BacDive: The core database for prokaryotic strain data

Since its initial release more than a decade ago, the bacterial diversity database BacDive (https://bacdive.dsmz.de) has grown tremendously in terms of content and functionality. Today, BacDive is a comprehensive resource covering the phenotypic diversity of prokaryotes with data on taxonomy, morphology, physiology, cultivation, and more. As the leading database for strain-level information on bacteria and archaea, it has been designated as an ELIXIR Core Data Resource and a Global Core Biodata Resource. These distinctions underscore its importance to the wider microbiological research community. As part of the newly established DSMZ Digital Diversity infrastructure, BacDive is now closely linked to several other databases of fundamental importance to the life sciences, including BRENDA, LPSN and SILVA. These databases will be further developed in a coordinated manner and benefit from frequent data exchange.

Here we present the current status and recent developments in BacDive. The database currently contains 2.6 million data points for 97,334 strains. This includes the world's largest collection of Analytical Profile Index (API) test results, which have now been fully translated into easily understandable and searchable data fields. Increasingly, the standardized high-quality data provided by BacDive is being used to train artificial intelligence models. The high-confidence genome-based predictions produced by our own models are now also being used to fill content gaps in the database. We further present a novel BacDive knowledge graph that provides powerful new search capabilities via a SPARQL endpoint to directly search and analyze the knowledge provided through BacDive in a standardized way, supported by a new descriptive ontology.