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

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

Source 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.