Journal: Gut Microbes

Article Title: Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics

doi: 10.1080/19490976.2023.2226921

Figure Lengend Snippet: Graphical representation of the time evolution of the gut microbiome ecology in the microbial community model.

Article Snippet: Simulations were carried out using the COBRA Toolbox and the Microbiome Modelling Toolbox, which is part of the COBRA Toolbox, in MATLAB version 2018b (MathWorks, Inc.) as a programming environment.

Techniques:

Journal: Gut Microbes

Article Title: Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics

doi: 10.1080/19490976.2023.2226921

Figure Lengend Snippet: Overview of the alteration of the microbiome-associated whole-body models.

Article Snippet: Simulations were carried out using the COBRA Toolbox and the Microbiome Modelling Toolbox, which is part of the COBRA Toolbox, in MATLAB version 2018b (MathWorks, Inc.) as a programming environment.

Techniques:

Journal: Computational and Structural Biotechnology Journal

Article Title: Deciphering and designing microbial communities by genome-scale metabolic modelling

doi: 10.1016/j.csbj.2024.04.055

Figure Lengend Snippet: Summarization of the characteristics and applications for the static and dynamic community-level GEMs.

Article Snippet: , Microbiome Modeling Toolbox2.0 , Large , MATLAB , ◆ Describe microbe-microbe and host-microbe interactions. ◆ User-friendly and easy to visualize. , Simulation and interpretation of pairwise microbe-microbe and host-microbe interactions . .

Techniques: Diffusion-based Assay, Convection, Functional Assay

Journal: Microbial Ecology

Article Title: Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

doi: 10.1007/s00248-024-02370-7

Figure Lengend Snippet: Summary of quantitative frameworks commonly employed to study microbial interactions with a brief discussion on its implementation, strengths and limitations

Article Snippet: Constraint model , Microbiome Modeling Toolbox (MMT)—constraint-based reconstruction and analysis framework (COBRA) : It allows visualizing microbe-microbe and host-microbe interactions , Microbiome Modeling Toolbox—MATLAB (Mathworks) , Relatively user friendly model for the analysis of microbe-microbe and host-microbe metabolic interactions , Computationally intensive. However, a version update reportedly has significantly reduced computation times by adopting parallelization , [ , ] .

Techniques: Ex Vivo, Construct, Sequencing, Transformation Assay, Gene Expression, Biomarker Discovery, In Silico, Combined Bisulfite Restriction Analysis Assay

Journal: Microbial Ecology

Article Title: Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

doi: 10.1007/s00248-024-02370-7

Figure Lengend Snippet: Summary of qualitative methods available to study microbial interactions with a description of the characterized microbial interactions/behavior

Article Snippet: Constraint model , Microbiome Modeling Toolbox (MMT)—constraint-based reconstruction and analysis framework (COBRA) : It allows visualizing microbe-microbe and host-microbe interactions , Microbiome Modeling Toolbox—MATLAB (Mathworks) , Relatively user friendly model for the analysis of microbe-microbe and host-microbe metabolic interactions , Computationally intensive. However, a version update reportedly has significantly reduced computation times by adopting parallelization , [ , ] .

Techniques: Fluorescence, Imaging, Electron Microscopy, Transmission Assay, Microscopy, Isolation, Concentration Assay, In Vitro, Cell Culture, Confocal Microscopy, Produced, Chromatography, Algae

Journal: Microbial Ecology

Article Title: Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

doi: 10.1007/s00248-024-02370-7

Figure Lengend Snippet: Summary of quantitative frameworks commonly employed to study microbial interactions with a brief discussion on its implementation, strengths and limitations

Article Snippet: , COBRA model with flux balance analysis: Novel use of constraint based microbial community modeling on an individual with episodic inflammation of GI tract , COBRA and Microbiome Modeling Toolbox—MATLAB (Mathworks) , Inclusion of flux balance analysis allowed for the adoption of the COBRA framework for understanding net metabolite production as a function of changes in gut microbiota composition , Does not account for inclusion of confounding factors such as antibiotic use. However, the model can integrate metagenomic and metabolite data efficiently to generate novel hypothesis for testing , [ ] .

Techniques: Ex Vivo, Construct, Sequencing, Transformation Assay, Gene Expression, Biomarker Discovery, In Silico, Combined Bisulfite Restriction Analysis Assay

Journal: Microbial Ecology

Article Title: Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

doi: 10.1007/s00248-024-02370-7

Figure Lengend Snippet: Summary of qualitative methods available to study microbial interactions with a description of the characterized microbial interactions/behavior

Article Snippet: , COBRA model with flux balance analysis: Novel use of constraint based microbial community modeling on an individual with episodic inflammation of GI tract , COBRA and Microbiome Modeling Toolbox—MATLAB (Mathworks) , Inclusion of flux balance analysis allowed for the adoption of the COBRA framework for understanding net metabolite production as a function of changes in gut microbiota composition , Does not account for inclusion of confounding factors such as antibiotic use. However, the model can integrate metagenomic and metabolite data efficiently to generate novel hypothesis for testing , [ ] .

Techniques: Fluorescence, Imaging, Electron Microscopy, Transmission Assay, Microscopy, Isolation, Concentration Assay, In Vitro, Cell Culture, Confocal Microscopy, Produced, Chromatography, Algae