Journal: bioRxiv

Article Title: Longitudinal flux balance analyses of a patient with Crohn’s disease highlight microbiome metabolic alterations

doi: 10.1101/2022.12.19.520975

Figure Lengend Snippet: In the timeline, generated with BioRender, the collection date, the measured blood concentration of complex reactive protein (CRP), as well as faecal lactoferrin, lysozyme, calprotectin, and secretory IgA (SecIGA) are reported. LS has episodic major increases in all of these inflammatory/immune biomarkers, as healthy values for each are CRP<1, lactoferrin<7.3, lysozyme<600, calprotectin<50, and SecIGA (30-275). The medical intervention between LS1 and LS2 consisted of ciprofloxacin, metronidazole, and prednisone. “Microbes” refers to the number of metabolic models identified in the metagenomic samples according to the threshold selected (see Methods) and that were included in each time point-specific microbial community model. The number of reactions and metabolites refers to the size of the condition-specific microbial community models at each time point.

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: Generated, Concentration Assay

Journal: bioRxiv

Article Title: Longitudinal flux balance analyses of a patient with Crohn’s disease highlight microbiome metabolic alterations

doi: 10.1101/2022.12.19.520975

Figure Lengend Snippet: (A) Stacked barplot representing the metagenomic phyla abundance of the gut microbiome in the different LS samples with a comparison to the Healthy Average (HeAve). For a similar barplot, which also shows the time variation of 10 abundant species superimposed on the LSphyla bars, see in Ref 30. (B) 3D principal component analysis computed on the species abundances mapped onto AGORA2 involved in the metabolic modelling for each time step and reflecting differential microbial compositions and abundances is shown (more details in the Method section). For a 2D PCA of the metagenomic species relative abundances of the 7 LS samples and the 34 HE samples, see of Ref. 11.

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: bioRxiv

Article Title: Longitudinal flux balance analyses of a patient with Crohn’s disease highlight microbiome metabolic alterations

doi: 10.1101/2022.12.19.520975

Figure Lengend Snippet: Top square : Class I microbe-metabolite relationships. Bottom square : Class II. Each pair of graphs represents representative specific gut microbiome species relative abundance over LS1-7 (top of pair) and a matched metabolite flux over LS1-7 (bottom of pair). For the species graph, the blue line represents the relative abundance of the microbe over LS1-7, while the red line represents the relative abundance of that microbe for HEAve.

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: bioRxiv

Article Title: Longitudinal flux balance analyses of a patient with Crohn’s disease highlight microbiome metabolic alterations

doi: 10.1101/2022.12.19.520975

Figure Lengend Snippet: (A) Heatmap of the net flux production of all metabolites with a summed net flux higher than ten mmol/gDW/day. Key metabolites commented on in the text have been highlighted in the heatmap. LF - Low flux; IF - Intermediate flux; HF - High flux (see text for more information). (B) Geom plot of reaction subsystem prevalence across the different time points. The colours of the circles refer to the “manually-attributed” group of each subsystem. The diameter of the circles is proportional to the abundance of the reactions in the modelled microbial communities.

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: