A highly anticipated academic conference was held on Sunday, September 21, 2025, where Dr. Jun Kunisawa, a leading researcher in intestinal bacteria, spoke about the deep relationship between intestinal flora and health.
The 9th Academic Conference of the Gut Flora Transplantation Clinical Research Society, featuring Dr. Kunisawa, a familiar face on the TV program “Hayashi Osamu’s Now!”, was attended by not only medical professionals with an interest in gut bacteria and cutting-edge medical care, but also the general public.
Based on Dr. Kunisawa’s research and insights, this article provides an easy-to-understand introduction to everything from the basics of gut bacteria to its latest applications and its potential for personalized nutrition.
Why do gut bacteria affect your health?
What are gut bacteria? Understanding the basics
Intestinal bacteria is a collective term for the countless microorganisms that live in our intestines.
The intestinal environment is made up of more than several hundred types of bacteria, and it is said that their number exceeds the number of cells in the human body.
These bacteria play essential roles in maintaining health, such as aiding digestion, synthesizing vitamins, and regulating the immune system.
For example, in his book “The Amazing World of the Gut Revealed from Examining 9,000 People,” Dr. Kunisawa states that “intestinal bacteria are ‘super organisms’ and can be described as ‘symbiotic organisms,'” emphasizing their importance.
Our health depends on the diversity and balance of our gut bacteria.
How gut bacteria affect your health
According to Dr. Kunisawa, intestinal bacteria are not just “digestive aids” but are deeply involved in the health of the entire body.
Our bodies are influenced not only by the nutrients absorbed by the intestines, but also by the various substances produced by intestinal bacteria.
Therefore, surprisingly, the condition of our intestines has a significant impact on the health of our entire body.
In fact, it has been shown that an imbalance in the intestinal environment (an imbalance in the intestinal flora) is associated with a variety of diseases, including obesity, diabetes, allergies, cancer, and mental health issues.
This is because metabolic products produced in the intestines travel through the bloodstream to the liver and brain, affecting the entire body’s metabolism, behavior, and even emotions.
Given this background, Dr. Kunisawa says, “Balancing your intestinal bacteria is the first step in preventing disease.”
How gut bacteria influence immunity
There is a close relationship between the intestinal environment and immune function, and it is believed that the balance of intestinal flora holds the key to immune strength.
Research by Professor Jun Kunisawa has also revealed that immune cells concentrated in the intestinal tract are activated by stimulation from intestinal bacteria, and that a regulatory mechanism that suppresses inflammation is activated.
Intestinal bacteria have a wide range of effects on our health, but one of their functions is the production of metabolic products.
Some of these metabolites play important roles in regulating immune function.
For example, gut bacteria that produce butyrate play a role in maintaining healthy epithelial cells in the large intestine.
Butyric acid is used as an energy source for the intestines, promotes the proliferation of epithelial cells, and strengthens the intestinal barrier function, acting like a gatekeeper to prevent the invasion of pathogens.
In addition, butyric acid also helps to reduce an overactive immune system.
For example, it prevents runaway allergies and autoimmune reactions by controlling the activity of immune cells that cause inflammation and assisting the function of regulatory T cells that suppress inflammation.
In his book “An Intellectual Adventure in a Strong Body and Bacteria,” Dr. Jun Kunisawa introduces examples of the relationship between allergies, autoimmune diseases, and the composition of intestinal bacteria, and states that improving the intestinal environment will lead to an improvement in the body’s “ability to protect itself.”
Diet to improve your intestinal environment
Foods that nourish gut bacteria
Dr. Kunisawa states that “food is a dialogue with intestinal bacteria,” and emphasizes the importance of consciously providing “good food” for intestinal bacteria in your daily diet.
“Nurturing intestinal bacteria” means increasing the number of good bacteria already living in the intestines and supporting their active function.
In other words, what we eat can greatly affect the “composition” and “activity” of the bacteria in our intestines.
When the bacteria become healthy, they will produce more useful metabolites.
One of the best foods is fiber.
Vegetables and seaweed that are rich in dietary fiber, and fermented foods (such as miso, natto, and yogurt) are typical foods that help cultivate good bacteria in the intestines.
