The composition of bacterial communities is a major factor in human health. Variations in the identity and abundance of species within a bacterial community affect its metabolic potential and hence have important medical implications. Such variations may also affect managed ecosystems such as bioreactors and agricultural fields. Thus, considering its medical and ecological implications, successful modeling of bacterial communities is likely to have broad consequences. Experimental and computational tools are now becoming available for the modeling of bacterial interactions, taking into account the identity of the interacting species and the available nutritional supplies. In this chapter, we review recent advances in the field of system biology and metabolic modeling, allowing a shift in focus from the species level to the community level, enabling a systematic exploration of species’ ecology and lifestyle, inter-species interactions, and community structure. These new approaches will hopefully provide a platform for the educated design of bacterial consortia optimized toward bioremediation and bio-production applications.