BacDive

BacDive (the Bacterial Diversity Metadatabase) is a

bacterial metadatabase that provides strain-linked
BacDive
information about bacterial and archaeal biodiversity.

Introduction
BacDive is a resource for different kind of metadata
like taxonomy, morphology, physiology, environment
and molecular-biology. [1][2][3][4][5][6][7][8] The
majority of data is manually annotated and curated.
With the release in December 2022 BacDive offers Content
information for 93,254 strains, including 19,313 type Description information about bacterial
strains. The database is hosted by the Leibniz Institute and archaeal strains
DSMZ - German Collection of Microorganisms and
Cell Cultures GmbH and is part of de.NBI (https://ww Data types metadata
w.denbi.de/) the German Network for Bioinformatics captured
Infrastructure, as well as Elixir (https://elixir-europe.or Contact
g/) the European Network for Bioinformatics. In
Research center Leibniz Institute DSMZ -
December 2022 BacDive was selected by the Global
German Collection of
Biodata Coalition (https://globalbiodata.org/) as a
Global Core Biodata Resource (GCBR). GCBRs are Microorganisms and Cell
considered critical data resources for the global Cultures GmbH
research endeavour in life sciences and biomedicine. Primary citation PMID 34718743 (https://pu
bmed.ncbi.nlm.nih.gov/347
Content and Features 18743)
Release date 2012
Access
Database
Website http://bacdive.dsmz.de/
The December release of the database encompassed Web service URL https://api.bacdive.dsmz.de/
over 1000 different data fields, 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" and "Strain availability". The database comprised 1,922,166 entries,
linked to the according strain and reference.[9] The data are retrieved from internal descriptions of culture
collections, expert-compiled compendia and primary scientific literature like species descriptions.

Data access

Data can be accessed either via a GUI or via the RESTful web service. Using the GUI the user can choose
between a simple search for searching strains by name, Culture collection number, NCBI Tax ID or
INSDC sequence accession number, or 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 PDF format (for single strains) or in CSV format for larger data sets (for multiple strains).
Via the RESTful web service portal (https://api.bacdive.dsmz.de/) BacDive content can be accessed
automaticly (a free registration is needed).To support the use of the API, software clients (https://api.bacdiv
e.dsmz.de/client_examples) in Python and R are available.

Other databases
For data that are outside the focus of BacDive, links to other databases are provided that deliver strain-
associated data:

SILVA
BRENDA
List of Prokaryotic names with Standing in Nomenclature
Straininfo.net (https://web.archive.org/web/20070702072654/http://www.straininfo.net/)
EBI
NCBI
MicrobeAtlas (https://microbeatlas.org/)

References
1. Söhngen, C; Boyke, B; Podstawka, A; Gleim, D; Overmann, J (October 13, 2013). "BacDive -
The Bacterial Diversity Metadatabase" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965
005). Nucleic Acids Research. 42 (Database issue): D592–D599. doi:10.1093/nar/gkt1058
(https://doi.org/10.1093%2Fnar%2Fgkt1058). PMC 3965005 (https://www.ncbi.nlm.nih.gov/p
mc/articles/PMC3965005). PMID 24214959 (https://pubmed.ncbi.nlm.nih.gov/24214959).
2. Fernández-Suárez, X. M.; Rigden, D. J.; Galperin, M. Y. (December 5, 2013). "The 2014
Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology
Database Collection" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965027). Nucleic
Acids Research. 42 (Database issue): D1–D6. doi:10.1093/nar/gkt1282 (https://doi.org/10.10
93%2Fnar%2Fgkt1282). PMC 3965027 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC396
5027). PMID 24316579 (https://pubmed.ncbi.nlm.nih.gov/24316579).
3. Cohan lab (October 23, 2015). "DSMZ's BacDive Bacterial Diversity Database" (http://cohan
lab.research.wesleyan.edu/2015/10/23/dsmzs-bacdive-bacterial-diversity-database/).
4. Abu-Jamous, Basel; Fa, Rui; Nandi, Asoke K. (2015). Integrative Cluster Analysis in
Bioinformatics (https://books.google.com/books?id=5XBuCAAAQBAJ&q=Bacdive&pg=PA7
7). John Wiley & Sons. p. 448. ISBN 9781118906552.
5. Zhulin, I. B. (August 1, 2015). "Databases for Microbiologists" (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC4505447). Journal of Bacteriology. 197 (15): 2458–2467.
doi:10.1128/JB.00330-15 (https://doi.org/10.1128%2FJB.00330-15). PMC 4505447 (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC4505447). PMID 26013493 (https://pubmed.ncbi.nl
m.nih.gov/26013493).
6. Söhngen, C; Podstawka, A; Boyke, B; Gleim, D; Vetcininova, A; Reimer, LC; Ebeling, C;
Pendarovski, C; Overmann, J (September 30, 2015). "BacDive - The Bacterial Diversity
Metadatabase in 2016" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702946). Nucleic
Acids Research. 44 (Database issue): D581–D585. doi:10.1093/nar/gkv983 (https://doi.org/1
0.1093%2Fnar%2Fgkv983). PMC 4702946 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC
4702946). PMID 26424852 (https://pubmed.ncbi.nlm.nih.gov/26424852).
7. Reimer, LC; Vetcininova, A; Sardà Carbasse, J; Söhngen, C; Gleim, D; Ebeling, C;
Overmann, J (September 17, 2018). "BacDive in 2019: bacterial phenotypic data for High-
throughput biodiversity analysis" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323973).
 Nucleic Acids Research. 47 (Database issue): D631–D636. doi:10.1093/nar/gky879 (https://
doi.org/10.1093%2Fnar%2Fgky879). PMC 6323973 (https://www.ncbi.nlm.nih.gov/pmc/articl
es/PMC6323973). PMID 30256983 (https://pubmed.ncbi.nlm.nih.gov/30256983).
8. Reimer, LC; Sardà Carbasse, J; Koblitz, J; Ebeling, C; Podstawka, A; Overmann, J (January
7, 2022). "BacDive in 2022: the knowledge base for standardized bacterial and archaeal
data" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728306). Nucleic Acids Research. 50
(Database issue): D741–D746. doi:10.1093/nar/gkab961 (https://doi.org/10.1093%2Fnar%2
Fgkab961). PMC 8728306 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728306).
PMID 34718743 (https://pubmed.ncbi.nlm.nih.gov/34718743).
9. "DSMZ's BacDive Bacterial Diversity Database" (https://bacdive.dsmz.de/). December 22,
2022.

External links
Simple search at BacDive (http://bacdive.dsmz.de)
Advanced search at BacDive (http://bacdive.dsmz.de/?site=advsearch)
Web services at BacDive (http://bacdive.dsmz.de/api/)

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