In particular, oligosaccharides and resistant starch, which act as prebiotics (food for good bacteria), play an important role.
For example, bananas, burdock, barley, and onions are rich in oligosaccharides, which support the growth of good bacteria.
Furthermore, when combined with the probiotics (good bacteria) contained in fermented foods, the effect of improving intestinal flora is further enhanced.
Eating habits to avoid and why
Dr. Kunisawa emphasizes that “your regular eating habits determine your intestinal environment,” and that “daily efforts are important for maintaining a healthy intestinal environment.”
In particular, there are warnings that a diet high in processed foods and high in fat and sugar increases the risk of an increase in bad bacteria and inflammatory bowel disease.
Specifically, they point out that consuming only soft drinks, snacks, and fried foods can increase the number of bacteria that produce harmful substances in the intestines, which can lead to inflammation.
In addition, a lack of dietary fiber can weaken the intestinal mucosal barrier.
How to get dietary fiber and its importance
One of the most important nutrients for gut bacteria is dietary fiber.
In particular, water-soluble dietary fiber serves as food for the beneficial bacteria in the intestines and helps produce short-chain fatty acids.
Dr. Kunisawa recommends incorporating a variety of dietary fiber sources into your daily diet, such as burdock, barley, seaweed, and natto.
However, rather than relying solely on certain foods, it is ideal to incorporate a balanced diet of root vegetables, beans, fruits, seaweed, etc., “a little bit every day.”
On the other hand, if you eat a lot of bread and meat at restaurants or eat instant foods, you are likely not getting enough dietary fiber, and you may be disrupting your intestinal environment without even realizing it.
Since modern people’s diets tend to be deficient in these nutrients, conscious intake is essential, which forms the foundation for good health.
The diverse health benefits of short-chain fatty acids
Short-chain fatty acids (SCFAs) are metabolic products produced by intestinal bacteria when they ferment dietary fiber.
You may not be familiar with the term short-chain fatty acids, but it is a very important term when talking about intestinal bacteria.
The most common examples are butyric acid, acetic acid, and propionic acid.
Butyric acid serves as an energy source for the intestines and helps maintain the barrier function of the intestinal wall, while acetic acid is involved in antibacterial action and regulating lipid metabolism.
Propionic acid is involved in glucose metabolism in the liver and is said to affect blood sugar control.
These short-chain fatty acids maintain a slightly acidic pH in the intestines, suppressing the growth of harmful bacteria, as well as suppressing inflammation and strengthening the intestinal mucosa.
Furthermore, it has been discovered that SCFAs are absorbed from the intestines, enter the bloodstream, and act on organs throughout the body, including the brain and liver.
For example, it is expected to have a variety of health benefits, such as improving mental health, preventing metabolic disorders, and even reducing the risk of some cancers.
Dr. Kunisawa suggests that by measuring the concentrations of these SCFAs, it may be possible to quantify the current health of the intestinal environment.
The relationship between gut bacteria and mental health
The impact of gut bacteria on the mind
The gut and brain are connected by a close network called the “gut-brain axis.”
Professor Kunisawa’s research has shown that certain intestinal bacteria affect the secretion of neurotransmitters such as serotonin and dopamine.
This means that the state of your gut can affect your mood and mental state.
For example, it has been reported that people prone to depression have significantly reduced levels of certain intestinal bacteria, such as bifidobacteria and lactobacillus, and this has raised new interest in the idea that improving the intestinal environment can lead to mental stability.
These beneficial bacteria are involved in the metabolism of tryptophan, a precursor to serotonin, and in the suppression of inflammatory cytokines, contributing to mental stability.
However, if these beneficial bacteria decrease due to a stressful lifestyle, a diet high in processed foods, or the use of antibiotics, the balance in the intestines is disrupted, which is thought to have a negative impact on the brain as a result.
Recently, research has begun on “mental-gut correlation care,” which involves improving the intestinal environment as part of the treatment and prevention of depression.
Interaction between stress and the intestinal environment
Dr. Kunisawa says, “It is important to keep your intestines in good condition in order to maintain mental health.”
“An Intellectual Adventure in a Strong Body and Bacteria” explains that the intestinal environment is prone to change under stress, and that beneficial bacteria may be able to suppress stress responses by activating the serotonin pathway.
