how to heal your gut with fermented Japanese food

How to heal your gut with fermented Japanese foods?

Do you have regularly digestive issues like being bloated or having gas or being constipated? Well, maybe your microbiome is unbalanced? It’s probably time to try some amazing japanese fermented foods to heal your gut!

When I went to Japan last year, I thought I already knew Japanese food (which I already loved). But trust me you have to go there and taste it for yourself. It’s so amazing!!! Not only was it super delicious but it was also so healthy (except for the occasional matcha desserts that I took…yum!).

Though, one thing that surprised me was how much they ate fermented foods. That made my stomach so happy! My stomach has had a lot of health issues over time, so it’s super sensitive to lots of foods and gets out of balance pretty easily. Combining eating fermented foods with the 9 cups of vegetables that I described in this other article has made me so much healthier!

If you also have a fragile stomach, food intolerances, a leaky gut or you simply feel that you need to feed your gut some foods to make it healthier, keep on reading!

What is your microbiome?

So, what is your microbiome exactly? Dr Sarah Ballantyne explains it in this way: “The term gut microbiota refers to the massive collection of microorganisms that inhabit our gastrointestinal tract”. We have approximately 30 to 100 trillion bacteria in the human gut. You probably already know about harmful bacteria, but we also have neutral and beneficial bacteria. Actually, when we have a good diversity of these helpful microorganisms in our bodies, this is a sign of being healthy.

The following study says that our gut is linked to our whole health, “How we digest our food, and even the food sensitivities we have are linked to our mood, behavior, energy, weight, food cravings, hormone balance, and immunity”. Further into the text, it says that the synergy between the nutrients we eat and our microbiome is what is going to decide how healthy we are. To know more, click on this link.

Knowing that what goes on in our gut affects way more than simply our digestion, actually gives us a lot of power to heal a lot of our problems! How you feel in your mind and in your body is greatly influenced by what you eat. Especially by eating regularly fermented foods!

When I was a teenager, I had had inflammation in my intestines for months, so I couldn’t digest well and I felt pain every day. I took a treatment for 6 months that turned out to have caused much more additional damage to my gut lining. When I saw another doctor, he told me my gut was basically destroyed. He had me take probiotics for a long time to repair the damage. When I finally discovered fermented food, that changed my gut health for the best!

What are the health benefits of fermented foods?

Unpasteurized fermented foods naturally have probiotics in them! Probiotics are live healthy bacteria that live in our gut and they help repair it!  

Probiotics are beneficial for a healthy immune system, they help with your digestive system, balance the gut bacteria, help reduce gas, constipation and diarrhea, lowers symptoms of inflammatory bowel disease (IBD) and more.

The importance of unpasteurized food

It’s important for the food to be unpasteurized, because if it’s pasteurized the food goes through a heating process that kills off all the bacteria, so you won’t have any of the beneficial probiotics left.

Why do we ferment foods?

We used to ferment foods a lot because this process prolongs the shelf-life of that food. But it goes way beyond that, it will actually increase the nutritional properties and gets rid of the toxic components (such as phytic acid, phytates, lectins, etc.) of the food. Read more about it here.

Try different fermented foods or drinks to get some variety of probiotics, it will be more powerful for your health.

Basically, by eating unpasteurized fermented foods, you can restore your microflora and heal your gut, let’s check out a few of my favorites!!!

4 Japanese foods to heal your gut

1. Miso

Miso is a fermented soybean paste. It can come from other sources such as other beans, rice or barley, but soybean is the most common one. It is also made with salt, water and koji which is good bacteria.

Not only is it low in calories, but it has numerous nutrients, such as a “high amount of protein, fiber, manganese and vitamin K…including copper, zinc, riboflavin and phosphorus”, says Dr. Axe in this article. It’s a great replacement of animal protein for vegetarians and vegans.

Click here if you want to make your own miso paste!!!

How to cook with miso paste?

If you cook it with your food to add flavor to your meal, I advise you to wait till the end, when your food is almost done and then add it, so you lose the least amount of nutrients and probiotics as possible. Also, you don’t need to use a lot, one to two teaspoons is sufficient for your meal, which is great because you know that your miso will last a while!

hoba miso to heal the gut
hoba miso to heal the gut

Hoba miso

Most of us know about it from tasting the famous Japanese miso soup or it is sometimes used in ramen. But, when I went to this town in the mountains called Takayama, they had this specialty, called hoba miso. It’s so delicious! They use a clay stove, called a shichirin, with a charcoal grill to cook on top of it some vegetables with some miso paste over some dried magnolia leaves. This system cooked it quite quickly and it tasted amazing!!! 

