Yet another key to miso's effectiveness as a medicine can be found in the unique lactobacillus fermentation process by which it is made. Not only does this process produce more isoflavones, but numerous studies have shown that fermentation of food with lactobacilli increases the quantity, availability, digestibility and assimilability of nutrients while promoting a healthy pH in the digestive system. What's more, lactobacillus fermentation kills dangerous pathogens both in the foods before they are eaten and in the intestines. One study, published in the Annals of Medicine in 1990, reports the effective use of freeze-dried lactobacillus bacteria for the treatment of salmonellosis, shigellosis, and antibiotic-induced diarrhea. This explains why these types of fermented foods are used in third world countries to prevent and treat various intestinal infections.

Beneficial bacteria found in the small intestine are also effective in fighting conditions such as constipation, yeast infections (candidiasis), and lactose intolerance. Now research is beginning to suggest that some friendly bacteria strains may combat more serious diseases such as coronary heart disease and cancer.

When the delicate ratio of friendly to dangerous bacteria in our digestive system is upset by the air we breathe, the food we eat, the water we drink, and the drugs we take, enzymes are produced that can change normal by-products of digestion into cancer causing toxins. Moreover, once cancer is established in the body, friendly bacteria can help destroy tumor cells. Research in Bulgaria involving patients with advanced stages of life threatening cancers has shown that ingestion of high doses of lactobacilli produced various forms of improvements, with some enjoying complete remission. Although this type of research involves taking large concentrated doses of beneficial bacteria, regularly eating foods high in these microorganisms, such as unpasteurized miso, can help maintain a healthy balance of bacteria in your digestive tract.

The benefits of lactobacilli in miso are usually associated with unpasteurized miso, however, research has shown that even heat treated lactobacilli are effective in reducing the risk of cancer. In one Japanese study scientists mixed the dead cells of lactic acid bacteria, isolated from miso, with a group of carcinogenic compounds called amines, which are commonly formed during the cooking and processing of some foods. Investigators were surprised to learn that the cell walls of some of the microorganisms found in miso bind and inactivate these dangerous food mutagens. This is yet another example of how including miso in the diet can be beneficial, particularly when eating high protein foods that have been burned or charred.