BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis

• Published in: Nucleic acids research Vol. 47; no. D1; pp. D631 - D636
• Main Authors: Reimer, Lorenz Christian, Vetcininova, Anna, Carbasse, Joaquim Sardà, Söhngen, Carola, Gleim, Dorothea, Ebeling, Christian, Overmann, Jörg
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 08-01-2019
• Subjects: Database Issue; Drug Resistance, Bacterial - genetics; Genetic Variation; Genome, Bacterial; Genomics - methods; Genomics - standards; Microbiota; Phenotype; Software
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gky879

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.