What Are Probiotics? A Look at the Microbes in Yogurt, Natto, and Nukazuke (Rice-Bran Pickles)

You may have noticed the word “probiotics” appearing more often on yogurt packaging and in health programs.

But when someone asks, “Does that mean lactic acid bacteria?” or “Are natto and nukazuke probiotics too?”, it can be surprisingly difficult to give a clear answer.

In this article, you’ll learn three things:

• What “probiotics” are and how they differ from fermented foods
• Which microbes are at work in yogurt, natto, and nukazuke
• Whether the microbes you eat take up residence in your gut, and how to include them in your daily diet

We’ll explain what international scientific organizations and government agencies have to say on the subject.

Probiotics are “live microorganisms” that research has shown can benefit health

Simply put, probiotics are “live microorganisms that, when consumed in adequate amounts, provide a health benefit.”

This is the definition set out in a 2014 consensus statement by the International Scientific Association for Probiotics and Prebiotics (ISAPP), an international organization of probiotic researchers. Japan’s Ministry of Health, Labour and Welfare’s eJIM website, which provides information on integrative medicine, also describes them as “live microorganisms that are thought to provide health benefits.”

Three key words in the definition

This definition contains three important phrases:

• Live: The microorganisms must be alive
• Adequate amounts: Their mere presence is not enough; the amount must be one that has been established through research
• Provide a health benefit: The benefit must have been demonstrated through research

In other words, “probiotics” is not a term for all foods that contain microbes. It refers to microbes that have been studied to determine which ones, in what amounts, provide what benefits.

“The microbes themselves” and “food for microbes” are different

A similar term is “prebiotics.” These are components that serve as food for microbes living in the gut, such as oligosaccharides and dietary fiber.

Learn more about the difference between “pro” (the microbes themselves) and “pre” (food for microbes) in this article.

Not all fermented foods are probiotics

A common misconception is that “fermented foods = probiotics.” ISAPP clearly explains that fermented foods and probiotics are not the same thing.

Fermented foods are “foods made with the help of microbes”

Fermented foods are made using the activity of microbes that grow or change the components of food. Examples include miso, soy sauce, bread, yogurt, natto, and nukazuke.

The key point is that “microbes were active during production” and “the microbes are alive when you eat the food” are two different things.

Heat treatment or pasteurization can kill the microbes

According to ISAPP, some fermented foods undergo processes such as pasteurization, heating, smoking, or filtration after they are made. These processes can kill or remove the microbes. In such cases, even fermented foods may not provide live microbes when eaten.

Even if live microbes are present, that alone isn’t enough

ISAPP also explains that even if a fermented food still contains live microbes, it may not meet the criteria for being called a “probiotic” if the benefits of those microbes have not been verified through research.

That doesn’t diminish the value of fermented foods. ISAPP’s materials also note that fermented foods can be a source of live microbes. Just understand that the term “probiotic” is used quite strictly.

Not all “lactic acid bacteria” are the same

Another thing to keep in mind is that even among “lactic acid bacteria,” characteristics differ by type. ISAPP’s materials state that scientists agree that “not all probiotics are the same.”

Even within the same group, microbes are divided into more specific types called “strains.” To use a human analogy, “lactic acid bacteria” is like a surname, while a “strain” is like an individual’s name. People with the same surname can have very different personalities. Research into potential benefits is conducted on individual strains like these.

Different microbes are at work in yogurt, natto, and nukazuke

So, which microbes are at work in familiar fermented foods? Let’s look at three: yogurt, natto, and nukazuke.

Yogurt: Made with lactic acid bacteria. Japan has a standard for the number of microbes

Yogurt is made by fermenting milk or similar products with lactic acid bacteria. In Japan, foods like yogurt are classified under the name “fermented milk” according to government regulations (the Ministerial Ordinance on Milk and Milk Products).

Two types of lactic acid bacteria have traditionally been used to make yogurt: Bulgarian bacillus and Streptococcus thermophilus. According to Meiji’s Yogurt Library, when these two are together, they produce substances the other needs, helping one another grow quickly.

In Japan, fermented milk must contain at least 10 million lactic acid bacteria (or yeast) per milliliter (a standard cited in materials submitted to the Ministry of Health, Labour and Welfare by an industry association).

Note that the types of microbes used and whether they are alive when eaten vary from product to product.

Natto: Made with “natto bacteria,” a type of Bacillus subtilis

The microbe used to make natto is natto bacteria. According to research information from Kyoto University, natto bacteria are a type of Bacillus subtilis, a microbe that naturally lives in places such as dead grass. They grow well on steamed soybeans, transforming them into natto.

