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Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves
Programme: SysMO
SEEK ID: https://fairdomhub.org/projects/2
Public web page: http://www.sysmo.net/index.php?index=54
Organisms: Clostridium acetobutylicum
FAIRDOM PALs: Sara Jabbari, Sebastian Curth, Graeme Thorn
Project created: 15th Jan 2009
Related items
- People (31)
- Institutions (8)
- Investigations (7)
- Studies (13)
- Assays (19)
- Data files (35+16)
- Models (7+4)
- SOPs (8+12)
- Publications (12)
- Presentations (21+8)
- Events (3)
- Samples (0+1)
Projects: COSMIC
Institutions: University of Rostock
Prof. Dr. Hubert Bahl
Head, Division of Microbiology, Institute of Biological Sciences
University of Rostock
Albert-Einstein-Str. 3
D-18051 Rostock
Projects: COSMIC
Institutions: University of Ulm
Expertise: Biotechnology, Molecular Biology, Microbiology
Tools: Protein, Mutant construction, Gaschromatographic analysis, DNA, Fermentation
Phd student
University of Ulm
Institute of Microbiology and Biotechnology
Albert-Einstein- Allee 11
89069 Ulm, Germany
Projects: COSMIC
Institutions: Beuth University of Applied Sciences Berlin
I am a biotechnologist with main focus on theoretical studies. Currently, I am working on the implementation of a parameter estimation algorithm on GPUs to reduce the computational burden of huge ODE systems.
I am a PAL and I am looking forward to communication with other SYSMO members.
Projects: COSMIC, SysMO-LAB, HUMET Startup
Institutions: Wageningen University & Research
Projects: COSMIC
Institutions: University of Goettingen
Expertise: pH dependent dynamic shift experiments of continuous cultures
Tools: Transcriptomics
Institutions: University of Ulm
Prof. Dr. Peter Dürre
Head, Department of Microbiology and Biotechnology, University of Ulm
89069 Ulm, Germany
Projects: COSMIC
Institutions: University of Goettingen
Expertise: Clostridium, Microarray printing, Microarray experiments with prokaryotes, Database design, Chemostats, HPLC, Anaerobic Microbiology, Programming, Molecular Biology, Microbiology
Tools: Groovy, HPLC, Molecular biology techniques (RNA/DNA/Protein), qRT-PCR, Microarray analysis, Fermentation, Java, Microbiology
I have a permanent position at the department of microbiology at the TU-München. As a microbiologist I am interested in the regulation of central metabolism in prokaryotic organisms with different types of energy metabolism such as Clostridia, Bacilli and acetic acid bacteria. Furthermore I worked as a software developer for several years in a bioinformatics company and I am very interested in bioinformatics and handling of large amounts of data.
Projects: COSMIC
Institutions: University of Rostock
Projects: COSMIC
Institutions: Beuth University of Applied Sciences Berlin

Roles: Project Coordinator
Expertise: Nonlinear Dynamics, Data integration, Dynamic optimization., Optimal experimental design, bioreactor models, dynamics of biological networks, parameter estimation, coupling metabolome and environome, rapid sampling experiments, Data Management, Mathematical modelling
Tools: Dynamic modelling, evaluation of process dynamics, continuous cultivation, Material balance based modeling, stimulus response experiments, Fermentation, Matlab, SBML
Process engineer, modeling biological systems since 1985.
Projects: COSMIC
Institutions: University of Rostock
biomathematician, PhD student at the University of Rostock, Systems Biology Group Rostock
Automated model building using Taverna workflows from KEGG-Database
Snapshots: No snapshots
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methods developed during COSMIC
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Despite a long history in using C. acetobutylicum, little is known about the regulation of the metabolic shift, the characteristics of key-regulatory elements as well as bottlenecks of the metabolism. Goal of the collaborative project ´COSMIC-2` (Clostridium acetobutylicum Systems Microbiology 2; part of ‘SysMO’) is to increase the knowledge of this clostridial metabolism and its regulatory patterns. The focus will be on the key regulatory and metabolic events that occur during the shift from the
...
Snapshots: No snapshots
Studies: Developement metabolomics protocol
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Clostridia are very ancient bacteria which evolved before the earth had an oxygen atmosphere. To them the air we breathe is a poison. To survive they produce a spore resting stage, resistant to physical and chemical agents.
Some species cause devastating diseases, such as the superbug Clostridium difficile. On the other hand, most are totally harmless, and make a wide range of chemicals useful to man. The best example is Clostridium acetobutylicum which makes butanol. Butanol is an alcohol, which
...