In other words, while stress can weaken the intestinal barrier function and allow harmful bacteria to proliferate, a healthy intestinal environment can increase stress resistance.
Understanding the connection between the gut and the mind can be said to be essential knowledge for modern people.
The forefront of intestinal bacteria research
Latest research results and their applications
In recent years, research on intestinal bacteria has evolved from simply classifying bacteria to understanding their functions and applying them to practical applications.
Professor Jun Kunisawa’s research team is using the latest metagenomics and multi-layered omics analysis to elucidate how the intestinal flora is involved in our metabolism, immunity, and even brain function.
This has led to the discovery, for example, that specific patterns of intestinal bacteria are involved in blood sugar control and the strength of the immune response.
These findings are expected to form the basis for disease prevention and personalized medicine, and to have a major impact on future dietary advice and treatments.
A relay of bacteria, a journey through the microbiota that connects us to health
The “microbial relay” refers to the passing of roles between various bacteria in the intestines, a process similar to “passing a baton.”
In “The Amazing World of the Gut Revealed from a Study of 9,000 People,” Dr. Kunisawa states that successful “cooperation between bacteria” is the key to a healthy intestinal environment.
Specifically, “saccharifying bacteria,” which break down dietary fiber and produce sugar, work first.
Next, lactic acid bacteria produce lactic acid, bifidobacteria produce lactic acid and the short-chain fatty acid acetic acid, and then other bacteria work to produce butyric acid and other acids. This bacterial relay continues, and bacteria survive by helping each other in the intestine.
(If you’re interested in the bacterial relay, I recommend reading “The Amazing World of the Gut Revealed from a Study of 9,000 People.”)
Intestinal bacteria and medicine notebook
The intestinal environment is greatly affected not only by daily diet but also by medications.
In particular, antibiotics eliminate the bad bacteria that cause infections, but they also reduce the good bacteria in the intestines, so the balance of intestinal bacteria can remain affected for some time after taking the drug.
Professor Kunisawa’s research has also focused on the relationship between drug use history and the composition of intestinal bacteria.
For example, it has been discovered that certain intestinal bacteria can break down drug ingredients, resulting in individual differences in the effectiveness of drugs.
These findings may lead to the development of personalized medicine in the future, such as determining whether a different drug may be more effective for people who have a certain bacterium.
In the future, efforts may be made to record data on intestinal environment, similar to a medicine notebook, leading to more appropriate prescriptions.
The potential of postbiotics
Postbiotics is a new perspective that suggests that dead bacteria and their metabolic products have a beneficial effect on the body.
According to Professor Kunisawa’s research, even dead bacteria can activate the intestinal immune system and suppress inflammation, thanks to their cell wall components and the butyric acid they produce.
This concept could lead to the development of foods containing heat-treated lactic acid bacteria and new functional foods that are different from probiotics, and is expected to become a new trend in future medical care and nutritional supplements.
Visualizing the intestinal environment opens up new avenues for healthcare
The era of precision nutrition and personalized nutrition
Dr. Kunisawa advocates the importance of “precision nutrition,” which optimizes dietary content based on gut bacterial profiles.
“The Amazing World of the Gut Revealed from a Study of 9,000 People” explains that the same food can raise blood sugar levels differently from person to person, and this is said to be a major hint for promoting the personalization of nutritional guidance.
It has become clear that the composition of intestinal flora leads to differences in food absorption and metabolism, and has different effects on health. Therefore, rather than providing “uniform nutritional guidance,” we are now in an era where dietary planning tailored to each individual’s intestinal environment is required.
Visualization of the intestinal environment and new healthcare
As the impact of intestinal bacteria on our health becomes increasingly clear, how can we visualize and utilize the “state of the intestinal environment” in the future?
On Sunday, September 21, 2025, at the 9th Academic Conference of the Intestinal Flora Transplantation Clinical Research Group, held at the Rihga Royal Hotel Osaka, Dr. Kunisawa gave a keynote speech titled “New possibilities for health care opened up by visualizing the intestinal environment.”
This event was successfully concluded with the participation of many attendees.
