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. 2019 Jan 8;47(D1):D631-D636.
doi: 10.1093/nar/gky879.

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

Lorenz Christian Reimer  1 , Anna Vetcininova  1 , Joaquim Sardà Carbasse  1 , Carola Söhngen  1 , Dorothea Gleim  1 , Christian Ebeling  1 , Jörg Overmann  1
Affiliations

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

Lorenz Christian Reimer et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
Novel features in the strain detail view. (A) Infobox comprising main strain identifier. (B) Table with metabolite data. (C) Navigation bar for a fast switching between thematic sections. (D) New isolation source section comprising isolation source category tags enabling systematically search of strains with the new microbial isolation source search. (E) Table for antibiotic susceptibility test data.
See this image and copyright information in PMC

References

    1. Reimer L.C., Söhngen C., Vetcininova A., Overmann J.. Mobilization and integration of bacterial phenotypic data—Enabling next generation biodiversity analysis through the BacDive metadatabase. J. Biotechnol. 2017; 261:187–193. - PubMed
    1. Weimann A., Mooren K., Frank J., Pope P.B., Bremges A., McHardy A.C.. From genomes to phenotypes: traitar, the microbial trait analyzer. mSystems. 2016; 1:e00101-16. - PMC - PubMed
    1. Söhngen C., Bunk B., Podstawka A., Gleim D., Overmann J.. BacDive - The bacterial diversity metadatabase. Nucleic Acids Res. 2014; 42:592–599. - PMC - PubMed
    1. Söhngen C., Podstawka A., Bunk B., Gleim D., Vetcininova A., Reimer L.C., Ebeling C., Pendarovski C., Overmann J.. BacDive – The bacterial diversity metadatabase in 2016. Nucleic Acids Res. 2016; 44:D581–D585. - PMC - PubMed
    1. Barberán A., Caceres Velazquez H., Jones S., Fierer N.. Hiding in plain sight: Mining bacterial species records for phenotypic trait information. mSphere. 2017; 2:e00237-17. - PMC - PubMed

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