While living in rural Japan we were surprised to see what a small part unfermented soy food products play in the traditional Japanese diet. Although we were served fermented soy foods, such as soy sauce, miso, and natto every day, our host never used soy milk and only served tofu about once a week. When we asked about this we were simply told that unfermented soy foods are hard to digest, although the processing of tofu partially eliminates this problem. This point of view is supported by research at Tokyo University of Agriculture, in Japan, which showed that most of the isoflavones in the diet of middle-aged Japanese women was attributed to tofu, natto, and miso.

Ancient Chinese agricultural documents dating back several thousand years show that in China soybeans were originally planted and cultivated for their nitrogen fixing ability. It was only after the discovery of fermentation, sometime during the Chou Dynasty (1134 B.C. - 246 B.C.), that soybeans became a part of the diet.

Although the ancient Chinese did not understand the problem with unfermented soybeans from a biochemical point of view, they clearly knew that unfermented soy foods were hard to digest, particularly for infants and young children. Modern scientific research has confirmed this ancient wisdom. According to modern studies and information collected by the Price Pottenger Nutrition Foundation, in Mesa, California, the soybean contains substances called "anti-nutrients" that disrupt the normal digestion and assimilation of protein and minerals. However, these substances are deactivated during the processes of fermentation and germination. Chief among these are trypsin inhibitors and phytic acid. Trypsin inhibitors block the action of trypsin and other enzymes needed for digestion of protein in the digestive tract. Although individuals differ greatly in their reaction to soy foods, these inhibitors can cause gastric distress, reduce protein digestion, and cause deficiencies in amino acid uptake in some people.

Phytic acid, which is commonly found in the hull or bran of seeds, is now known to block the uptake of essential minerals, such as calcium, iron, magnesium, copper, and zinc, in the digestive tract. The soybean has one of the highest phytate levels of all the grains and legumes that have been studied. Moreover, the soybean is highly resistant to normal phytate reducing techniques, such as long, slow cooking.

Advances in food technology have made it possible to isolate soy proteins to make many types of soy foods that are rapidly replacing meat and dairy in vegetarian fare, infant formula, and in the diets of poor people in third world countries. Although the processing of tofu and soy milk does eliminate much of the anti-nutrients in these foods, their over-consumption can cause health problems in some people. Of more concern are the breakfast cereals, baked goods, convenience foods, smoothes, and meat and dairy substitutes that are made with textured soy protein and soy isolates. Another concern with these highly processed soy foods is that the high temperature of processing denatures fragile proteins that can interfere with their digestion and assimilation.

The key to healthy soy foods consumption is fermentation. According to Sally Fallon, author of Nourishing Traditions and a spokesperson for the Price Pottenger Nutrition Foundation, anti-nutrients are actually part of the seed's natural germination timing mechanism. Phytic acid coats the seed and protects it until it is time for germination. Trypsin inhibitors are involved in activating the seed germination process. Both of these anti-nutrients are consumed and destroyed during the miso fermentation process. In a sense, says Fallon, "fermentation has the same effect on the soybean as germination." Fallon's explanation is supported by several scientific studies. For example, when researchers at the Department of Nutrition at the University of the Ryukyus, in Okinawa, Japan, compared the trypsin inhibitor concentration of fermented and unfermented foods, they found that unfermented foods had a much higher concentration of trypsin inhibitors than fermented foods. The trypsin inhibitor concentration of heat treated soy milk was more than 35 times the concentration found in miso!