builder tool. The standardized and programmatically accessible data will foster new approaches for the design of cultivation media to target the vast majority of uncultured microorganisms.

Figure 1.

Example showing the medium viewer page for DSMZ medium 1634. (A) The medium toolbar, (B) unique number and name of the medium, (C) the recipe can be modified by selecting a strain or changing the volume, (D) the main solution recipe; all other solutions can be found on the page below, (E) a summary of all the important metadata, (F) a QR-code to move seamlessly to mobile devices, (G) the final gas composition for cultivation, (H) an overview on all associated strains with links to detail pages, (I) the final concentrations of all ingredients in the medium.

Figure 2.

Showcase screenshot of the medium finder. Different search criteria are applied for (A) the presence of compounds with defined concentrations, (B) for the absence of compounds, (C) a defined gas phase, (D) the presence of certain solutions. (E) More search criteria can be added. (F) The search parameters are summarized. (G) All found media are shown in detail and matching search conditions are highlighted.

Figure 3.

Screenshot of the medium builder. The name of the cultivation medium (A) can be defined in the toolbar at the top of the page, as well as various actions, such as saving the medium to the database, which will generate a unique key phrase (B). The key phrase can in turn be used to load and edit the medium. The recipe editor (C) is used to modify the recipe by adding compounds, solutions, steps, and equipment. Metadata include the authors of the cultivation medium (D), the medium metadata (E), strains that are known to grow on the medium (F) and the final gas composition (not shown). The shown cultivation medium was taken as a use case (20) and published under the medium number P1.