**Core Concept**
Metachromatic granules are specialized organelles found in certain types of bacteria, particularly those belonging to the genus Corynebacterium. These granules contain lipids and are responsible for the bacteria's ability to synthesize mycolic acids, which are essential components of their cell walls.

**Why the Correct Answer is Right**
Metachromatic granules are stained by the Methyl Violet dye in the Albert's stain, which is a type of Gram stain. The Methyl Violet dye binds to the lipids present in the metachromatic granules, causing them to appear as purple or violet structures under the microscope. This staining reaction is a key diagnostic feature of Corynebacterium diphtheriae, a bacterium that causes diphtheria.

**Why Each Wrong Option is Incorrect**
**Option A:** This option is incorrect because Methyl Violet is not specific to any other type of bacterial structure or component.
**Option B:** This option is incorrect because while Acid Fast stain may highlight certain types of bacteria, it is not used to stain metachromatic granules specifically.
**Option C:** This option is incorrect because Gram stain, which uses Crystal Violet, does not specifically highlight metachromatic granules.

**Clinical Pearl / High-Yield Fact**
It's essential to note that the presence of metachromatic granules in a bacterium is a key diagnostic feature of Corynebacterium diphtheriae. The presence of these granules, along with the bacterium's characteristic morphology, can help confirm the diagnosis of diphtheria.

**Correct Answer: D. Methyl Violet.**