In many Asian traditions, soybeans have always undergone processes of fermentation and aging before they have been consumed. Soy sauces, soy curds (made into tofu), soy pastes (made into miso), and other soy products like tempeh have all been traditionally produced through methods that take time and revolve around the ability of microorganisms (mostly "friendly bacteria" that are very desirable inhabitants of our digestive tract) to convert the cooked soybeans into a more digestible, nutrient-rich, and health-supportive food. I've seen studies, for example, comparing soy foods fermented with the bacterium Bifidobacterium to non-fermented soy foods. In these studies (conducted on mice) the fermented foods were able to support the skin and connective tissue of the animals (by increasing the production of a substance called hyaluronic acid) in a way that the non-fermented products were not. Two phytoestrogens (called genistein and daidzen) were also found to be present in the fermented foods but not detectable in the non-fermented versions.
Research has clearly shown that soy proteins become more digestible with fermentation. A significant percentage of soy proteins get broken down into shorter protein strands (called polypeptides) or even into single amino acids during the process of fermentation. These protein forms require less chemical activity in our digestive tract and are much better prepared for digestion than whole, intact proteins.
I've also seen studies that examined traditional fermentation process used to make soy sauce (shoyu), and these studies suggest that the antioxidant properties of soy sauce and the potentially cancer-preventive properties of soy sauce are both related to the process of fermentation. In addition, these studies show that the risk of allergy to soy is decreased through the process of fermentation. This conclusion makes sense to me, because many food allergies involve our immune system's response to food proteins, and the proteins in soy are clearly changed during the fermentation process.
From a manufacturing standpoint, however, there are challenges with traditional fermentation methods for soy. Proper fermenting takes time, adds complexity to production, and may not match with existing consumer expectations in terms of texture or taste. Lengthy fermentation processes may also bring a cost factor into production. Preservation of unique characteristics in the final food product can also be an issue. The vast majority of soy products in the marketplace today is not fermented and therefore would be expected to lack the unique health benefits provided by soy foods that have been prepared using traditional fermentation methods.
While there appear to be special health benefits from the consumption of traditionally fermented soy foods, non-fermented soy foods can still make a very nourishing contribution to your diet. We definitely like some of the unique health-supporting aspects of fermented soy foods (and other fermented foods as well), but we encourage you to consider all types of whole soy products and their great potential for improving health and nourishment. (Please note that we prefer organic soybeans and foods made from them since they are not grown from genetically modified seeds.)