We are currently accepting applications for [Archive Streaming].
For those who were unable to attend on the day, please take this opportunity to view the latest insights.
Visualizing the intestinal environment has the potential to reveal the key to health, which has been a “black box” until now, and fundamentally change the future of medicine.
This is a rare opportunity to hear Professor Kunisawa speak, so please apply.
For details of Professor Kunisawa’s lecture, please click here.
Frequently Asked Questions (Q&A)
Q1. How long does it take to improve your intestinal environment?
Improvement in the intestinal environment varies from person to person, but changes are often seen within 2 weeks to 3 months.
It is important to review your diet and continually incorporate fermented foods and dietary fiber into your diet.
Q2. Are probiotics and supplements really effective?
Some probiotics and supplements have even been shown to be clinically effective.
However, some products may work better than others, so if you don’t feel any effect, try changing the product or focusing on consuming natural foods.
Q3. How can you check your gut bacteria?
Nowadays, by using private intestinal flora test kits, you can easily find out the balance and diversity of your intestinal bacteria at home.
This collaboration between testing and medical care has been attracting attention in recent years.
Q4. Is it important for children and the elderly to maintain a healthy intestinal environment?
It’s very important.
A child’s intestinal environment determines their future health, and for the elderly, it is involved in maintaining their immune system and cognitive function.
Take care of your intestines by following an age-appropriate diet.
Q5. Is it true that stress can cause poor intestinal health?
Yes, that’s true.
Severe stress can weaken the intestinal barrier function and lead to an increase in harmful bacteria.
Conversely, there is also research that suggests that improving your intestinal environment can increase your resistance to stress.
References
1. Jun Kunisawa, “The Amazing World of the Intestine Revealed from a Study of 9,000 People: An Intellectual Adventure into a Strong Body and Bacteria”
2. Jun Kunisawa, “Revolutionizing the Intestine with ‘Good Enzymes'”
3. Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):e1002533. doi:10.1371/journal.pbio.1002533
4. Hosomi K, Saito M, Park J, Kunisawa J, et al. Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota. Nat Commun. 2022;13:4477. doi:10.1038/s41467-022-32015-7
5. Furusawa Y, Obata Y, Fukuda S, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013;504:446-450. doi:10.1038/nature12721
6. Nagatake T, Kunisawa J, Arita M, et al. Dietary ω-3 fatty acid exerts anti-allergic effect through conversion to 17,18-epoxyeicosatetraenoic acid in the gut. Sci Rep. 2015;5:9750. doi:10.1038/srep09750
7. Taitz JJ, Tan J, Ni D, et al. Antibiotic-mediated dysbiosis leads to activation of inflammatory pathways. Front Immunol. 2024;15:1493991. doi:10.3389/fimmu.2024.1493991
8. Ryan FJ, Clarke M, Lynn MA, et al. Bifidobacteria support optimal infant vaccine responses. Nature 2025;641:456-464. doi:10.1038/s41586-025-08796-4
9. Schaub AC, Schneider E, Vazquez-Castellanos JF, et al. Clinical, gut microbial and neural effects of a probiotic add-on therapy in depressed patients: a randomized controlled trial. Transl Psychiatry 2022;12:227. doi:10.1038/s41398-022-01977-z
10. Tanabe M, Kunisawa K, Saito I, et al. High-cellulose diet ameliorates cognitive impairment by modulating gut microbiota and metabolic pathways in mice. J Nutr. 2025;155(6):1689-1699. doi:10.1016/j.tjnut.2025.04.004
11. Mutoh N, Kakiuchi I, Hiraku A, et al. Heat-killed Lactobacillus helveticus improves mood states: a randomized, double-blind, placebo-controlled study. Benef Microbes 2023;14(2):109-118. doi:10.3920/BM2022.0048
12. Bermingham KM, Linenberg I, Polidori L, et al. Effects of a personalized nutrition program on cardiometabolic health: a randomized controlled trial. Nat Med. 2024;30:1888-1897. doi:10.1038/s41591-024-02951-6
Supervisor: Dr. Hideaki Shima, Ph.D. in Agriculture (Symbiotics Co., Ltd.)
Release date: June 25, 2025
Update date: October 15, 2025
