INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium

Granda, Pablo Alejandro Araujo; Gras, Anna; Gisbert, Marta Ginovart; Moulton, Vincent

doi:10.1016/j.jtbi.2016.05.017

Cited by 10 publications

(16 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The basic principles of the bacterial model and protocol system developed here are taken from the INDISIM model (Ginovart et al, 2002 ; Gras and Ginovart, 2006 ; Gras et al, 2011a ; Granda et al, 2016 ). The basic entities of our model represent bacterial cells of the two P .…”

Section: Methodsmentioning

confidence: 99%

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

et al. 2018

Self Cite

View full text Add to dashboard Cite

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.

show abstract

Section: Methodsmentioning

confidence: 99%

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…Using these MMRs we created an IBM called INDISIM-Paracoccus [27], [31], [48], [49], which is designed to study the de-nitrification process carried out by the bacteria P. denitrificans in order to explore the consequence of different priorities in the individual use of electron-acceptors on the denitrification pathway [27].…”

Section: The Developed Computational Tool: Mbt-toolmentioning

confidence: 99%

“…These metabolic reactions could be used to design the individual metabolism model as well as to parameterize the IBM models. In this sense, we think that the MbT-Tool's outputs are a convenient means to advance with this type of model [27], [31], [55].…”

Section: Final Remarksmentioning

confidence: 99%

“…Models such as individual-based models (IBMs) [24], [25], [26], [27], metabolic energy-based modelling (EBMs) [28], reaction-centric models (RCMs) [29], and even, deterministic-population models (DPMs) [30] can obtain useful information from a MMR. The reason is that these reactions, or the stoichiometry between chemical species described in the metabolic sub-model, can help in understanding how the microbial interactions happen and why microbial systems behave as they do.…”

Section: Introductionmentioning

confidence: 99%

“…In this context, the principal aim of this contribution is to develop a computational tool to write MMRs for processes driven by a range of microbes based on the Thermodynamic Electron Equivalents Model (TEEM), a methodology proposed by Perry L. McCarty [4], [7], [8], [9], [11], which is the baseline of many current bio-technological studies [4], [27], [31].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process

Granda

Gras

Gisbert

2016

Computational and Structural Biotechnology Journal

Self Cite

View full text Add to dashboard Cite

Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs) using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics) can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc). MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

show abstract

INDISIM-Denitrification, an individual-based model for study the denitrification process

Granda

Gras

Gisbert

et al. 2020

Journal of Industrial Microbiology and Biotechnology

Self Cite

View full text Add to dashboard Cite

Denitrification is one of the key processes of the global nitrogen (N) cycle driven by bacteria. It has been widely known for more than one hundred years as a process by which the biogeochemical N-cycle is balanced. To study this process, we develop an individual-based model called INDISIM-Denitrification. The model embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM and is designed to simulate in aerobic and anaerobic conditions the cell growth kinetics of denitrifying bacteria. INDISIM-Denitrification simulates a bioreactor that contains a culture medium with succinate as a carbon source, ammonium as nitrogen source and various electron acceptors. To implement INDISIM-Denitrification, the individual-based model INDISIM was used to give sub-models for nutrient uptake, stirring and reproduction cycle. Using a thermodynamic approach, the denitrification pathway, cellular maintenance and individual mass degradation were modelled using microbial metabolic reactions. These equations are the basis of the sub-models for metabolic maintenance, individual mass synthesis and reducing internal cytotoxic products. The model was implemented in the open-access platform NetLogo. INDISIM-Denitrification is validated using a set of experimental data of two denitrifying bacteria in two different experimental conditions. This provides an interactive tool to study the denitrification process carried out by any denitrifying bacterium since INDISIM-Denitrification allows changes in the microbial empirical formula and in the energy-transfer-efficiency used to represent the metabolic pathways involved in the denitrification process. The simulator can be obtained from the authors on request.

show abstract

INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium

Cited by 10 publications

References 46 publications

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process

INDISIM-Denitrification, an individual-based model for study the denitrification process

Contact Info

Product

Resources

About