Kim2021 - Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917

  public model
Model Identifier
BIOMD0000001062
Short description
Escherichia coli Nissle 1917 (EcN) is an intestinal probiotic that is effective for the treatment of intestinal disorders, such as inflammatory bowel disease and ulcerative colitis. EcN is a representative Gram-negative probiotic in biomedical research and is an intensively studied probiotic. However, to date, its genome-wide metabolic network model has not been developed. Here, we developed a comprehensive and highly curated EcN metabolic model, referred to as iDK1463, based on genome comparison and phenome analysis. The model was improved and validated by comparing the simulation results with experimental results from phenotype microarray tests. iDK1463 comprises 1463 genes, 1313 unique metabolites, and 2984 metabolic reactions. Phenome data of EcN were compared with those of Escherichia coli intestinal commensal K-12 MG1655. iDK1463 was simulated to identify the genetic determinants responsible for the observed phenotypic differences between EcN and K-12. Further, the model was simulated for gene essentiality analysis and utilization of nutrient sources under anaerobic growth conditions. These analyses provided insights into the metabolic mechanisms by which EcN colonizes and persists in the gut. iDK1463 will contribute to the system-level understanding of the functional capacity of gut microbes and their interactions with microbiota and human hosts, as well as the development of live microbial therapeutics.
Format
SBML (L3V1)
Related Publication
  • Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917.
  • Kim D, Kim Y, Yoon SH
  • International journal of molecular sciences , 2/ 2021 , Volume 22 , Issue 4 , PubMed ID: 33672760
  • Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea.
  • Escherichia coli Nissle 1917 (EcN) is an intestinal probiotic that is effective for the treatment of intestinal disorders, such as inflammatory bowel disease and ulcerative colitis. EcN is a representative Gram-negative probiotic in biomedical research and is an intensively studied probiotic. However, to date, its genome-wide metabolic network model has not been developed. Here, we developed a comprehensive and highly curated EcN metabolic model, referred to as iDK1463, based on genome comparison and phenome analysis. The model was improved and validated by comparing the simulation results with experimental results from phenotype microarray tests. iDK1463 comprises 1463 genes, 1313 unique metabolites, and 2984 metabolic reactions. Phenome data of EcN were compared with those of Escherichia coli intestinal commensal K-12 MG1655. iDK1463 was simulated to identify the genetic determinants responsible for the observed phenotypic differences between EcN and K-12. Further, the model was simulated for gene essentiality analysis and utilization of nutrient sources under anaerobic growth conditions. These analyses provided insights into the metabolic mechanisms by which EcN colonizes and persists in the gut. iDK1463 will contribute to the system-level understanding of the functional capacity of gut microbes and their interactions with microbiota and human hosts, as well as the development of live microbial therapeutics.
Contributors
Submitter of the first revision: Dohyeon Kim
Submitter of this revision: Mikal Daou
Modellers: Mikal Daou, Dohyeon Kim

Metadata information


Curation status
Non-curated

Modelling approach(es)

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Model files

iDK1463.xml SBML L3V1 annotated representation of Escherichia coli Nissle 1917 11.26 MB Preview | Download

Additional files

iDK1463.zip iDK1463 FROG report using MATLAB 42.06 KB Preview | Download
idk1463.omex Frog report with annotated model 709.19 KB Preview | Download
miniFROG Report_Kim2021.xlsx iDK1463 miniFROG report 55.32 KB Preview | Download

  • Model originally submitted by : Dohyeon Kim
  • Submitted: Apr 18, 2022 7:59:16 AM
  • Last Modified: Aug 12, 2022 1:43:33 PM
Revisions
  • Version: 5 public model Download this version
    • Submitted on: Aug 12, 2022 1:43:33 PM
    • Submitted by: Mikal Daou
    • With comment: Automatically added model identifier BIOMD0000001062
  • Version: 4 public model Download this version
    • Submitted on: Aug 12, 2022 1:40:19 PM
    • Submitted by: Mikal Daou
    • With comment: Added annotation
  • Version: 3 public model Download this version
    • Submitted on: Apr 18, 2022 7:59:16 AM
    • Submitted by: Dohyeon Kim
    • With comment: Upload miniFROG report for iDK1463

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Curator's comment:
(added: 12 Aug 2022, 13:43:14, updated: 12 Aug 2022, 13:43:14)
This model is curated using FROG standards. We used COBRApy and FROG Matlab toolbox to curate the model. FROG Report , miniFROG Report can also be accessed from the model files page.