This question comes up a lot. And, yes, its a pre-biotic. "Prebiotics are compounds in food that induce the growth or activity of beneficial microorganisms such as bacteria and fungi. The most common example is in the gastrointestinal tract, where prebiotics can alter the composition of organisms in the gut microbiome, according to Wikipedia.
Cacao is fermented and to make it confusing, its also not. You see, during the fermentation the cacao bean pulp undergoes anaerobic and aerobic fermentation. Its actually the most complex food fermentation in the world! Many different types of families of microorganisms live in cacao fermentation, Lactobacillales, Acetobacter, Yeasts and pulp enzymes. Even fungi are present!
The breakdown of proteins and carbohydrates inside the bean, is how flavor precursors are made. But the beans have to be dried and rested before starting the chocolate making process which gives you the final flavor. Chocolate flavor ends up being largely based on fermentation.
The pulp surrounding the beans create carbon dioxide (carbonation), also ethanol. And even an oxygen free environment. This is when yeasts eat the sugary sucrose, fructose and glucose. It burps and would get you drunk. Better yet, the ethanol cures and begins to sterilize the bean's germ.
Once the cacao can breathe again and it gets turned or flipped, the ethanol and acids (citric, malic, lactic) get oxidized into vinegar like bacteria.
Now including the enzymatic breakdown in the beans, it will no longer grow. But thats not because the inside of the bean was fermented. The outside of it was. The result of the pulp fermenting is the curing of the bean into usable cacao.
So yes and no. Cacao was present for the fermentation of the pulp. That pulp is removed in chocolate making. Whats used is the cured bean. So the cacao bean it self has not fermented. Almost a catch-22 but folks just say cacao is fermented. Its quicker.