Introduction
In October 2000, the research initiative GenoMik was launched by the Federal Ministry of Education and Research. The intention was to stimulate and to support genome research on microorganisms (bacteria and archaea) within competence networks. As a result of an evaluation process, three competence networks were selected and granted, one in Bielefeld on “Genome research on bacteria relevant for agriculture, environment and biotechnology”, one in Göttingen on “Genome research on bacteria for the analysis of biodiversity and its further use for the development of new production processes“, and one in Würzburg on “Genome research on pathogenic bacteria - PathoGenoMik”. The Würzburg Network rests on the expertise and the reputation of the Chair of Microbiology, the Institute of Hygiene and Microbiology and the Research Center for Infectious Diseases, all located at the University of Würzburg.
The three networks were funded for a first three year period beginning Mai/June 2001. Early in 2004 the networks were evaluated by a board of internationally recognized experts which attested excellent scientific achievements within the last three years. The very positive evaluation resulted in a second granting period for the three German-wide networks. The PathoGenoMik network which fully integrated the former independent Stuttgart network will be supported by the BMBF with a total of more than 7 million Euro until June 2006.
Structure
Since July 2004, the newly organized competence network PathoGenoMik consists of 43 research groups from 14 Universities, the Max-Planck-Institute for Infection Biology (Berlin), the GBF (Braunschweig), the Robert-Koch-Institute (Wernigerode), the Robert Bosch Hospital (Stuttgart), the Institute for Molecular Biotechnology (Jena) and the three companies Milupa (Friedrichsdorf), Combinature (Berlin) and Selecore (Göttingen) which are organized in four alliances and a central management unit. Several groups from partner countries which are active in the BMBF-organized initiative ERA-NET Pathogenomics are integrated in the network as associated members.
The four alliances are each headed by a coordinator either from Würzburg (W. Goebel, M. Frosch, J. Hacker) or from Stuttgart (R. Schmid) and are subdivided into nine project groups, each headed by a project group leader. The four coordinators together with the project group leaders form the steering committee of the network. The coordination of the bioinformatics for the PathoGenoMik network and their integration into the Bielefeld bioinformatics platform GenDB will be supervised by T. Dandekar (Würzburg).
Alliance I: Gram-positive cocci
Coordinator: J. Hacker
Project Group 1: Staphylococci
(J. Hacker, G. Bierbaum, M. Hecker, F. Götz, C. von Eiff)
Project Group 2: Streptococci, Pneumococci and Entercococci
(R. Hakenbeck, A. Podbielski, G. Chhatwal, E. Domann)
Alliance II: Intracellular bacteria, especially Chlamydia, Listeria, Mycobacterium and Legionella
Coordinator: W. Goebel
Project Group 3: Listeria
(T. Chakraborty, W. Goebel, A. Bacher, T. Fuchs, S. Scherer, J. Wehland, J. Schmitt, A. Szalay)
Project Group 4: Mycobacterium, Chlamydia and Legionella
(S. Kaufmann, T. Meyer, A. Vente, G. Glöckner, M. Steinert, K. Heuner)
Alliance III: Gram-negative pathogenic bacteria
Coordinator: M. Frosch
Project Group 5: Helicobacter
(S. Suerbaum, C. Josenhans, M. Achtman, D. Beier)
Project Group 6: Neisseria, Haemophilus, Bordetella and Pseudomonas
(M. Frosch, J. Reidl, R. Gross, U. Göbel, C. Guzman, B. Tümmler, H. Kolmar)
Project Group 7: Escherichia coli
(J. Heesemann, H. Karch, A. Schmidt, U. Dobrindt)
Alliance IV: Technology
Coordinator R. Schmid
Project Group 8: Diagnostic microarrays
(R. Schmid, W. Ludwig, C. Knabbe, W. Witte)
Project Group 9: Sample reconditioning
(T. Bachmann)
Central Services
Network management:
(W. Goebel, M. Kuhn)
Technical Support Facility:
(W. Goebel, M. Frosch, J. Hacker, J. Kreft)
Bioinformatics:
(T. Dandekar, J. Kreft, R. Lampidis)
Research
Bacteria pathogenic for humans which are of high scientific interest and also of high potential for the development of new diagnostic tools and new therapeutics will again be the focus of the research of the competence network PathoGenoMik in the second funding period. The selected bacterial species are investigated by internationally recognized German groups which - thanks to the financial support received through the PathoGenoMik network - have established themselves in the field of microbial genomics in a way which - despite strong international competition - may even open possibilities to commercially exploit the results obtained up to know and hopefully obtained within the next two years.
Each of the research areas now organized in 9 Project Groups follows strongly integrated and largely application-oriented aims. The basis of the envisaged research in all project groups are the information content of the publicly available bacterial genome sequences, which were largely established within the PathoGenoMik network. This information will be used by bioinformatics approaches as well as with modern high-throughput methods (DNA-arrays, transcriptomics, proteomics, genome wide mutations, IVET-approaches) to analyse the relevance of the genome content for the outcome of the diseases caused by these bacteria. This functional "pathogenomik"-approach will focus on the development of new diagnostic tools („pathoarrays“), antibacterial substances and vaccines. The fusion with the formerly independent Stuttgart network (bringing in expertise in technology in DNA-array design and array production and in DNA purification) and the close cooperation of the Bioinformatics group of the PathoGenoMik network with the Bielefeld-based bioinformatics platform GenDB will mainly contribute to reach these goals.