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

  • Author(s): Thiele, Ines
  • Hyduke, Daniel R
  • Steeb, Benjamin
  • Fankam, Guy
  • Allen, Douglas K
  • Bazzani, Susanna
  • Charusanti, Pep
  • Chen, Feng-Chi
  • Fleming, Ronan MT
  • Hsiung, Chao A
  • De Keersmaecker, Sigrid CJ
  • Liao, Yu-Chieh
  • Marchal, Kathleen
  • Mo, Monica L
  • Özdemir, Emre
  • Raghunathan, Anu
  • Reed, Jennifer L
  • Shin, Sook-Il
  • Sigurbjörnsdóttir, Sara
  • Steinmann, Jonas
  • Sudarsan, Suresh
  • Swainston, Neil
  • Thijs, Inge M
  • Zengler, Karsten
  • Palsson, Bernhard O
  • Adkins, Joshua N
  • Bumann, Dirk
  • et al.
Abstract

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.

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