Natto bacteria also produce spores. Spores are like a “dormant form” enclosed in a shell, which microbes produce to survive harsh conditions.

Important: People taking warfarin, a medication that reduces blood clotting, are advised to avoid natto. According to Japan’s Pharmaceuticals and Medical Devices Agency (PMDA), vitamin K in natto and natto bacteria that produce vitamin K in the large intestine can weaken the medication’s effect. If you take medication, follow your doctor’s or pharmacist’s instructions.

Nukazuke: Made with two types of microbes, lactic acid bacteria and yeast

Nukazuke is a traditional Japanese fermented food made by pickling vegetables in a “nukadoko,” or rice-bran bed. According to materials from Fukushima University, the distinctive tartness and aroma of nukazuke are produced mainly through fermentation by lactic acid bacteria and yeast.

Yeasts are a group of microbes also used to make bread and alcoholic beverages. A defining feature of nukazuke is that these two types of microbes—lactic acid bacteria and yeast—work together.

Important: Pickles and miso are foods whose salt content is worth keeping an eye on. According to the Ministry of Agriculture, Forestry and Fisheries, the daily target for salt intake is less than 7.5 g for adult men and less than 6.5 g for adult women (Dietary Reference Intakes for Japanese, 2025). Meanwhile, the average daily salt intake in Japan was 9.8 g (2023 National Health and Nutrition Survey). Consider how much you eat in the context of the salt in your other dishes.

Most of the microbes you eat don’t take up residence in your gut—they “pass through”

Here’s a question many people wonder about: “If I eat yogurt, do those microbes take up residence in my gut?”

Normally, they don’t take up residence in the gut

ISAPP’s materials state that probiotics generally do not colonize the gut. “Colonize” means taking up residence in the gut and continuing to live there.

The microbes you eat pass through your digestive system like travelers, and most eventually leave your body.

They interact with things as they pass through

Does that mean they’re of no use if they don’t take up residence? ISAPP’s materials explain that as probiotics pass through the gut, they interact with intestinal cells and microbes that are already there.

Think of the microbes you eat not as “residents” of your gut, but as “travelers passing through.” Even if they don’t settle in, they can still encounter things along the way.

That’s why the idea is to “take them every day”

A Japanese provisional translation of materials from the International Dairy Federation also states that most probiotics are thought not to colonize the gut permanently. It goes on to explain that daily intake is considered important.

Rather than eating a lot at once and stopping, the idea is to make them a regular, manageable part of your daily diet. This is the approach suggested for probiotics. When adding foods containing microbes to your meals, it’s a good idea to focus on what you can stick with.

“The more you take, the better” isn’t necessarily true

ISAPP’s materials also state that more microbes do not necessarily mean greater effects. What matters is the amount and type of microbe that have been verified through research. With foods, too, prioritize what’s easy to keep up rather than increasing the amount you eat.

How can you include them in your daily diet?

Now, let’s move from the research to everyday meals.

Add “one item” to your usual meals

Rather than doing anything special, an easy way to make this a habit is to add one food made with the help of microbes to your usual meals.

• Breakfast: Top yogurt with fruit such as banana. On days you have rice, add a serving of natto
• Lunch or dinner: Have miso soup or a small serving of nukazuke on the side
• Snacks: Choose plain yogurt instead of a sweet snack some days

Eat a variety instead of relying on one food

Different microbes are at work in yogurt, natto, and nukazuke. Rather than focusing on just one, try including a variety of fermented foods in your meals, in amounts that feel manageable.

It can also help to include foods containing dietary fiber, which feeds gut microbes, such as vegetables, beans, seaweed, and mushrooms. For more about the microbes that live in your gut, see our article on the gut microbiome.

Things to keep in mind

• Be mindful of how much you eat of foods that contain salt, such as pickles and miso
• If you take medication or have a chronic condition, consult your doctor about changes to your diet
• eJIM explains that the risk of adverse effects from probiotics may be greater for people with serious illnesses or weakened immune systems. If you are considering supplements, it advises you to consult a healthcare professional first
• If digestive discomfort persists, don’t try to address it with food; see a healthcare provider

Frequently asked questions

Q. Are heated or dead microbes useless?

This article cannot say whether they are “useful” or “not useful.” This is still an area of active research. However, microbes killed by heating or other processes do not fit the definition of “live microbes,” so they are not called probiotics. In 2021, ISAPP proposed a definition for “postbiotics”: non-living microbes and their components that provide a health benefit.

Q. Should I eat natto or yogurt?

You don’t need to choose one over the other. They contain different microbes, so choose what you enjoy and can keep eating comfortably as part of your usual diet. As noted above, if you take warfarin, follow your doctor’s or pharmacist’s instructions regarding natto.

