Network inference is being applied to studies of microbial ecology to visualize and characterize microbial communities. Network representations can allow examination of the underlying organizational structure of a microbial community, and identification of key players or environmental conditions that influence community assembly and stability. Microbial co-association networks provide information on the dynamics of community structure as a function of time or other external variables. Community metabolic networks can provide a mechanistic link between species through identification of metabolite exchanges and species specific resource requirements. When used together, co-association networks and metabolic networks can provide a more in-depth view of the hidden rules that govern the stability and dynamics of microbial communities.