Surface-enhanced Raman spectroscopy (SERS) of bacteria infused with silver or gold colloids reflects the different biochemicals in the immediate, nano-vicinity of the particles. In particular we demonstrate high sensitivity to flavins, important coenzymes usually associated with the cell wall. Varying the type of colloid, the laser excitation wavelength and the chemical protocols enables us to observe spectral signatures from different biochemical components of the microorganism. Specifically, we can switch between normal Raman, resonance Raman, and SERS, altering the relative spectral contributions of the various cell constituents.