Microbial strain data

Microbial strains in culture collections

Here, we define a microbial strain as all clones derived from a pure isolate, sharing identical phenotypic characteristics and a 99,99% genomic identity. To preserve and distribute important microbial strains, they are deposited in culture collections that provide access for researchers and industry. An instance of a strain at a culture collection is called deposit and gets a unique identification number, also known as culture collection number (CCNo). According to the WDCM, there are more than 800 culture collections world wide, with a combined number of more than 4 million microbial deposits.

Standardized microbial data

In a lot of cases culture collections provide an online catalogue of their available strains (e.g. DSMZ, CECT, Westerdijk Institute). The information about the strains in these catalogues are often lacking deeper biological knowledge, even if this knowledge is available at the collection. Another issue is that all of these collections hold their data in different formats. Approaches in the past like MCL, CABRI, MINE and ISO 21710, were either focused only on a minimal set of information to resolve the identity of a strain, failed to find widespread application due to limited IT resources in the respective collections or they have not been maintained and therefore are insufficient for modern requirements. In consequence, the access to as well as the exchange of microbial strain data is laborious and prevents the effective utilization of a gigantic number of important resources for the research community and for the bioindustrial use.

What is the goal of the new standard?

The EU project Bioindustry 4.0 brings together experts from multiple culture collections, research infrastructures and microbial databases to improve the access to microbial strain data. The new standard will be the keystone to build a new unified Strain Discovery Database to search for strains by their biological traits independently from the culture collections catalogues that provide the strains. To reach this goal we define a technical standard format covering all data fields to hold, share and compare the strain data from different sources. Starting with the integration of data from DSMZ, CECT and the Westerdijk Institute, the open concept of the system will not only enable the distribution of the data, but also the contribution of data by other collections.

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