Soy and Your Gut Microbiome: How Soy Foods Affect Your Gut Health

The gut microbiome, or gut microbiota, refers to the microorganisms — including bacteria, fungi, and viruses — that live in the digestive tract. The gut microbiata has evolved to have a mutually beneficial relationship with humans. It thrives on the nutrients in the foods we eat and, in exchange, protects us against diseases and helps us glean important nutrients from our diet. While scientists still have much to learn about our gut microbiome, most gut bacteria can be categorized as beneficial or potentially harmful, based on what they metabolize and produce.

Soy and Your Gut Health

Bacteria that specialize in converting carbohydrates into energy are considered potentially beneficial. Examples of these include Lactobacillus and Bifidobacteria. Beneficial, or “good,” gut bacteria assist with disease prevention, maintaining your immune system and aiding your metabolic health. Research has explored how bacteria found in soy foods, especially fermented soy products like miso and natto, may help promote a healthier gut by feeding your good gut bacteria.

Is Soy Good for Gut Health?

Nutrients and compounds from foods that can nourish your gut microbiome and encourage growth of good bacteria are known as “prebiotics.” Prebiotics are essentially your good bacteria’s food.

Soy has four major components that may act as prebiotics:


A type of carbohydrate found in soybeans. Oligosaccharides aren’t digested in the small intestine. Instead, they enter the large intestine, where most of your gut bacteria reside, and provide fuel for good bacteria.


More research on soy protein and gut health is needed. However, findings from animal studies have been encouraging and have helped provide insights for future research on soy protein and the gut microbiota.


Researchers believe isoflavones, plant-based compounds from foods like soybeans, make their way to the colon where they can interact directly with the microbiota.


Fiber fuels your gut bacteria and supports digestive health.

Soy Foods and Dietary Fiber

Consuming high amounts of dietary fiber is associated with a diverse gut microbiome and reduced levels of obesity. Soybeans are a great source of dietary fiber, as one serving of soybeans has around eight grams.

Edamame                 SoyNuts

Soy foods that use the entire soybean, such as edamame or soy nuts, are higher in fiber than other soy foods like tofu or soy milk, that may be more processed.

The Benefits of Fermented Soy Foods

Fermented soy foods, like miso and natto, are popular in Asian countries and are gaining popularity in the U.S. When soy products are fermented, the process of fermentation creates changes to soy’s composition that may positively affect your microbiome. One study on tempeh made from soybeans and tempeh made from common beans found that soybean tempeh stimulated the growth of Bifidobacterium, a gut bacterium that is considered potentially beneficial, while tempeh from common beans didn’t. 

Japanese researchers studied the effects of natto—a fermented food made from whole soybeans—on the microbiome. The study followed seven healthy volunteers who consumed 50 grams of natto daily for two weeks. Participants in the study had an increase in two types of good gut bacteria, Bacillus subtilis and Bifidobacterium, and a decrease in Clostridium perfringens, a potentially harmful bacteria. A similar study was conducted using miso soup that contained natto and yielded similar results. 

Another study, following volunteers who drank fermented soy milk, found that fermented soy milk increased the amount of Bifidobacterium and Lactobacillus bacteria, as well as increased the ratio of a good bacteria to a potentially harmful bacteria among participants. 


Now that you know about the benefits of soy on your gut microbiome, why not add some of this versatile bean to your diet? If you want to get a boost of beneficial nutrients and plant compounds, whip up one of the delicious soy recipes on our site. And to learn where soy foods come from, visit our Soy Farms page.