Microbial strain data

Microbial strains and culture collections

When a scientist isolates a microorganism (e.g. Bacteria, Yeast, ...) the isolate and all clones of it is called from now on a strain. If the strain can be deposited at culture collections. Culture collections are BRC's (Biological resource centers) and the collections provide access to the biological resources (the microbial strains) for researchers and/or industry. Every culture collection gives each strain in their collection a unique identification number (aka culture collection number (CCNo)).

Number of microbial strains

There are more than 800 culture collections world wide according to WDCM, with a combined number of more than 4 million microbial cultures. A culture is a strain at a culture collection. The combined number of microbial strains is unknown because one strain can be deposited in multiple culture collections and there is no complete matching of the microbial resources of all culture collections. StrainInfo is trying to provide an overview on which culture belongs to which strain. There is also BacDive, the largest database for standardized bacterial information, that accumulates cultures and associated biological knowledge to strains.

Standardized microbial data

In a lot of cases culture collection provide an online catalogue of their available strains (e.g. DSMZ, CECT, CBS (Westerdijk Institute), CCUG). The information 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 collection do hold their data in different formats. There is no overarching standardization of microbial strain data in use, even if there have been attempts to introduce standards to microbial strain data (MCL, CABRI, MINE, ...)

Why now a new standard?

The EU project Bioindustry 4.0 brings together experts from multiple culture collections, research infrastructures and microbial databases. The goal is to implement a new strain discovery database that integrates the data from the DSMZ and their database BacDive, from the CECT and the MIRRI consortium, as well as from the Westerdijk Institute and their collections of fungi (CBS) and bacteria (NCCB).