Japanese Diet and Microbiome

Alexandra (Sasha) Fedorova
8 min readJun 1, 2018


My recent interest in human microbiome led me to explore the traditional Japanese diet. Not the weight loss diet, but their way of eating. In this post I will share the few bits that I learned about these fascinating subjects.

Human microbiome is the community of microbes that live inside us. Of particular interest is the microbiome of our guts. Researchers have linked the composition of the gut microbiome to various diseases, obesity, and even personality traits. Furthermore, using germ-free mice (special mice cultivated in the lab to have absolutely zero microbes in their guts), the researchers were able to demonstrate interesting causal effects. For example, if you inject the microbiome of an obese person into a germ-free mouse, the mouse gets fat. If you inject the microbiome of a skinny person, the mouse gets skinny. There are even documented human cases, such as this one (pg. 17), where a young girl’s epilepsy was treated via a fecal transplant from a healthy donor (you put a healthy person’s poo inside the gut of a sick person).

There is a plethora of books and scientific articles written on the subject, and this whole field is breathtaking. Yet, I was frustrated to find very little actionable information. Short of transplanting the feces of my ironman-runner friend into my own gut, what can I do to make my and my family’s microbiomes healthier? The most concrete statement I’ve seen is “eat more fiber, less fat and sugar”. How much more? How much less?

The search for actionable information got me thinking about entire populations of humans that obviously “got something going for them”. For example, my sister, who lives in France, keeps talking about these French women who eat croissants and cheese, yet remain slim throughout their lives. I also thought of Japanese girls in my ballet class, who are not simply fit, but are as lean as bodybuilders in competition season (without all the bulk). They do the same ballet exercises as the rest of us, but their body fat percentage is much lower, and they are super strong!

I had two questions in mind: Is there something about the Japanese or the French microbiome that sets it apart from everyone else’s? If so, can I make my own microbiome look more “Japanese” or “French” by changing my diet? And will this bring the health benefits that the owners of these microbiomes typically enjoy?

My search led to this fascinating paper that analyzed the microbiomes of people from Japan, Russia, France, China, the United States and other countries in Europe, Asia and South America. Figure 2 in this paper revealed fascinating information.

Firmicutes are not the “fat” bacteria. The first thing that jumped at me is that the Japanese as well as most Europeans had a lot more Firmicutes and a lot fewer Bacteroidetes than the Americans. (Both Firmicutes and Bacteroidetes are a sort of “classes” of bacteria). Interestingly, in the North American literature Firmicutes are considered the “fat” bacteria and the Bacteroidetes the “skinny” bacteria. So if you have a higher proportion of the former to the latter you are more likely to be fat and vice versa. But we all know that the US population has a much higher obesity rate (about 30%) than the French and the Japanese (9% and 3% respectively). So, go figure! My guess is that the Firmicutes were named the “fat” bacteria based on the studies done on the American subjects, but these findings may not apply when you compare people from different food cultures.

Japanese microbiome is unique. This paper concluded that the Japanese microbiome is unique in a couple of ways. The most striking difference is the abundance of Bifidobacterium, bacteria that’s part of the Actinobacteria class. These bacteria are present in kefir and some probiotic yogurts. Interestingly, the French, the other “skinny” nation, also have a pretty high proportion of Bifidobacterium compared to the rest of the studied nations. The Japanese have nearly 18% of Bifidobacterium, the Austrians about 10%, the French about 8%, the rest — fewer than 5%.

Ok, so the Japanese have the highest longevity and the lowest obesity rate in the world and also the highest span of healthy life years. And their gut microbiome is unique. Is this because of what they eat? Can you change your microbiome to look “Japanese” by changing the way you eat and can you reap the associated health benefits? The people who study this stuff still don’t know the answers to these questions, but, I thought, it does not hurt to find out for myself.

I decided to find out exactly how the Japanese people eat, and then try to eat like this myself. Incidentally, just before diving into the Japanese diet, I sampled my own microbiome at ubiome.com, so I have a “before” snapshot of my gut’s microbiome. I also scrupulously record what I eat every day (I like to measure things), so there will be loads of lovely data to analyze.

My research on Japanese diet led me to a book by Naomi Moriyama, Japanese Women Don’t Get Old or Fat: Secrets of my Mother’s Tokyo Kitchen. Naomi paints a vivid, almost palpable, picture of what the Japanese might have on their plates every breakfast, lunch and dinner. This is an awesome book to read, but I’ll summarize what I learned here.

To me, there are three key points about the Japanese diet: the kinds of food they eat, the diversity of foods present at each meal, and how the food is presented.

