Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms

  public model
Model Identifier
BIOMD0000000932
Short description 
Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in Bacillus subtilis biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995. The system involves three differential equations and a single bilinear term. We specifically select parameters that are suitable for the biological scenario of biofilm oscillations. We perform computer simulations and a detailed analysis of the system including bifurcation analysis and quasi-steady-state approximation. We also discuss the feedback structure of the system and the correspondence of the simulations to biological observations. Our theoretical work suggests potential scenarios about the oscillatory behaviour of biofilms and also serves as an application of a previously described chemical oscillator to a biological system.
Format
SBML (L2V4)
Related Publication
  • Differential equation-based minimal model describing metabolic oscillations in Bacillus subtilis biofilms.
  • Garde R, Ibrahim B, Kovács ÁT, Schuster S
  • Royal Society open science , 2/ 2020 , Volume 7 , Issue 2 , pages: 190810 , PubMed ID: 32257302
  • Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
  • Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in Bacillus subtilis biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995. The system involves three differential equations and a single bilinear term. We specifically select parameters that are suitable for the biological scenario of biofilm oscillations. We perform computer simulations and a detailed analysis of the system including bifurcation analysis and quasi-steady-state approximation. We also discuss the feedback structure of the system and the correspondence of the simulations to biological observations. Our theoretical work suggests potential scenarios about the oscillatory behaviour of biofilms and also serves as an application of a previously described chemical oscillator to a biological system.
Contributors
Submitter of the first revision: Ahmad Zyoud
Submitter of this revision: Ahmad Zyoud
Modellers: Ahmad Zyoud

Metadata information

is (2 statements)
BioModels Database MODEL2004140001
BioModels Database BIOMD0000000932

hasTaxon (1 statement)
isDerivedFrom (7 statements)
Mathematical Modelling Ontology Ordinary differential equation model
NCIt Metabolic
Environment Ontology biofilm
TEDDY TEDDY_0000072
Gene Ontology glutamate metabolic process

hasProperty (5 statements)
Mathematical Modelling Ontology Ordinary differential equation model
Gene Ontology glutamate metabolic process
TEDDY TEDDY_0000072
Environment Ontology biofilm
NCIt Metabolic

isDescribedBy (2 statements)
Curation status
Curated
Modelling approach(es)
ordinary differential equation model
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Model files
Garde2020.xml SBML L2V4 Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms_Curated 34.67 KB Preview | Download

Additional files
Garde2020-Fig2.sedml sed-ml L1V2 Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms_Curated-Fig2 6.42 KB Preview | Download
Garde2020-Fig4.sedml sed-ml L1V2 Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms_Curated-Fig4 6.41 KB Preview | Download
Garde2020.cps COPASI version 4.27 (Build 217) Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms_Curated 65.03 KB Preview | Download

  • Model originally submitted by : Ahmad Zyoud
  • Submitted: Apr 14, 2020 4:07:50 PM
  • Last Modified: Apr 14, 2020 4:07:50 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Apr 14, 2020 4:07:50 PM
    • Submitted by: Ahmad Zyoud
    • With comment: Automatically added model identifier BIOMD0000000932
Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
A

ammonia 		1.0 mmol
Gp

CHEBI:32484 ; C25233 		1.0 mmol
Gi

CHEBI:32484 ; C25234 		1.0 mmol
B

biomass production 		1.0E11 mmol
Reactions
Reactions Rate Parameters
A => compartment*k3*A k3 = 4.0
=> Gp; A compartment*(k1*GE*Gp-k2*A*Gp) GE = 30.0; k2 = 5.3; k1 = 0.3426
Gp => Gi compartment*k4*Gp k4 = 2.0
Gi => A compartment*k5*Gi k5 = 2.3
=> B; A, Gp compartment*b*A*Gp*B b = 0.1
Curator's comment:
(added: 14 Apr 2020, 16:06:41, updated: 14 Apr 2020, 16:06:41)
Figure 2 and 4 were reproduced by using Copasi 4.27 (Build 217)