Q. Should I eat a lot of yogurt every day?

The materials discussed in this article indicate that more microbes are not necessarily better. Rather than eating a lot, focus on making yogurt a manageable part of your daily diet.

Summary: Foods containing microbes—“daily, varied, and manageable”

Here are the three main takeaways:

• Probiotics are “live microbes” that research has shown provide a health benefit when consumed in adequate amounts. Not all fermented foods are probiotics
• Yogurt contains lactic acid bacteria, natto contains natto bacteria, and nukazuke contains lactic acid bacteria and yeast. Even familiar fermented foods contain different microbes
• Most of the microbes you eat pass through your gut without taking up residence. Daily intake is considered important for probiotics, so at mealtimes, it’s better to “keep it up without overdoing it” than to eat “a lot at once”

One thing you can do starting today is add a serving of yogurt or natto to tomorrow’s breakfast.

Take a look at these related articles as well:

• How is kestose different from lactic acid bacteria and bifidobacteria supplements? Understanding “food for microbes” versus “the microbes themselves”
• What is the gut microbiome? A simple guide to “good,” “bad,” and “opportunistic” bacteria

Why not add kestose to your daily gut-health routine?

The information above is general information about probiotics and fermented foods. It does not demonstrate the effects of kestose.

Kestose is not a microbe itself; it is an oligosaccharide that serves as food for beneficial bacteria. Nakaya Shoten’s kestose is made with 100% kestose, an oligosaccharide consisting of three sugar units. It comes in 30 packets of 3 g each. Add one packet a day to yogurt or a drink as a guide. It has a mild sweetness.

• Kestose, 3 g, 30 packets (one-time purchase)
• Kestose, 3 g, 30 packets (subscription)

For details such as pricing, please see the product page.

This article provides general information about diet. It is not intended to diagnose, treat, or prevent disease. If you have concerns about your health, have a chronic condition, or have ongoing symptoms, please consult a doctor.

Sources

• ISAPP, “A roundup of the ISAPP consensus definitions” (definitions by Hill et al. 2014, Salminen et al. 2021, and Marco et al. 2021) https://isappscience.org/a-roundup-of-the-isapp-consensus-definitions-probiotics-prebiotics-synbiotics-postbiotics-and-fermented-foods/
• ISAPP, “Probiotics: Common Misconceptions,” Japanese version (2020) https://isappscience.org/wp-content/uploads/2020/06/Pro_Myths_Japanese.pdf
• Ministry of Health, Labour and Welfare, eJIM, “Oral Probiotics” https://www.ejim.mhlw.go.jp/public/overseas/c02/09.html
• International Dairy Federation (IDF), FAQ, provisional Japanese translation by the Japan National Committee https://www.j-milk.jp/jidf/wp-content/uploads/2015/06/j-probiotics.pdf
• Japan Fermented Milk and Lactic Acid Bacteria Beverage Association, “Request Regarding the Cultivation Temperature for Component Standards for Low-Temperature Fermented Milk” (2014; materials for a Ministry of Health, Labour and Welfare council meeting) https://www.mhlw.go.jp/file/05-Shingikai-11121000-Iyakushokuhinkyoku-Soumuka/0000036811.pdf
• Meiji Yogurt Library, “Yogurt Components” https://www.meiji.co.jp/yogurtlibrary/laboratory/yogurt/02/01/
• Kyoto University, “Mechanism Behind the Struggle Between Soybeans and Natto Bacteria Revealed” (2020) https://www.kyoto-u.ac.jp/ja/research/research_results/2020/201029_2.html
• Keitaro Kimura, “New Developments in Natto Research: Exploring Co-evolution Through Natto Bacteria and Phages,” Journal of the Society for Biotechnology, Japan, 90(6) https://www.sbj.or.jp/wp-content/uploads/file/sbj/9006/9006_tokushu-2_3.pdf
• Pharmaceuticals and Medical Devices Agency (PMDA), Drug Q&A, “I take warfarin and have been advised to avoid natto, chlorella, green juice, and similar products. Why?” https://www.pmda.go.jp/safety/consultation-for-patients/on-drugs/qa/0016.html
• Fukushima University, press release, “Launch of ‘Assorted Nukazuke’ Made with Lactic Acid Bacteria Isolated from Fermented Products in Fukushima Prefecture” (2026) https://www.fukushima-u.ac.jp/press/Files/2026/08/206_02.pdf
• Ministry of Agriculture, Forestry and Fisheries, Food Education Navigator (daily salt intake targets) https://www.maff.go.jp/j/syokuiku/minna_navi/topics/topics5_04.html