Cataloging microbes: Scientists prepare proteomic database of bacteria

BREMEN, Germany—MS specialist Bruker Daltonik announced a collaboration with the German Collection of Microorganisms and Cell Cultures (DSMZ) to identify and classify microbes from their proteomic profiles

Randall C Willis
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BREMEN, Germany—Mass spectrometry specialist Bruker Daltonik GmbH announced recently a collaboration with the German Collection of Microorganisms and Cell Cultures (DSMZ) to identify and classify microbes from their proteomic profiles. The work will combine Daltonik's technical expertise and its new BioTyper system, which it introduced in March at Pittcon 2006 in Orlando, with the DSMZ's vast repository of biological samples.
"Bruker Daltonik had the expertise in the instrumentation, the sample preparation and the data interpretation using sophisticated pattern matching approaches," says Dr. Wolfgang Pusch, director of clinical proteomics and biomarker analysis at Bruker Daltonik. "However, we did not have the expertise in microbiology or access to broad strain collections covering considerable parts of the taxonomical kingdoms of bacteria, archaea, yeasts and fungi. So it made a lot of sense to approach the DSMZ."
Under the terms of the agreement, Bruker Daltonik offers support from dedicated application scientists and the necessary data interpretation tools with support from the development team. In return, it will get access to reference spectra generated from the comprehensive strain collection, which it will incorporate into a reference database it is establishing for future BioTyper support. Financial terms of the three-year collaboration, however, were not disclosed.
An independent nonprofit organization, the DSMZ has a mission to collect, maintain, store and perform research on biological materials of relevance to fields such as applied biology, healthcare and biotechnology. Thus, says Dr. Erko Stackebrandt, DSMZ managing director, it will use the MALDI TOF technology to identify specific organisms from the clinical environment. The organization can then use this information to classify microbes and perform clinical and diagnostic research.
As Stackebrandt explains: "Searching for novelty at the strain level may increase the chance of finding novelty at the genomic and phenotypic level."
For Bruker Daltonik, the move is part of a larger effort to support and collaborate with the wider scientific community. "Our current business strategy for the BioTyper is to build up collaborations wherever possible," says Pusch. "This is actually a win/win scenario, as both parties benefit. The customer gets high-level support and access to the necessary data interpretation. And we establish close relationships with our customers and can build up larger libraries of microbial strains for upcoming software versions."
Likewise, the BioTyper is yet another component of the spectrum of systems biology platforms Bruker Daltonik has released over the last few years. Aside from the proteomic capabilities of the BioTyper, the company also offers access to the metabolic and genomic worlds through its Metabolic Profiler platform and its partnership with Sequenom, respectively.
Bruker Daltonik views the BioTyper, in its current guise, as a microbe-identification and classification tool because it focuses on the most abundant proteins in the cells, such as the ribosomal proteins. At the same time, Dr. Frank Laukien, president and CEO of Bruker BioSciences, would not rule out the possibility of drug screening capabilities as a subject for future system development.
Regardless, efforts like that at the DSMZ will greatly facilitate the general understanding of infectious disease organisms and are therefore likely to have significant impact in both drug discovery as well as disease diagnosis.

Randall C Willis

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