BacDive

Last updated
BacDive
BacDive logo.png
Content
Descriptioninformation about bacterial and archaeal strains
Data types
captured
metadata
Contact
Research center Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
Primary citation PMID   26424852
Release date2012
Access
Website http://bacdive.dsmz.de/
Web service URL http://bacdive.dsmz.de/api/

BacDive (the Bacterial Diversity Metadatabase) is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity.

Contents

Introduction

BacDive is a resource for different kind of metadata like taxonomy, morphology, physiology, environment and molecular-biology. [1] [2] [3] [4] [5] [6] The majority of data is manually annotated and curated. With the release in July 2018 BacDive offers information for 63,669 strains. [7] The database is hosted by the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH and is part of de.NBI the German Network for Bioinformatics Infrastructure.

Content and Features

Database

The July 2018 release of the database encompassed over 600 different data fields, divided into the categories "Name and taxonomic classification", "Morphology and physiology", "Culture and growth conditions," "Isolation, sampling and environmental information." "Application and interaction", "Molecular biology" and "Strain availability". The database comprised 712,958 entries, linked to the according strain and reference. [7] The data are retrieved from internal descriptions of culture collections, expert-compiled compendia on strains and primary scientific literature.

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 the main fields like taxonomy or strain ID, 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 web service portal not only BacDive content, but also the taxon reference list Prokaryotic Nomenclature Up-To-Date can be accessed.

Other databases

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

Related Research Articles

In taxonomy, Methanopyrus is a genus of the Methanopyraceae.

BRENDA is an information system representing one of the most comprehensive enzyme repositories. It is an electronic resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction. Kinetic properties of the corresponding reactants are described in detail. BRENDA contains enzyme-specific data manually extracted from primary scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a web-based user interface that allows a convenient and sophisticated access to the data.

The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. As both a bioinformatics and a cheminformatics resource, DrugBank combines detailed drug data with comprehensive drug target information. DrugBank has used content from Wikipedia. Wikipedia also often links to Drugbank.

<i>Shigella boydii</i> species of bacterium

Shigella boydii is a Gram-negative bacterium of the genus Shigella. Like other members of the genus, S. boydii is a nonmotile, nonsporeforming, rod-shaped bacterium which can cause dysentery in humans through fecal-oral contamination.

MicrobesOnline

MicrobesOnline is a publicly and freely accessible website that hosts multiple comparative genomic tools for comparing microbial species at the genomic, transcriptomic and functional levels. MicrobesOnline was developed by the Virtual Institute for Microbial Stress and Survival, which is based at the Lawrence Berkeley National Laboratory in Berkeley, California. The site was launched in 2005, with regular updates until 2011.

The Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH was founded 1969 as the national culture collection in Germany. This independent non-profit organization is dedicated to the acquisition, characterization, identification, preservation, distribution of Bacteria, Archea, fungi, plasmids, bacteriophages, human and animal cell lines, plant cell cultures and plant viruses. The organization is member of the German Wissenschaftsgemeinschaft Gottfried Wilhelm Leibniz and of worldwide organizations like the European Culture Collections' Organisation (ECCO), the World Federation for Culture Collections (WFCC), and the Global Biodiversity Information Facility (GBIF).

Mycoplasma capricolum is a species of Mycoplasma bacteria. It is primarily a pathogen of goats, but has also been found in sheep and cows.

PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank. The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London. As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of Janet Thornton at the European Bioinformatics Institute (EBI).

The Laminin database, is a database of non-collagenous extracellular matrix proteins.

Bacillus halodurans is a rod-shaped, Gram-positive, motile and spore-forming bacterium found in soil. In a genomic comparison with Bacillus subtilis, B. halodurans strain C-125 - originally an unclassified Bacillus strain - was found to contain unique genes and sigma factors that may have aided its adaptation to more alkaline environments.

Oceanobacillus iheyensis is a bacterium, the type species of its genus. It is a deep-sea species, having been isolated from a depth of 1,050 metres (3,440 ft), and is extremely halotolerant and alkaliphilic. Its type strain is HTE831. Oceanobacillus iheyensis HTE831 is an alkaliphilic and extremely halotolerant Bacillus-related species isolated from deep-sea sediment.

