StrainInfo – A central database for resolving microbial strain identifiers

Poster presented at VAAM 2023.

StrainInfo – A central database for resolving microbial strain identifiers

Microbial strains can be known by a myriad of different strain designations, culture collection numbers and sequence accessions, which poses a challenge to the communication of research findings, as well as the comparison and reuse of data. Culture collection numbers, like DSM 5522 or ATCC 43876 are the most commonly used strain identifiers for microorganisms. They have the advantage of being unique, stable and subject to the high quality standards of culture collections. Nevertheless, each collection receiving a culture of the same strain assigns their own number at deposition. Different designations are thus used throughout publications and databases, making it difficult for scientists to draw connections between them.

Here we present the StrainInfo database, a service that collects and curates culture collection numbers as well as their relations and links them with different sources of information, such as publications and sequence accession numbers. This facilitates the connecting of data describing the same strain. The database builds on the idea of the defunct StrainInfo.net web services, which were developed at the LMG (Ghent University) between 2000 and 2015. It uses archived data and functionalities from the original database combined with newly collected data and additional features. The information is provided through a modern and intuitive web user interface, which enables users to easily find corresponding strain identifiers and links to associated data, and through a web API, that allows for direct integration of strain identity resolution into workflows and other databases.

In the future, StrainInfo additionally aims to provide a central registry service for cultures, allowing microbiologists to register strain designations and receive persistent identifiers prior to deposition and publication.