BacDive in 2025: the core database for prokaryotic strain data

• Isabel Schober
• Julia Koblitz
• Joaquim Sardà Carbasse
• Christian Ebeling
• Marvin Leon Schmidt
• Adam Podstawka
• Rohit Gupta
• Vinodh Ilangovan
• Javad Chamanara
• Jörg Overmann
• Lorenz Christian Reimer

Departments

Microbial Ecology and Diversity Bioinformatics, IT & Databases

Abstract

In 2025, the bacterial diversity database BacDive is the leading database for strain-level bacterial and archaeal information. It has been selected as an ELIXIR Core Data Resource as well as a Global Core Biodata Resource. Since its initial release more than ten years ago, BacDive (https://bacdive.dsmz.de) has grown tremendously in content and functionalities, and is a comprehensive resource covering the phenotypic diversity of prokaryotes with data on taxonomy, morphology, physiology, cultivation, and more. The current release (2023.2) contains 2.6 million data points on 97 334 strains, reflecting an increase by 52% since the previous publication in 2021. This remarkable growth can largely be attributed to the integration of the world-wide largest collection of Analytical Profile Index (API) test results, which are now fully integrated into the database and searchable. A novel BacDive knowledge graph provides powerful search options through a SPARQL endpoint, including the possibility for federated searches across multiple data sources. The high-quality data provided by BacDive is increasingly being used for the training of artificial intelligence models and resulting genome-based predictions with high confidence are now used to fill content gaps in the database.

• DOI: 10.1093/nar/gkae959
• PubMed: 1234556

Associated Projects

Cite this activity

@article{Schober2025,
  Title = {BacDive in 2025: the core database for prokaryotic strain data},
  Author = {Schober, Isabel and Koblitz, Julia and Sardà Carbasse, Joaquim and Ebeling, Christian and Schmidt, Marvin Leon and Podstawka, Adam and Gupta, Rohit and Ilangovan, Vinodh and Chamanara, Javad and Overmann, Jörg and Reimer, Lorenz Christian},
  Editor = {},
  Journal = {Nucleic acids research},
  Year = {2025},
  Pages = {D748–D756},
  Volume = {53},
  Doi = {10.1093/nar/gkae959},
  Abstract = {In 2025, the bacterial diversity database BacDive is the leading database for strain-level bacterial and archaeal information. It has been selected as an ELIXIR Core Data Resource as well as a Global Core Biodata Resource. Since its initial release more than ten years ago, BacDive (https://bacdive.dsmz.de) has grown tremendously in content and functionalities, and is a comprehensive resource covering the phenotypic diversity of prokaryotes with data on taxonomy, morphology, physiology, cultivation, and more. The current release (2023.2) contains 2.6 million data points on 97 334 strains, reflecting an increase by 52% since the previous publication in 2021. This remarkable growth can largely be attributed to the integration of the world-wide largest collection of Analytical Profile Index (API) test results, which are now fully integrated into the database and searchable. A novel BacDive knowledge graph provides powerful search options through a SPARQL endpoint, including the possibility for federated searches across multiple data sources. The high-quality data provided by BacDive is increasingly being used for the training of artificial intelligence models and resulting genome-based predictions with high confidence are now used to fill content gaps in the database.},
}

TY  - JOUR
AU  - Schober, Isabel
AU  - Koblitz, Julia
AU  - Sardà Carbasse, Joaquim
AU  - Ebeling, Christian
AU  - Schmidt, Marvin Leon
AU  - Podstawka, Adam
AU  - Gupta, Rohit
AU  - Ilangovan, Vinodh
AU  - Chamanara, Javad
AU  - Overmann, Jörg
AU  - Reimer, Lorenz Christian
TI  - BacDive in 2025: the core database for prokaryotic strain data
T2  - Nucleic acids research
PY  - 2025
SP  - D748–D756
VL  - 53
DO  - 10.1093/nar/gkae959
AB  - In 2025, the bacterial diversity database BacDive is the leading database for strain-level bacterial and archaeal information. It has been selected as an ELIXIR Core Data Resource as well as a Global Core Biodata Resource. Since its initial release more than ten years ago, BacDive (https://bacdive.dsmz.de) has grown tremendously in content and functionalities, and is a comprehensive resource covering the phenotypic diversity of prokaryotes with data on taxonomy, morphology, physiology, cultivation, and more. The current release (2023.2) contains 2.6 million data points on 97 334 strains, reflecting an increase by 52% since the previous publication in 2021. This remarkable growth can largely be attributed to the integration of the world-wide largest collection of Analytical Profile Index (API) test results, which are now fully integrated into the database and searchable. A novel BacDive knowledge graph provides powerful search options through a SPARQL endpoint, including the possibility for federated searches across multiple data sources. The high-quality data provided by BacDive is increasingly being used for the training of artificial intelligence models and resulting genome-based predictions with high confidence are now used to fill content gaps in the database.
ER  - 

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