 | |
| Content | |
|---|---|
| Description | information 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 34718743 |
| Release date | 2012 |
| Access | |
| Website | http://bacdive.dsmz.de/ |
| Web service URL | https://api.bacdive.dsmz.de/ |
BacDive (the Bacterial Diversity Metadatabase) is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity.
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 information for 93,254 strains, including 19,313 type strains. 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, as well as Elixir the European Network for Bioinformatics. In December 2022 BacDive was selected by the Global Biodata Coalition as a Global Core Biodata Resource (GCBR). GCBRs are considered critical data resources for the global research endeavour in life sciences and biomedicine.
The December release of the database encompassed 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 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 BacDive content can be accessed automatically (a free registration is needed).To support the use of the API, software clients in Python and R are available.
For data that are outside the focus of BacDive, links to other databases are provided that deliver strain-associated data:
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization, clinical effects of mutations as well as similarities of biological sequences and structures.
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.
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.
The Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, located in Braunschweig, is a research infrastructure in the Leibniz Association. Also the DSMZ is the world's most diverse collection of bioresources. These include microorganisms as well as more than 840 human and animal cell cultures, over 1,500 plant viruses, over 940 bacteriophages, and 250 plasmids. Since 2010, the scientific director of the Leibniz Institute DSMZ has been Jörg Overmann, a microbiologist with a PhD from the University of Konstanz. He holds a professorship in microbiology at the Technical University of Braunschweig. Since August 2018, he has led the institute with leadership with Bettina Fischer as administrative director.
Mycoplasma capricolum is a species of Mycoplasma bacteria. It is primarily a pathogen of goats, but has also been found in sheep and cows. The species requires external sources of cholesterol to grow or survive, but the uptaken fatty acid is not used as a substrate for energy production but rather for phospholipid synthesis instead.
Afifella is a genus in the phylum Pseudomonadota (Bacteria). Afifella are found in marine and estuarine settings, including microbial mats. They are anaerobes, with one cultured representative capable of photosynthesis.
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.
Herbaspirillum rhizosphaerae is a Gram-negative mesophilic bacterium of the genus Herbaspirillum isolated from rhizosphere soil of Allium victorialis var. platyphyllum on Ulleung Island in Korea.
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.
BASys is a freely available web server that can be used to perform automated, comprehensive annotation of bacterial genomes. With the advent of next generation DNA sequencing it is now possible to sequence the complete genome of a bacterium within a single day. This has led to an explosion in the number of fully sequenced microbes. In fact, as of 2013, there were more than 2700 fully sequenced bacterial genomes deposited with GenBank. However, a continuing challenge with microbial genomics is finding the resources or tools for annotating the large number of newly sequenced genomes. BASys was developed in 2005 in anticipation of these needs. In fact, BASys was the world’s first publicly accessible microbial genome annotation web server. Because of its widespread popularity, the BASys server was updated in 2011 through the addition of multiple server nodes to handle the large number of queries it was receiving.
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 bioniformatic 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.
Enterococcus raffinosus is a bacterial species of the Gram-positive genus Enterococcus, named for its facultative anaerobic metabolism, including the ability to ferment the trisaccharide raffinose. This mesophilic microaerophile has optimal growth at 37°C in Columbia Blood Medium. It has an ovoid morphology categorized as coccal with arrangement singly, in pairs, or short chains.
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.
Carbohydrate Structure Database (CSDB) is a free curated database and service platform in glycoinformatics, launched in 2005 by a group of Russian scientists from N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences. CSDB stores published structural, taxonomical, bibliographic and NMR-spectroscopic data on natural carbohydrates and carbohydrate-related molecules.
Exiguobacterium undae is a species of Bacilli. Its discovery was published in the International Journal of Systematic and Evolutionary Microbiology. This species has the ability to metabolize arabinose, cellulose, fructose, and glucose. It may undergo fermentation by utilizing D-glucose, D-mannitol, D-ribose, and glycogen. E. undae is motile and it contains peritrichous flagella.
Ligilactobacillus animalis is a non-motile, homofermentative species in the Gram-positive genus Ligilactobacillus, initially isolated from the dental plaque of primates and intestinal samples of a dog and mouse. L. animalis has optimal growth at 37°C on MRS agar, making this species mesophilic. The first reported isolates could ferment cellobiose, fructose, glucose, lactose, maltose, melibiose, raffinose, and salicin, but not xylose. The genome size of the type strain is 1.89 Mbp and the G/C content is 41.1%.
BacDive ID (P2946) (see uses )