Fig. 3

Number of each type of interaction predicted to occur between pairs of the nine bacterial species (D esulfovibrio piger, Bacteroides thetaiotaomicron, Bacteroides caccae, Bacteroides ovatus, Eubacterium rectale, Marvinbryantia formatexigens, Collinsella aerofaciens, Escherichia coli, and Clostridium symbiosium) inoculated into the guts of gnotobiotic mice under different metabolic conditions in [52] and used in Case Study 2. The metabolic conditions simulated in MMinte were “Complete”, “Complete/10” and “Complete/100”. There are 380 metabolites in the “Complete” metabolic conditions and they exist as highly available. The metabolic condition “Complete/10” contains the same metabolites as “Complete” but at 10 times lower availability and “Complete/100” contains the same metabolites as “Complete” but at 100 times lower availability. Please see file Diet.txt for a complete list of the metabolites, and their availabilities represented as uptake metabolic fluxes. The effect of being in a community on the growth rate of each species (positive +, negative -, or no effect 0) determines the kind of interaction occurring. The interactions are defined as: mutualism: + +; parasitism: + −; commensalism: + 0; competition: − −; amensalism: − 0; neutralism or no interaction: 0 0)