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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Author

Listed:
  • Yara Seif

    (University of California)

  • Erol Kavvas

    (University of California)

  • Jean-Christophe Lachance

    (Université de Sherbrooke)

  • James T. Yurkovich

    (University of California
    University of California)

  • Sean-Paul Nuccio

    (University of California)

  • Xin Fang

    (University of California)

  • Edward Catoiu

    (University of California)

  • Manuela Raffatellu

    (University of California)

  • Bernhard O. Palsson

    (University of California
    University of California
    University of California
    Technical University of Denmark)

  • Jonathan M. Monk

    (University of California)

Abstract

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.

Suggested Citation

  • Yara Seif & Erol Kavvas & Jean-Christophe Lachance & James T. Yurkovich & Sean-Paul Nuccio & Xin Fang & Edward Catoiu & Manuela Raffatellu & Bernhard O. Palsson & Jonathan M. Monk, 2018. "Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06112-5
    DOI: 10.1038/s41467-018-06112-5
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    Cited by:

    1. Mohammad H. Mirhakkak & Xiuqiang Chen & Yueqiong Ni & Thorsten Heinekamp & Tongta Sae-Ong & Lin-Lin Xu & Oliver Kurzai & Amelia E. Barber & Axel A. Brakhage & Sebastien Boutin & Sascha Schäuble & Gian, 2023. "Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Huimin Ye & Sabrina Borusak & Claudia Eberl & Julia Krasenbrink & Anna S. Weiss & Song-Can Chen & Buck T. Hanson & Bela Hausmann & Craig W. Herbold & Manuel Pristner & Benjamin Zwirzitz & Benedikt War, 2023. "Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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