BacDive

Overview

BacDive (Bacterial Diversity Metadatabase) is the world’s largest and most comprehensive database for standardized bacterial information at the strain level. Maintained by the Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures), BacDive mobilizes and integrates research data from diverse sources to make bacterial diversity information freely accessible to the scientific community.

Key Features

• Comprehensive Coverage: Over 99,000 bacterial strains with 21,168 type strains
• Standardized Information: Morphology, physiology, growth conditions, isolation sources, and genomic data
• Global Core Biodata Resource: Recognized as both an ELIXIR Core Data Resource and Global Core Biodata Resource
• Digital Object Identifiers: All strain data are referenced by DOIs for permanent citability
• Open Access: Freely available under Creative Commons Attribution 4.0 International License

Data Content

BacDive provides comprehensive information across multiple categories:

Morphological Traits

• Cell shape, size, and arrangement
• Gram staining properties
• Motility characteristics
• Colony-forming properties

Physiological Traits

• Oxygen tolerance (aerobe, anaerobe, facultative)
• Temperature optima and ranges
• pH preferences
• Metabolic capabilities
• Chemotaxonomy

Growth Conditions

• Culture media requirements
• Temperature ranges
• Oxygen requirements
• Special growth conditions

Isolation and Sampling

• Geographic origin
• Isolation sources
• Environmental context
• Collection information

Molecular Data

• GC content
• Genome sequences
• 16S rRNA sequences
• Taxonomic classification

Access Methods

• Web Interface: Interactive browsing and search at https://bacdive.dsmz.de/
• Advanced Search: Filtering by multiple parameters
• TAXplorer: Taxonomic exploration tool
• API: RESTful web services at https://api.bacdive.dsmz.de/
• API Test Finder: Tool for testing API queries

Special Collections

BacDive provides statistics and focused access to:

• Well-known culture collections
• Specific bacterial groups
• Type strain collections
• Isolation source compilations

Applications

• Comparative microbiology and taxonomy
• Selection of reference strains for research
• Culture optimization and strain characterization
• Ecological and environmental studies
• Systems biology and knowledge graph integration
• Biotechnology and industrial applications

Integration

BacDive data is integrated into multiple knowledge graphs and resources:

• KG-Microbe (microbial knowledge graphs)
• NCBITaxon (taxonomic classifications)
• Environmental ontologies
• Genomic databases

Support and Funding

BacDive is supported by:

• de.NBI (German Network for Bioinformatics Infrastructure)
• ELIXIR Europe
• DZIF (German Center for Infection Research)
• NFDI4Biodiversity
• NFDI4Microbiota

Citation

When using BacDive, please cite the database and relevant publications. Each strain entry includes a DOI for permanent citation.

For more information, visit https://bacdive.dsmz.de/