1. where is the cell from. bacterial or multi-cell organism, human or other non-model organism. This will limit the application of the technologies. Like the metabolome, there are many metabolites haven't be identified up to now. But for bacterial, their metabolites have been identified relatively well.
2. however, as the rule of from simple to complex. If we want to predict the behavior of the bacterial, technologically, the transcriptome+metabolome may be the preferred. Because these two techniques have been developed relatively mature and can give confident results. Further, metabolome linked closely and directly to behavior.