Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome
Fig 3
Steady states and node perturbations in the gut microbiome model.
A) Heatmap of the three steady states in the gut microbiome model. These steady states are identical to steady states identified in the three experimental groups. B) The effect of node perturbations represented by four heatmaps. On the Y-axis of each of the four heatmaps are nodes (genera) in each steady state. On the x-axis of each of the four heatmaps are the steady states found under normal model conditions (i.e. no node perturbations) and also the specific perturbation of a single network node. The two heatmaps in the left column of the figure demonstrate the effect of addition (forced overabundance) of individual genera, and the two heatmaps in the right column of the figure demonstrate the effect of removal (knockout) of individual genera. The top row heatmaps show the effect of node perturbations on the clindamycin treated group and the bottom row heatmaps show the effect of node perturbations on the clindamycin+ C. difficile treatment group. *Genus abundance of 0 means present in 0% of asynchronous simulations and is indicated in blue; Genus abundance of 1 means present in all (100%) of asynchronous simulations, shown in yellow. n = 1000 simulations were applied for all Boolean model simulations.