Fig. 2

Network and number of the different types of interaction for operational taxonomic units in Case Study 1 under “Complete” and “Complete/10” metabolic conditions. 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. Please see file Diet.txt for a complete list of the metabolites, and their availabilities represented as uptake metabolic fluxes. It can be seen from the figure that a 10 fold reduction in metabolite availability resulted in a significant decrease in the number of positive interactions predicted to occur between the members of this community, with parallel increase in the number of negative interactions. MMinte first creates a network based on the information on the file listing the associations between pairs of OTUs to be analyzed. If pairs of OTUs are not listed in the file as having some level of association, no edges between them are represented. This network is then used as the basis for the depiction of the kind of interactions that are predicted to occur between the OTUs. In the network, the shading of the nodes indicates how close the match between the sequence of the OTU is to the sequence of the genome assigned to it. This can be seen in the details from the full networks plotted. The darker the node, the higher the similarity. The length and thickness of the links reflect the association values on the initial file provided by the user. The shorter and thicker the line, the higher the association value. The color of the links reflect the kind of interaction. The red, green and grey represent whether the interaction between the two species is predicted to be negative, positive or no interaction is predicted, respectively