Shoyu is the Japanese
word for soy sauce
There are many varieties of shoyu, however the real difference these days is whether it has been naturally brewed or has been concocted chemically.
The process of brewing soy sauce naturally has three phases: koji-making, brine fermentation, and refining.The following information is adapted from material from http://www.kikkoman.com, the site for the best known authentic shoyu.
1. Koji-making: To begin the process, soybeans and wheat are blended under controlled conditions. Next, a mould, (a range of aspergillus is used by different brewers), is introduced and the mixture is allowed to mature for at least three days in large, perforated vats through which air is circulated.
2. Brine Fermentation: The resulting culture, or koji, is then transferred to fermentation tanks, where it is mixed with salt-water brine to produce a mash called moromi. The next and most critical step is for the moromi to ferment for several months using osmophilic lactic acid bacteria and yeasts. During this time, the soybeans and wheat mature into a semi-liquid, deeply reddish-brown mash. It is this long process of fermentation that creates the many flavour and fragrance compounds that build the distinctive richness of shoyu.
3. Refining: Following the months of moromi fermentation, the raw shoyu is separated from the cake by pressing it through layers of filtration cloth. The liquid which emerges from this filtration is then refined, pasteurized and packaged as finished shoyu.
The manufacture of non-brewed soy sauce is an entirely different matter. Soybeans are boiled with hydrochloric acid for 15 to 20 hours. After most of the amino acid is removed, the mixture is chilled down to halt the hydrolytic reaction. The amino acid liquid is then neutralized, pressed through a filter, mixed with active carbon and purified through filtration.
Colour and flavor are introduced to this hydrolyzed vegetable protein mixture by adding caramel colour, corn syrup for sweetness, and salt. The mixture is then refined and packaged.
There really is no comparison between naturally brewed soy sauces and the caramel coloured liquid often sold as "soy sauce". Technically, they are both sauces made from soy. But only brewed, dermented shoyu conveys the richness that has made this condiment such a pervasive part of world cooking.
For some further information on koji see About Koji - A Starter For Making Saké