2. Natto

natto on rice

This one is one of my favorites. But it wasn’t always. The first couple of times I ate some, I was so surprised by it’s strange consistency (kind of slimy) and it’s strong smell (in the same way as cheese, but has more of a nutty smell). I didn’t think it was my cup of tea, but turned out that once I got past that, I started loving it. Actually, when I was in Japan, I would eat it for breakfast most mornings.

So, let me explain to you what is this special food and why it’s totally worth eating regularly! Just like miso, natto is fermented soybeans, but the process to make it and the bacteria in it are different. It’s also not in the form of a paste but you see clearly the soybeans that are stringy and slimy.

Benefits of natto

Though, don’t let this stop you because natto is a superfood! With one gram of natto, you are already close to the quantity of the healthy bacteria that you would get by eating a whole serving of other fermented foods! Your gut will definitely thank you for this 😉 read more about in this study.

In addition to that, natto will help you have healthy bones. It has a high quantity of calcium and is rich in vitamin K2. Read about how it reduces the risk of bone fracture in this article

Natto is also beneficial to the heart. Its enzyme helps get rid of blood clots and the vitamin K2 prevents calcium deposit in the arteries.

I won’t go into more details, but natto has amazing nutrients that help with not only your digestive system, bones, heart but your immune system as well. It’s also rich in vitamin C, iron, zinc, selenium and copper.

What are you waiting for? Check out my video on how to prepare it and why you should eat natto beans? And if you don’t like it, invite your friends over. I promise, you will get a good laugh out of it!

3. Shoyu

Shoyu is the Japanese word for soy sauce. This one I know that most of you are familiar with, even if you don’t eat out at Asian restaurants. There are several types of soy sauces, some are of better quality than others. My favorite is tamari which you can often find some that are gluten free. Yes, usually soy sauce is made by fermenting soybeans with wheat. So, if you are trying to cut down or avoid it, look for some gluten free tamari!

Also, avoid soy sauce with Monosodium glutamate (MSG) in it. Not only is this unhealthy but it’s often found in chemically made soy sauce.

It does have a high sodium intake, but thanks to its strong flavor, you won’t be putting that much on your food, so it’s healthier than your basic salt.

It has antioxidant properties, it could reduce seasonal allergies and it helps with the gut health. For these reasons, I do enjoy putting some on my food in certain quantities but don’t over do it. I am also careful about which one I buy, because there are some very unhealthy ones out there. I look for the natural fermented organic soy sauce and gluten free.

4. Tsukemono

Tsukemono is Japanese pickled vegetable. While I was in Japan, they very often served, in restaurants, several bowls of different types of foods in small quantities. One of them was usually a mix of fermented vegetables, like carrots, cabbage, radish and especially other local ones that I wasn’t really sure what they were…but at least they tasted good! Sometimes, they were fermented with vinegar or miso (better).

The fermentation process will give these veggies lots of probiotics which as you now know are so healing for your gut!

fermented vegetables

What to be careful about when eating fermented foods?

If you are not used to eating any of these foods, start out gradually. Don’t just drink a full bottle of kombucha, while having a miso soup and some fermented veggies on the side. Your gut needs to get used to the change. If you consume too much fermented food from the beginning, you could get bloated.

If you have any intolerance or allergy to soy, do not eat natto, miso or shoyu.

You should also avoid eating fermented foods if you have candida, read this article to know why

What other fermented foods do I love to eat or drink?

So, what other fermented foods do I eat or drink on a regular basis to heal the gut? I go for kombucha, water or fruit kefir, tempeh and unpasteurized fermented vegetables found in Europe, such as fermented beets, sauerkraut, etc.

Kombucha is my favorite probiotic-rich drinks. When I have stomach issues, I love to drink kombucha with ginger in it.


If I am making my own fermented drink, kefir is pretty cool because you can make it super fast! Unlike some foods that take weeks or months to ferment, this drink can be made within 2-3 days, depending on how warm it is in your home.

 One of my husband’s favorites is kimchi, it’a Korean dish that is made with fermented cabbage and spices. My husband loves spicy foods, so it’s great for him. Me, spices are an issue for my stomach, so I can’t really enjoy it…


Tempeh is from Indonesia and it’s so easy to cook it with your veggies and a little tamari sauce. It’s simple but delicious! It’s also made of fermented soybean but it’s more compact and solid than the other soy fermented foods we discussed in this article.

Heal your gut with fermented foods!

So, after exploring all the benefits of introducing some unpasteurized fermented foods or drinks into your diet, it is worth trying a few, maybe even that weird sounding natto 😉. Since they heal the gut, immune system, they boost the nutritional properties and lower toxins or antinutrients from the food you eat, they will change your life.

Have you tried any of these foods or drinks? Which one is your favorite? Let us know in the comments!

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