The kinds of food they eat. The Japanese diet is dominated by fish, vegetables, rice, miso soup, sea weed, soybeans, noodles and fruit. In contrast to the Western diet, there is little meat, bread and cheese. Japanese eat a ton of rice. The trick is, I think, that rice fills you up, but it’s less melt-in-your-mouth than bread, so you end up eating less and feeling more full. So a fish-and-rice meal would be better than a fish sandwich for maintaining your waste line. Miso soup also fills you up and adds the feeling of “comfort” to your meal. Fish, vegetables and fruits are obviously healthy. Fruits are consumed in small quantities, so you don’t get overloaded on sugar. Soybeans contain lots of fiber.

The diversity of foods present at each meal. What I found striking is how many foods are present at each Japanese meal, including breakfast. In my home country it is common to have just a plate of pasta and a piece of chicken for dinner. Or just a bowl of yogurt for breakfast. Western meals are a lot less diverse than Japanese meals: you might get a salad and a plate of pasta or meat and potatoes at a “traditional” restaurant. On a Japanese lunch or dinner table, you would see rice, several kinds of vegetables, fish (or occasionally meat or chicken), miso soup and perhaps also some noodles. I think that when a meal is diverse, it satisfies you with fewer calories (unless it is served as a buffet), because you get to experience many tastes and entertain multiple senses. Also, the presence of bulky rice, satisfying fats and proteins, and water-rich vegetables fills you up. In contrast, if you get a boring pasta dish, your stomach might get full before you satiate your other senses, and you might keep eating to get that extra comfort even if you are already full.

How the food is presented. That, in my opinion, is a crucial part of why the Japanese people stay so healthy. In Japan, the food is served in tiny portions on individual plates, presented all at once. In the Western world, the food is served in courses, one large dish after another. As a result, here is what happens to me at a typical Western restaurant. I come to a restaurant. It’s late in the day, I am tired and starving. What’s the first thing that appears at the table? Deliciously smelling fresh white bread with butter. I usually avoid white bread, but at this point I am too weak to resist. The glass of wine that is served at the same time makes any act of will power impossible. By the time I finish the bread, I am almost full, but here comes the appetizer, larger in size than I want or need, but I am hungry so I finish it. By the time the main course comes I am completely full, but I eat it anyway, because, well, I ordered it. In the end, I leave the restaurant completely over-full.

Contrast that to what happens when the food is presented Japanese style. I have many small portions of different foods presented to me all at once. I can taste a little bit of everything, satisfying all my senses. When the rice or noodles appear before me at the same time as vegetables and salmon, it is easier for me to convince myself to eat vegetables and fish before gorging on a second helping of Udon.

My understanding of the Japanese diet is based on a single book by Naomi Moriyama and on what I saw in Japanese restaurants, so it is most certainly limited. However, my impression is that, apart from sushi, Japanese-style dishes are very quick to make: whip up a bowl of miso soup by adding hot water to miso paste, quickly sautée some fish and vegetables on a hot frying pan, boil some rice. For everyday cooking, I find this very convenient.

Rather than cooking authentic Japanese meals, I decided to adopt from the Japanese diet the three principles: the kinds of food they eat, the diversity of foods served at eat meal and the presentation. Other than that, I don’t practice the Japanese diet to the letter. I eat brown, not white, rice and also quinoa and boiled buckwheat. I add butter to my rice and vegetables. I do have a piece of cheese and some yogurt and kefir every day, and I have not completely given up whole-grain bread. I do eat some soybeans in the form of edamame, but mostly I eat chickpeas and other kind of beans. Making sure my family eats fish every day is challenging, but I try. I find miso soup and dried seaweed delicious and easy to get, so I have them every day. And drinking buckets of green tea — no problem! I do stick to portion sizes and presentation. I take pleasure in serving food in elegantly arranged small dishes. Here are a few examples of my Japanese-ish meals.

1: Breakfast. One-egg omelette, cheese, smoked salmon, sautéed broccoli and cauliflower. 2: Lunch. Sautéed broccoli and cauliflower, miso soup, buckwheat, sautéed chickpeas, sautéed wild salmon, ratatouille. 3. Brunch. Buckwheat, green tea, coconut flower cookie, yogurt, ratatouille, crab cake, avocado.

I also got a “yumbox” for my daughter, for packing school meals. It has six compartments, and is inspired by a Japanese bento box. The idea is that each compartment hosts a different food group. It reminds me to give diverse food to my daughter and teaches her to eat healthy.

Yumbox. Cheese, dried mango, egg white, brown rice, 85% dark chocolate, raw broccoli and cauliflower.

As I started following the Japanese diet, I was able to cut my calories intake by 500/day without feeling hungry. I eat about 20 grams of fiber per 1000 calories (twice as much as an average Westerner) and on most days I eat less sugar (added and naturally occurring) than fiber.

What about the microbiome? Will my “Japanese” diet make my microbiome look more like that of a Japanese? Will I become healthier and leaner? Time will tell, but I am looking forward to resampling my gut microbiome in a couple months to find out!



Alexandra (Sasha) Fedorova

I research computer systems, raise young scientists and consult in the area of systems performance. I am a professor at the University of British Columbia.