Snapshots: No snapshots
Studies: Investigation of different pH values for metabolic shift
Assays: test
Snapshots: No snapshots
Studies: Effect of pH on the metabolome, Effect of pH on the proteome, Effect of pH upon the transcriptome, Identification of clusters of co-regulated and anti-regulated genes, Modelling the effect of pH on the metabolic shift
Assays: Comparison of the proteome between pH 5.7 (acidogenesis) and pH 4.5 (sol..., Comparison of the transcriptome between pH 5.7 (acidogenesis) and pH 4.5..., Comparison of the transcriptome between pH 5.8 (acidogenesis) and pH 4.5..., Identification of dynamically similar transcript profiles, Steady state study of the effect of gene regulation on yields of end-pro..., Study of the end products of the acidogenesis and solventogenesis pathways, Time-dependent simulations
Conversion from KEGG Reactome Information to SBTOOLBOX2 format.
Person responsible: Sebastian Curth
Snapshots: No snapshots
Investigation: Modular Model Building
Assays: Example for model derivation from KEGG, Integration of data into the model
Annotation retrieval
Person responsible: Sebastian Curth
Snapshots: No snapshots
Investigation: Modular Model Building
Assays: No Assays
Creation of the KEGG based Reactome
Person responsible: Sebastian Curth
Snapshots: No snapshots
Investigation: Modular Model Building
Assays: Graph Analysis, KEGG Data Mining
Person responsible: Sebastian Curth
Snapshots: No snapshots
Investigation: General Method Development
Assays: Theoretical calculation of quenching time and quenching temperature
We developed a new metabolomics protocol, which involved a comparison of different harvesting techniques, quenching solutions and extraction methods.
Person responsible: John Raedts
Snapshots: No snapshots
Investigation: Identification of regulatory metabolites in the...
Investigation of the dynamic switch at pH values between 5.8 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7 and 4.5).
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH upon the transcriptome
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: No Data files
Comparison of the transcriptome at steady state in acidogenesis and at steady state in solventogenesis.
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH upon the transcriptome
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: Transcriptome data of Clostridium acetobutylicu..., Transcriptome data of Clostridium acetobutylicu...
Investigation of all steady state pH-values between pH 5.7 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7).
Contributor: Sara Jabbari
Assay type: Proteomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH on the proteome
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: Standard operating procedure to analyze the int...
Data files: Proteome Reference maps of Clostridium acetobuy..., Proteome of Clostridium acetobutylicum growing ...
Measurements of acetone, butanol, acetate, butyrate and ethanol taken during dynamic shift (pH 5.8, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5) and at steady state (pH 5.7, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5).
Contributor: Sara Jabbari
Assay type: Metabolomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH on the metabolome
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: End products of Clostridium acetobutylicum grow..., End products of Clostridium acetobutylicum grow...
Contributor: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Snapshots: No snapshots
Investigation: Investigation on the effect of pulsed metabolit...
Study: Effect of acid pulses during acidogenesis and s...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: Chemostat Fermentation B, Chemostat Fermentation C
Contributor: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Snapshots: No snapshots
Investigation: Investigation on the effect of pulsed metabolit...
Study: Effect of acid pulses during acidogenesis and s...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: Chemostat Fermentation B, Chemostat Fermentation C, Fermentation D, Fermentation E, Fermentation F, Fermentation G
Contributor: Sebastian Curth
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Investigation on the effect of pulsed metabolit...
Study: Effect of acid pulses during acidogenesis and s...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: No Data files
We developed a new metabolomics protocol, which involved a comparison of different harvesting techniques, quenching solutions and extraction methods. Cell leakage and metabolite recovery was determined by ATP measurements
Contributor: John Raedts
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Identification of regulatory metabolites in the...
Study: Developement metabolomics protocol
Organisms: No organisms
SOPs: 2 hidden items
Data files: No Data files
Contributor: John Raedts
Assay type: Metabolomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Identification of regulatory metabolites in the...
Study: Developement metabolomics protocol
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: Extraction protocol
Data files: No Data files
Contributor: Daniel Hönicke
Assay type: Transcriptomics
Technology type: Microarray
Snapshots: No snapshots
Investigation: Altering the expression pattern in Clostridium ...
Study: Influence of cysteine/sulfate negative mutants ...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (batch)
SOPs: No SOPs
Data files: Data DNA microarray analyses of C. acetobutylic...