Experimental factor ontology ontology

Experimental factor ontology, also known as EFO, is an open-access ontology of experimental variables particularly those used in molecular biology. The ontology covers variables which include aspects of disease, anatomy, cell type, cell lines, chemical compounds and assay information. EFO is developed and maintained at the EMBL-EBI as a cross-cutting resource for the purposes of curation, querying and data integration in resources such as Ensembl, ChEMBL and Expression Atlas.

Sulfolobus tokodaii is a thermophilic archaeon. It is acidophilic and obligately aerobic. The type strain is 7. Its genome has been sequenced.

BacMap is a freely available web-accessible database containing fully annotated, fully zoomable and fully searchable chromosome maps from more than 2500 prokaryotic species. BacMap was originally developed in 2005 to address the challenges of viewing and navigating through the growing numbers of bacterial genomes that were being generated through large-scale sequencing efforts. Since it was first introduced, the number of bacterial genomes in BacMap has grown by more than 15X. Essentially BacMap functions as an on-line visual atlas of microbial genomes. All of the genome annotations in BacMap were generated through the BASys genome annotation system. BASys is a widely used microbial annotation infrastructure that performs comprehensive bionformatic analyses on raw bacterial genome sequence data. All of the genome (chromosome) maps in BacMap were constructed using the program known as CGView. CGView is a popular visualization program for generating interactive, web-compatible circular chromosome maps. Each chromosome map in BacMap is extensively hyperlinked and each chromosome image can be interactively navigated, expanded and rotated using navigation buttons or hyperlinks. All identified genes in a BacMap chromosome map are colored according to coding directions and when sufficiently zoomed-in, gene labels are visible. Each gene label on a BacMap genome map is also hyperlinked to a 'gene card'. The gene cards provide detailed information about the corresponding DNA and protein sequences. Each genome map in BacMap is searchable via BLAST and a gene name/synonym search.

Rhodococcus opacus is a bacterium species in the genus Rhodococcus. It is moderately chemolithotrophic. Its genome has been sequenced.

METAGENassist is a freely available web server for comparative metagenomic analysis. Comparative metagenomic studies involve the large-scale comparison of genomic or taxonomic census data from bacterial samples across different environments. Historically this has required a sound knowledge of statistics, computer programming, genetics and microbiology. As a result, only a small number of researchers are routinely able to perform comparative metagenomic studies. To circumvent these limitations, METAGENassist was developed to allow metagenomic analyses to be performed by non-specialists, easily and intuitively over the web. METAGENassist is particularly notable for its rich graphical output and its extensive database of bacterial phenotypic information.

Hahella gaghwensis is a marine strain of Gram-negative, aerobic, and obligately halophilic bacteria of the gammaproteobacteria. Unlike its relative, H. chejuensis, H. ganghwensis is obligately halophilic, and both have distinctly different metabolic capabilities and fatty acid content.

Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the gene ontology to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.

BacMet is an antimicrobial resistance database. It tracks bacterial genes that give resistance to antibacterial biocides and metals.

References

  1. Söhngen, C; Boyke, B; Podstawka, A; Gleim, D; Overmann, J (October 13, 2013). "BacDive - The Bacterial Diversity Metadatabase". Nucleic Acids Research. 42 (Database issue): D592–D599. doi:10.1093/nar/gkt1058. PMC   3965005 . PMID   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". Nucleic Acids Research. 42 (Database issue): D1–D6. doi:10.1093/nar/gkt1282. PMC   3965027 . PMID   24316579.
  3. Cohan lab (October 23, 2015). "DSMZ's BacDive Bacterial Diversity Database".
  4. Abu-Jamous, Basel; Fa, Rui; Nandi, Asoke K. (2015). Integrative Cluster Analysis in Bioinformatics. John Wiley & Sons. p. 448. ISBN   9781118906552.
  5. Zhulin, I. B. (August 1, 2015). "Databases for Microbiologists". Journal of Bacteriology. 197 (15): 2458–2467. doi:10.1128/JB.00330-15. PMC   4505447 . PMID   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". Nucleic Acids Research. 44 (Database issue): D581–D585. doi:10.1093/nar/gkv983. PMC   4702946 . PMID   26424852.
  7. 1 2 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". Nucleic Acids Research. 47 (Database issue): D631–D636. doi:10.1093/nar/gky879. PMC   6323973 . PMID   30256983.