Open Access Highly Accessed Research article

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

Ines Thiele12, Daniel R Hyduke3, Benjamin Steeb4, Guy Fankam3, Douglas K Allen5, Susanna Bazzani6, Pep Charusanti3, Feng-Chi Chen7, Ronan MT Fleming18, Chao A Hsiung7, Sigrid CJ De Keersmaecker9, Yu-Chieh Liao7, Kathleen Marchal9, Monica L Mo3, Emre Özdemir10, Anu Raghunathan11, Jennifer L Reed12, Sook-Il Shin11, Sara Sigurbjörnsdóttir13, Jonas Steinmann13, Suresh Sudarsan14, Neil Swainston1516, Inge M Thijs9, Karsten Zengler3, Bernhard O Palsson3, Joshua N Adkins17 and Dirk Bumann4*

Author affiliations

1 Center for Systems Biology, University of Iceland, Reykjavik, Iceland

2 Faculty of Industrial Engineering, Mechanical Engineering & Computer Science University of Iceland, Reykjavik, Iceland

3 Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA

4 Infection Biology, Biozentrum, University of Basel, Basel, Switzerland

5 USDA-ARS, Plant Genetics Research Unit, Donald Danforth Plant Science Center, St Louis, MO, USA

6 Technical University Braunschweig, Institute for Bioinformatics & Biochemistry, Braunschweig, Germany

7 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan

8 Science Institute, University of Iceland, Reykjavik, Iceland

9 Centre of Microbial and Plant Genetics, Department of Microbial & Molecular Systems, Katholieke Universiteit Leuven, Leuven, Belgium

10 Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, Lausanne, Switzerland

11 Department of Infectious Diseases, Mount Sinai School of Medicine, New York City, NY, USA

12 Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA

13 Faculty of Life & Environmental Sciences, University of Iceland, Reykjavik, Iceland

14 Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Dortmund, Germany

15 School of Computer Science, The University of Manchester, Manchester, UK

16 The Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK

17 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

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Citation and License

BMC Systems Biology 2011, 5:8  doi:10.1186/1752-0509-5-8

Published: 18 January 2011

Abstract

Background

Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem.

Results

Here, we describe a community-driven effort, in which more than 20 experts in S. Typhimurium biology and systems biology collaborated to reconcile and expand the S. Typhimurium BiGG knowledge-base. The consensus MR was obtained starting from two independently developed MRs for S. Typhimurium. Key results of this reconstruction jamboree include i) development and implementation of a community-based workflow for MR annotation and reconciliation; ii) incorporation of thermodynamic information; and iii) use of the consensus MR to identify potential multi-target drug therapy approaches.

Conclusion

Taken together, with the growing number of parallel MRs a structured, community-driven approach will be necessary to maximize quality while increasing adoption of MRs in experimental design and interpretation.