The pathways that are studied to explain metabolism are all centered on a sugar being the starting point, the nutrient the microbe is generally expected to use for energy and growth. However, what if the microbe is growing in a medium lacking sugars but rich in protein? Nutrient gelatin would be an example of a medium where a protein (gelatin) is the main course for the microbe's feast.
The answer lies in other pathways that enter and leave the main pathways of metabolism - glycolysis and the TCA Cycle. These pathways take intermediate molecules formed by enzymes along the way of glycolysis and the TCA Cycle for energy production and divert them to building amino acids and nucleotides and vitamins. These twelve intermediates are called precursors, and from them some microbes can make everything necessary for cell growth.
The pathways connected to glycolysis and the TCA Cycle by the precursors are typically reversible. That is, they also serve as entryways to get amino acids and other molecules from digestion INTO glycolysis and the TCA Cycle for energy production. In this way non-sugar nutrients like amino acids from proteins can accomplish energy production and supply everything needed for glycolysis and the TCA Cycle without having any sugar to start with. Pretty clever!
So a microbe growing on a protein diet would have lots of amino acids available but no sugars for metabolism. Its amino acids would be metabolized by these side pathways and enter energy production via a precursor molecule. And by doing this, it would be able to make ATP as effectively as a bacterium growing on a sugar-rich growth medium.
The first step in converting some amino acids into precursors is often either (1) removal of the "amino" group (-NH2, a process called deamination) or removal of the "acid" group (or "carboxyl group", -COOH, a process called decarboxylation). There are biochemical tests to detect these processes in bacterial cultures.
To explore this in greater detail, go to VUMIEtm 2012 and follow the directions in MDM Exercise 13 "Amino Acid Metabolism". Your instruction will clarify what documentation should be turned in - Virtual Lab Report, MDM Exercise 13, or other.
When you are done, you may be asked to take a quiz over this material.