Online Laboratory Magazine


Unlimited access to microbiological research data

The scientists Dr. Lorenz Reimer, Joaquim Sardà and Prof. Dr. Jörg Overmann from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures have extended the database BacDive extensively with the update in April 2019.

Since 2012, the bioinformaticians of the DSMZ have been developing BacDive (the Bacterial Diversity Metadatabase), a database that is unique in the world and makes data on bacteria and archaea that are not yet available freely accessible. The development follows the FAIR principles, according to which scientific data should be findable, accessible, interoperable and re-usable.

More than 600 data fields available

The possibilities of using BacDive are continuously being expanded, currently scientists can use more than 600 data fields to search for microbiological information. The repertoire includes initial species descriptions and metabolic profiles as well as data on enzymatic activities and antibiotic resistance. In addition, BacDive offers 9,000 Analytical Profile Tests (API) for over 5,000 bacterial strains, the largest publicly available API data collection worldwide.

External Data Integration and Interoperability

In order to provide the scientific community with a comprehensive database, the DSMZ scientists also continuously maintain the microbiological metadata of other European collections in BacDive. With the current update, DSMZ integrated data from more than 19,505 bacterial strains from the Swedish Culture Collection University of Gothenburg (CCUG). BacDive thus provides up-to-date information on 80,584 bacteria and archaea. For scientific work with cross-source data sets, the various information sources must be linked as directly as possible via unique identifiers.

For example, direct links to the 16S rRNA sequence of a bacterial strain in the database SILVA or to the enzymes involved in metabolic reactions in the database BRENDA have been established. Via links in PubMed, NCBI Taxonomy, NCBI Nucleotide, but also in species descriptions of Wikipedia, users can access the structured metadata in BacDive.

» BacDive

Source: Leibniz Institute - German Collection of Microorganisms and Cell Cultures GmbH