Bac''Dive'' (The Bacterial Diversity Database) is the worldwide largest
database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...
for standardized
bacterial and
archaeal strain-level information.
Bac''Dive'' is a comprehensive resource containing diverse data on
bacterial and
archaeal strains, including taxonomy, morphology, physiology, sampling and environmental data and sequence information.
The database is built on a base of curated data from culture collections. In 2025 Bac''Dive'' contains information on 99,392 strains, including 21,168 type strains.
The database is hosted by the
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH and is part of the integrated DSMZ Digital Diversity infrastructure. Bac''Dive'' is a member of
de.NBI - the German Network for Bioinformatics Infrastructure, as well as
ELIXIR
An elixir is a sweet liquid used for medical purposes, to be taken orally and intended to cure one's illness. When used as a dosage form, pharmaceutical preparation, an elixir contains at least one active ingredient designed to be taken orall ...
. The
Global Biodata Coalition designated Bac''Dive'' a Global Core Biodata Resource (GCBR) in 2022. In 2023, Bac''Dive'' was additionally named as an
ELIXIR
An elixir is a sweet liquid used for medical purposes, to be taken orally and intended to cure one's illness. When used as a dosage form, pharmaceutical preparation, an elixir contains at least one active ingredient designed to be taken orall ...
Core Data Resource.
Database content
Bac''Dive'' was initially released in April 2012 to standardize and make publicly available strain data of culture collections, other compendia, and publications. The first release, contained 89,758 entries for 18,157 strains and 179 different used data fields.
Today (as of December 2024), the database encompassed over 1000 different data fields. The database now comprises 2,709,516 entries for 99,392 strains. Each entry is linked to a reference. Data for each strain is divided into the categories "Name and taxonomic classification", "Morphology", "Culture and growth conditions, "Physiology and metabolism", "Isolation, sampling and environmental information." "Safety information", "Sequence information".
Since 2023 high-quality predicted data produced using machine learning models trained on curated ''BacDive'' data can be found in an additional section titled "Genome-based predictions".
Data access
Data can be accessed either via a
GUI, via the RESTful
web service
A web service (WS) is either:
* a service offered by an electronic device to another electronic device, communicating with each other via the Internet, or
* a server running on a computer device, listening for requests at a particular port over a n ...
., or via a
SPARQL endpoint.
The GUI offers a simple search featuring auto-completion for searching strains by name, culture collection number, NCBI Tax ID or INSDC sequence accession number. Additionally, the user can use the advanced search, which enables the search in 130 data fields and gives the opportunity of complex queries by combining several fields. Data can be downloaded in
CSV format for one or multiple strains.
Via th
RESTful web service portalBac''Dive'' content can be accessed automatically (a free registration is needed). To support the use of the API
software clientsin Python and R are available.
Other databases
For data that are outside the focus of Bac''Dive'', links to other databases are provided.
Other databases within the DSMZ Digital Diversity infrastructure:
*
BRENDA
*
List of Prokaryotic names with Standing in Nomenclature
List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclatu ...
Media''Dive''*
SILVA StraininfoPhage''Dive''
External databases:
* EBI
* ChEBI
* NCBI
MicrobeAtlas
References
External links
Simple search at Bac''Dive''Advanced search at Bac''Dive''Web services at Bac''Dive''
{{Webarchive, url=https://web.archive.org/web/20160917104006/http://bacdive.dsmz.de/api/ , date=2016-09-17
Metadata
Biological databases
Biodiversity databases
Online databases