My stepfather is a chemist and produces a lot of E number chemicals, like sweeteners, flavourings etc including MSG.
From what I’ve learned over the years of talking to him, most of the flavourings are created in a similar way to yoghurt. You take a natural product like tomato, soy, mushroom, leaves of a specific plant etc and you introduce a bacteria culture to it, the bacteria culture “eats” the product and creates a bi-product which is either refined or used in further fermentations to produce chemicals which coincidentally have certain properties which people are willing to pay for. Either they colour a food, flavour a food, thicken a food, preserve a food, or any of the other additive qualities people look for.
He produces his MSG at almost zero cost, because he extracts a certain chemical from mushrooms and garlic used as a supplement for race horses and is left with a lot of bio waste. So he worked out if he added a certain bacteria culture, he could produce MSG for free since the bacteria stays alive so long as you feed it regularly.
Flavourings can also occur naturally in a similar way within a plant or in nature where a chemical reaction takes place without human interaction, so certain animal glands can be harvested for dyes or certain insects can be used for flavourings.
If you want a primitive, non industrial version of what my stepfather does, look up how people used to and still produce “royal blue” dye by fermenting shellfish.
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