DSMZ relaunches free expert-curated bacterial nomenclature database
Merge of Prokaryotic Nomenclature Up-to-date (PNU) with List of Prokaryotic names with Standing in Nomenclature (LPSN)
(Braunschweig, 19th February 2020): On February 17th the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH launched a new website (https://lpsn.dsmz.de) that offers free access to the recently merged two renowned bacterial nomenclature databases, i.e. Prokaryotic Nomenclature Up-to-date (PNU) and List of Prokaryotic names with Standing in Nomenclature (LPSN). The Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures GmbH is not only the largest Biological Resource Centre in Europe but also provides a growing range of bioinformatic services to industry and the scientific community. Integrating LPSN into the DSMZ digital collection and connecting it with other popular databases will increase visibility and usability of these services and create various opportunities for synergy. Long-term maintenance of endangered databases is not an end in itself but is a necessary prerequisite for mastering the scientific challenges of the future.
Prokaryotic Nomenclature Up-to-date (PNU)
Prokaryotic Nomenclature Up-to-date (PNU) started as a by-product of the DSMZ strain catalogue in the 1990s but developed into a standalone service for nomenclature and taxonomy of microorganisms, as a searchable website and as a downloadable file. In 2015, an Application Programming Interface (API) was added to PNU to allow for programmatic access to the data. In 2018, PNU switched to a distinct database infrastructure and to a semi-automated data collection approach, which considerably accelerated the collection of the literature data. In 2019, the scope of the data was substantially increased. However, PNU still only made a small part of the information contained in the internal DSMZ databases accessible to the public, for example, the validly published names of genera, species and subspecies.
List of Prokaryotic names with Standing in Nomenclature (LPSN)
The List of Prokaryotic names with Standing in Nomenclature (LPSN) was founded by the French veterinary microbiologist Jean P. Euzéby in 1997, and rapidly became established as a key resource for microbial taxonomy. LPSN provides the validly published names of prokaryotes of all taxonomic categories in addition to a rich collection of notes and a variety of pages with background information on the rules of nomenclature of microorganisms, including orthography and etymology. When Euzéby retired in 2013, microbiologist Aidan C. Parte, who had considerable experience in editing journals and books on taxonomy, took over as curator of LPSN. LPSN has remained immensely popular with microbiologists since then, but due to the tremendous growth in the number of microbial names proposed every year it became increasingly difficult to maintain.
Since there was considerable overlap between the goals and the content of LPSN and PNU, it was a natural progression for the two services to become one, taking advantage of the higher profile of LPSN and the superior technology that forms the backbone of PNU. In 2019, Aidan Parte and DSMZ agreed to merge the two databases and integrate them into DSMZ’s infrastructure. After integrating all data at the level of individual taxon names, a new LPSN website (https://lpsn.dsmz.de) was created with particular emphasis on easy access to comprehensive and up-to-date information on microbial nomenclature.
DSMZ Digital Collection
As a member of the Leibniz Association, DSMZ is an essential part of the research infrastructure of Germany and as such is particularly suited for the long-term maintenance of scientific databases. The integrated PNU-LPSN database now forms the basis of the new LPSN website, the PNU API, the DSMZ strain catalogue, the Type (Strain) Genome Server (TYGS) and the bacterial metadatabase BacDive, all hosted at DSMZ. TYGS, the successor to the highly cited Genome-to-Genome Distance Calculator (GGDC), allows for genome-based taxonomy, yielding whole-genome phylogenies along with species and subspecies boundaries. BacDive is the world’s largest database for standardized bacterial phenotypic information, mobilized from collections and enriched with literature data. Within hundreds of data fields BacDive offers systematic access to countless data, including the world’s largest API® test collection.
Sven-David Müller, Head of Public Relations, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH
Phone: ++49 (0)531/2616-300
About the Leibniz Institute DSMZ
The Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures is the world’s most diverse collection of biological resources (bacteria, archaea, protists, yeasts, fun-gi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). Microorganisms and cell cultures are collected, investigated and archived at the DSMZ. As an institution of the Leibniz Association, the DSMZ with its extensive scientific services and biological resources has been a global partner for research, science and industry since 1969. The DSMZ is the first registered collection in Europe (Regulation (EU) No. 511/2014) and certified according to the quality standard ISO 9001:2015. As a patent depository, it offers the only possibility in Germany to deposit biological material in accordance with the requirements of the Budapest Treaty. In addition to scientific services, research is the second pillar of the DSMZ. The institute, located on the Science Campus Braunschweig-Süd, accommodates more than 73,000 cultures and biomaterials and has 198 employees. www.dsmz.de
The Leibniz Association
The Leibniz Association connects 96 independent research institutions that range in focus from the natural, engineering and environmental sciences via economics, spatial and social sciences to the humanities. Leibniz Institutes address issues of social, economic and ecological relevance. They conduct knowledge-driven and applied basic research, maintain scientific infrastructure and provide research-based services. The Leibniz Association identifies focus areas for knowledge transfer to policy-makers, academia, business and the public. Leibniz institutions collaborate intensively with universities – in the form of “Leibniz ScienceCampi” (thematic
partnerships between university and non-university research institutes), for example – as well as with industry and other partners at home and abroad. They are subject to an independent evaluation procedure that is unparalleled in its transparency. Due to the importance of the institutions for the country as a whole, they are funded jointly by the Federation and the Länder, employing some 19,100 individuals, including 9,900 researchers. The entire budget of all the institutes is approximately 1.9 billion Euros. www.leibniz-gemeinschaft.de