"Omics" studies reported to date have dealt with either thoroughly characterized single species or poorly explored meta-microbial communities. However, these techniques are capable of producing highly informative data for the analysis of interactions between two organisms. We examined the bacterial interaction between Escherichia coli O157:H7 (O157) and Bifidobacterium longum (BL) as a pathogenic-commensal bacterial model creating a minimum microbial ecosystem in the gut using dynamic omics approaches, consisting of improved time-lapse 2D-nuclear magnetic resonance (NMR) metabolic profiling, transcriptomic, and proteomic analyses. Our study revealed that the minimum ecosystem was established by bacterial adaptation to the changes in the extracellular environment, primarily by O157, but not by BL. Additionally, the relationship between BL and O157 could be partially regarded as that between a producer and a consumer of nutrients, respectively, especially with regard to serine and aspartate metabolism. Taken together, our profiling system can provide a new insight into the primary metabolic dynamics in microbial ecosystems.