Abstract
The bacterial metadatabase BacDive (http://bacdive.dsmz.de) has become a comprehensive resource for structured data on the taxonomy, morphology, physiology, cultivation, isolation and molecular data of prokaryotes. With its current release (7/2018) the database offers information for 63 669 bacterial and archaeal strains including 12 715 type strains. During recent developments of BacDive, the enrichment of information on existing strains was prioritized. This has resulted in a 146% increase of database content over the past three years. Especially rich datasets were integrated from 4782 manual annotated species descriptions in the International Journal of Systematic and Evolutionary Microbiology which yielded standardized phenotypic data for 5468 type strains. Another important improvement of content was achieved through the mobilization of 8977 Analytical Profile Index (API®) test results that constitute physiological data for the identification of 5237 strains. BacDive offers a unique API® data collection with respect to size and diversity. In addition, data on fatty acid profiles and antibiotic susceptibility tests were integrated. A revised graphical user interface and new search tools such as the API® test finder, the TAXplorer, or the Microbial Isolation Source Search significantly improve the user experience.
Highlights
Prokaryotes express a wide variety of phenotypic traits with high relevance for research and development
Hotspots for bacterial metadata are the initial species descriptions in primary literature as well as databases maintained by biological resource centers (BRC) (1)
Both sources are difficult to access, and searches for particular phenotypic data are often cumbersome. This is of particular relevance, as whole genome sequences are rapidly growing in numbers (to date, 10 957 genomes are found in the NCBI genome database) and are increasingly used for the prediction and analysis of bacterial phenotypes
Summary
Prokaryotes express a wide variety of phenotypic traits with high relevance for research and development. BacDive offers annotated data from IJSEM species descriptions for a total of 5468 strains (https://bacdive.dsmz.de/advsearch?site= advsearch&searchparams%5B84%5D%5Bsearchterm% 5D=IJSEM&advsearch=search). Phylum, class, family, genus, species, subspecies, the full scientific name and type strain status Size, morphology, utilized substrates, active enzymes, antibiotic resistance, murine types, lysis/ decomposition Cultivation media compositions, growth temperatures, pH, salt concentrations Isolation source, geographic location, environmental conditions at sampling time, utilized enrichment media Medical, biotechnical or industrial application, risk group classification Genotype information e.g. INSDC sequence accession numbers, sequence length, GC-content Depository history, holding biological ressource center, culture collection identifiers
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