Speaking the same language: Changing the way to share microbial strain data

Researchers worldwide are working with millions of microbial strains, with about 530.000 strains registered in the Global Catalogue of Microorganisms (gcm.wdcm.org). The data on these microorganisms is exchanged in different, largely unstructured ways. This hinders comparative analyses and synthesis of data. To facilitate data sharing and contribute to more open and FAIR data, we developed and applied a new common data format and established a technical infrastructure for exchanging microbial strain data in a systematic approach.

While there have been several attempts in the past to establish standards suitable for the exchange of microbial data, these were limited to just basic strain data for identification and growth conditions and also lacked a technical concept for making this standard accessible and effectively usable for the wider microbial research community. Here we present a new approach, that aims to establish a modular standard gradually integrating various data. The data that now can be accommodated by this standard include basic growth conditions and detailed information about the metabolism and even kinetic growth parameters of microbial strains.

The key to effectively establishing the standard as a common basis for data exchange, is to create a technical infrastructure to share these data. Customizable tools for data export and import will be developed, to simplify data transfer. Two of the largest microbial strain databases, the bacterial diversity database BacDive (bacdive.dsmz.de) and the MIRRI-IS, the microbial resource research infrastructure MIRRI database (mirri.org), have joined forces to develop a new open system that makes use of this new format and enables data contributions by researchers. The format will be developed by experts from DSMZ and MIRRI within the Bioindustry 4.0 Project (Grant agreement ID: 101094287). The data about the ~250.000 microbial strains provided by the partners, will be made available in this new data standard to enable industrial exploitation of microbial biodiversity. Beyond the project, a permanent governance structure will be established to keep the new standard flexible and up to date.