There are 4 broad categories of molecule in your body:
Of these, you acquire most of the first three by consuming them, breaking them down into building blocks, and reassembling as needed. Nucleic acids are used in much, much smaller quantities and are mostly produced in your body instead of absorbed through your food.
Each of these can also be broken down by your body and burned for energy; this is the calorie content.
To some extent, your body can convert each one into the others as long as you have sufficient calories, but an ideal diet contains some of each three. In particular, certain fats are almost impossible to make, and if you don't consume them, you can die, and if you don't get enough protein, you'll run out of nitrogen and can't make any more - but honestly, except in very specific circumstances, this isn't something you need to worry about (though "specific circumstances" can include an eating disorder). Additionally, there are 20 kinds of amino acid (what proteins are made of), and the body can't produce 9 of them; vegans need to be careful to make sure they get enough of them, but it's not that hard (people who eat animal products usually get enough without any issues).
Micronutrients refers to certain substances that your body needs to survive and can't make for itself, but only needs in tiny amounts - milligrams a day or less for the most part. These are what you know as vitamins and minerals.
When people talk about fermented foods and probiotics, what they're mostly talking about it trying to affect your gut microflora, the bacteria (etc.) that live in your intestine.
While science in recent years has made it clear that your gut microflora affect a wide array of things (most clearly weight gain), the details are still uncertain and being researched. A lot of people who make claims about eating certain things leading to mental effects like greater focus, better mood, etc. are pseudoscience at best, unfortunately.