Creator: Sebastian Curth
Contributor: Sebastian Curth
Investigations: General Method Development
Creator: Thomas Rimpf
Contributor: Thomas Rimpf
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
call
ConvertStdModel2SBTtest('Conti_Ferm_Std', 'CD_Transcriptomic.csv', 'glucose.csv', 'OD.csv',0)
Creator: Sebastian Curth
Contributor: Sebastian Curth
Investigations: Modular Model Building
Studies: Automated Model Building
transcriptome, glucose, biomass data inside
Creator: Sebastian Curth
Contributor: Sebastian Curth
Investigations: Modular Model Building
Studies: Automated Model Building
acetic acid pulse 100mM
acetic acid step 50mM, 70mM
Creator: Sebastian Curth
Contributor: Sebastian Curth
- automated integration of transcriptomic and reactome data to differential equations
- structure of the paths is maintained
- continuous fermentation model in standard format for data integration, two component model (cell and fermenter)
call >> Kegg2SBToolbox2('model_map.txt', 'reactions_compounds_final.csv','extracellular.txt','testmodel.txt') for an example
where
model_map is the desired mapping of species,
reaction_compounds_final.csv is the entire network,
extracellular.txt is a manual
...
Creator: Sebastian Curth
Contributor: Sebastian Curth
Investigations: Modular Model Building
Studies: Automated Model Building
acetic acid addition
step experiment:
50mM, 70mM, 100mM, 120mM
pulse
200mM
Creator: Sebastian Curth
Contributor: Sebastian Curth
pulse acetic acid: 70mM (2x), 80mM,
shift to 4.5,
pulse acetic acid: 70mM
Creator: Sebastian Curth
Contributor: Sebastian Curth
Creator: Sebastian Curth
Contributor: Sebastian Curth
Investigations: Modular Model Building
Studies: Automated Model Building
An ODE model of the gene regulation network governing sporulation initiation in Bacillus subtilis to be run in Matlab.
The network incorporates four sporulation-related signals: nutrient supply, DNA damage, the products of the competence genes and the bacterial population size.
Run execute_bacillus_sporulation_initiation.m to simulate the model. This file also contains the signal-related parameters which can be altered to investigate the effect of competing signals.
Some results for this model
...
Creator: Sara Jabbari
Contributor: Sara Jabbari
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Not specified
Organism: Bacillus subtilis
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Here, we use hyperbolic tangents to fit experimental data of AB fermentation in C. acetobutylicum in continous culture at steady state for different external pHs. The estimated parameters are used to define acidogenic and solventogenic phase. Furthermore, an transition phase is identified which cannot be assigned to acidogenesis or solventogenesis.
Several plots compare the fits to the experimental data.
Creator: Thomas Millat
Contributor: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
This function estimates the parameters of growth functions of the acid-forming and solvent-forming population observed in 'forward'-shift experiments of phosphate-limited continuous cultures of C. acetobutylicum. The parameters are used in the 'Two-Populations'-Model of the pH-induced metabolic shift.
It assumed that the found behaviour of the optical density during these experiments results from a phenotypic switch caused by the changing pH level.
Creator: Thomas Millat
Contributor: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
This model assumes a phenotypic switch between an acid- and solvent-forming population caused by the changing pH levels. The two phenotypes differ in their transcriptomic, proteomic, and ,thus, their metabolomic profile. Because the growth rates of these phenotypes depends on the extracellular pH, the initiation of the pH-shift results in a significant decline of the acidogenic population. Simultaneously, the solvent-forming population rises and establishes an new steady state.
The model is build
...
Creators: Thomas Millat, Graeme Thorn, Olaf Wolkenhauer, John King
Contributor: Thomas Millat
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Matlab
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
The fitted function describes the pH-drop during 'forward'-shift experiments and the increase of the pH during 'reverse'-shift experiments. The estimated parameters are used to compute the changing pH level in the models of the pH.induced metabolic shift in continuous cultures under phosphate limitation of C. acetobutylicum. Furthermore, the parameters can be applied to join different independent experiments into a single data set.
To fit the changing pH level, an exponential function and a
...
Creator: Thomas Millat
Contributor: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
input: array of investigated quenching temperatures and volumetric flows
output: quenching time and coil length as function of quenching temperature, and quenching time as function of temperature for varying coil lengths
Creator: Sebastian Curth
Contributor: Sebastian Curth
Model type: Algebraic equations
Model format: Matlab package
Environment: Matlab
Organism: Not specified
Investigations: General Method Development
Studies: Development of a rapid quenching system
Modelling analyses: Theoretical calculation of quenching time and q...
An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum, incorporating the effect of pH upon gene regulation and subsequent end-product levels.
The zip file containes 4 models (in SBML), each representing slightly different experimental conditions.
Creators: Sara Jabbari, Sylvia Haus
Contributor: The JERM Harvester
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Clostridium acetobutylicum
Investigations: The effect of pH upon the metabolic shift in Cl...
Studies: Modelling the effect of pH on the metabolic shift
Modelling analyses: Steady state study of the effect of gene regula..., Time-dependent simulations
Creator: John Raedts
Contributor: John Raedts
Investigations: Identification of regulatory metabolites in the...
