A quick run-down of your GI (gastrointestinal) system:
You put food in your mouth. Your saliva contains the first round of digestive enzymes, and starts to break down simple carbs into sugar, which are then absorbed directly into your bloodstream. (This is why simple carbs are basically the same thing as sugar.)
The rest of the food slides down your esophagus, your esophageal sphincter opens and the food empties into your stomach. In your stomach is, among other things, HCl (hydrochloric acid), and that’s phase 1 of breaking down proteins.
Once your stomach has done its thing, food gets dumped into your small intestine. You should have a boatload of good bacteria (or probiotics, mostly from the lactobacillus family) in there, and this is also where your gall bladder empties bile to help with fat absorption, and where your pancreas releases digestive enzymes. Digestive enzymes break more complex food molecules (proteins, carbohydrates, and fats) down into simpler, absorbable molecules, and then these molecules get absorbed into your bloodstream. Probiotics help with this process, and also function as a “good” army, defending your body from invasion from nastier microbes.
Once your small intestine has removed all the useful parts of your food, what’s left over gets dumped into your colon, where you have a different set of good bacteria (mostly from the bifidobacillus family). Your colon absorbs and adds water as needed to bulk up the waste and make it solid. Then, if all goes well, you eliminate.