Seif2018 - Strain specific Salmonella Genome Scale Models (GEMs)

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Original code
Related Publication
  • Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits.
  • Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM
  • Nature communications , 9/ 2018 , Volume 9 , Issue 1 , pages: 3771
  • Department of Bioengineering, University of California, San Diego, La Jolla, USA.
  • Salmonella strains are traditionally classified into serovars based on their surface antigens. While increasing availability of whole-genome sequences has allowed for more detailed subtyping of strains, links between genotype, serovar, and host remain elusive. Here we reconstruct genome-scale metabolic models for 410 Salmonella strains spanning 64 serovars. Model-predicted growth capabilities in over 530 different environments demonstrate that: (1) the Salmonella accessory metabolic network includes alternative carbon metabolism, and cell wall biosynthesis; (2) metabolic capabilities correspond to each strain's serovar and isolation host; (3) growth predictions agree with 83.1% of experimental outcomes for 12 strains (690 out of 858); (4) 27 strains are auxotrophic for at least one compound, including L-tryptophan, niacin, L-histidine, L-cysteine, and p-aminobenzoate; and (5) the catabolic pathways that are important for fitness in the gastrointestinal environment are lost amongst extraintestinal serovars. Our results reveal growth differences that may reflect adaptation to particular colonization sites.
Contributors
Yara Seif, Rahuman Sheriff

Metadata information

Curation status
Non-curated
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Model file

Strain_specific_models_Salmonella.zip Original code and representation of Salmonella Genome Scale Models (GEMs) 53.33 MB Preview | Download

Additional files

  • Model originally submitted by : Yara Seif
  • Submitted: 07-Nov-2018 11:51:27
  • Last Modified: 07-Nov-2018 11:51:27
Revisions
  • Version: 4 public model Download this version
    • Submitted on: 07-Nov-2018 11:51:27
    • Submitted by: Rahuman Sheriff
    • With comment: Edited model metadata online.