Studies: Developement metabolomics protocol
Assays: Test extraction methods
Protocol for transfer of plasmids into Clostridium
acetobutylicum ATCC 824 by electroporation
Creators: None
Contributor: Ying Zhang
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
ClosTron mutants should always be subjected to Southern blot analysis to ensure that only
one intron insertion has occurred.
Creators: Ying Zhang, Nigel Minton
Contributor: Ying Zhang
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
A protocol to improve conventional, recombination-based gene knock-out methodologies thtough the provision of negative selection markers, pyrE or codA.
Creators: Ying Zhang, Nigel Minton
Contributor: Ying Zhang
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Protocol for transfer of plasmids into
Clostridium spp. by conjugation
Creators: Ying Zhang, Nigel Minton
Contributor: Ying Zhang
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
A refined and streamlined procedure to generate mutant in a wide range of different clostridial species, using group II intron retargeting methodologies.
Creators: Ying Zhang, Nigel Minton
Contributor: Ying Zhang
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Holger Janssen
Contributor: The JERM Harvester
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Holger Janssen, Tomas Fiedler
Contributor: Holger Janssen
Investigations: The effect of pH upon the metabolic shift in Cl...
Studies: Effect of pH on the proteome
Abstract (Expand)
Authors: Holger Janssen, Désireé Krausse, Ralf-Jörg Fischer, Hubert Bahl, Peter Dürre, Armin Ehrenreich, Grimmler Christina,Liebl Wolfgang
Date Published: 6th Jan 2011
Journal: J. Mol. Microbiol. Biotechnol.
PubMed ID: 21212688
Citation:
Abstract (Expand)
Authors: None
Date Published: 3rd May 2013
Journal: Appl. Microbiol. Biotechnol.
PubMed ID: 23640360
Citation:
Abstract (Expand)
Authors: None
Date Published: 1st Feb 2013
Journal: Microbial Biotechnology
Citation:
Abstract:
Authors: Matthias Reuss, Schaub Jochen,Schiesling Carola,Dauner Michael
Date Published: 2006
Journal: Biotechnol Progress
DOI: 10.1021/bp050381q
Citation:
Abstract (Expand)
Authors: Katrin Schwarz, Wouter Kuit, Armin Ehrenreich, Servé Kengen, Grimmler Christina
Date Published: 1st Mar 2012
Journal: Journal of Biotechnology
DOI: 10.1016/j.jbiotec.2012.03.018
Citation:
Abstract (Expand)
Authors: None
Date Published: 11th Nov 2010
Journal: Methods Mol. Biol.
PubMed ID: 21063964
Citation:
Abstract (Expand)
Authors: None
Date Published: 2011
Journal: BMC Syst Biol
Citation:
Abstract (Expand)
Authors: Thomas Millat, Olaf Wolkenhauer, Frey Simone,Sott Kristin,Smedh Maria,Dahl Peter,Goksör Mattias
Date Published: 2011
Journal: Mol. BioSyst.
DOI: 10.1039/c005305h
Citation:
Abstract (Expand)
Authors: Holger Janssen, Christina Döring, Armin Ehrenreich, Hubert Bahl, Ralf-Jörg Fischer, Voigt Birgit,Hecker Michael
Date Published: 1st Aug 2010
Journal: Appl Microbiol Biotechnol
DOI: 10.1007/s00253-010-2741-x
Citation:
Abstract (Expand)
Authors: Sara Jabbari, John King, Williams Paul
Date Published: 30th Nov 2009
Journal: Math Biosci
PubMed ID: 20214910
Citation:
This presentation reports about the results from an investigation of a ClosTron-mutant lacking CoA-transferase activity. Using our two-population model developed for the wild type of C. acetobutylicum, we analyse the changes in the formation of products caused by that mutation. In particular, we focus on the investigation of the acid re-assimilation after the initiation of the pH shift. Our comparison of experimental data and simulation unravels that an CoA-independent re-assimilation mechanism
...
Creator: Thomas Millat
Contributor: Thomas Millat
The acetone-butanol-ethanol (ABE) fermentation of Clostridium acetobutylicum attracts new attention because it provides a potential alternative for the synthesis of value added chemicals to petroleum and other fossil reserves. This fermentative metabolic process comprises two distinct metabolic states that differ in their product spectrum. Growing on starch or sugars the predominant fermentation products are acetate and butyrate during acidogenesis (high pH). In contrast, C. acetobutylicum produces
...
Creator: Thomas Millat
Contributor: Thomas Millat
Start Date: 18th Sep 2013
End Date: 18th Sep 2013
Event Website: Not specified
Country: Germany
City: Berlin
Progress Meeting
Start Date: 23rd Dec 2011
End Date: 23rd Dec 2011
Event Website: Not specified
Country: Germany
City: Berlin
Start Date: 5th Apr 2012
End Date: 5th Apr 2012
Event Website: Not specified
Country: Germany
City: Berlin