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For decades, doctors viewed the trillions of microorganisms living in our digestive system as passive passengers that simply coexisted with us. Today, science tells a very different story.
Researchers now recognize that the gut microbiome, the vast community of bacteria, fungi, and other microbes living in our intestines, plays an active role in many aspects of health — from metabolism and immunity to brain function and healthy aging. As microbiome research rapidly advances, it is changing the way scientists understand disease and opening new possibilities for personalised healthcare.
Dr. Jeremy Lim, co-founder of AMILI, Southeast Asia’s first precision health company focused on modifying the gut microbiome to improve human health, touches on the various ways your gut microbiome affects your health, and how it is reshaping the future of personalised medicine.
The term microbiome refers to the collection of microorganisms that live in and on the human body. The largest and most complex microbial community resides in the gut.
"The right way to think about microbes is that they are trillions of little biological factories," Dr. Lim explains. "They produce important molecules that can benefit—or sometimes harm—our health."
While these microbes were once thought to be harmless "commensals," scientists now know they perform essential functions. In many ways, they act like tiny biological factories, producing substances that influence the body, including neurotransmitters, vitamins, and other molecules involved in metabolism and immune regulation.
The gut microbiome is estimated to contain trillions of microorganisms, making it one of the most important ecosystems in the human body.
The microbiome evolved alongside humans over thousands of years. However, modern lifestyles have introduced factors that can disrupt this delicate ecosystem.
"I put it to all of you that most of us probably have less-than-ideal microbiomes," Dr. Lim states. "Modern living has inflicted a lot of collateral damage on our resident microbes."
Several aspects of modern living may negatively impact the gut microbiome, including:
Dr. Lim also referenced a study by Dr. Justin Sonnenburg, a leading microbiologist at Stanford University, which found that tobacco, toxins, and other chemicals encountered in daily life can cause collateral damage to the gut's resident microbes.
When the balance of microbes in your gut is disrupted—a condition known as dysbiosis—researchers have linked it to a growing list of health conditions. For example, diets rich in simple sugars can disrupt the intestinal barrier, trigger intestinal inflammation, and negatively affect host metabolism.
This has led to increased interest in concepts such as the gut-brain axis, gut-immune axis, and gut-lung axis, which describe the complex communication networks between the microbiome and different organs throughout the body.
One of the most exciting areas of microbiome research is its relationship with the brain.
Scientists have discovered that gut microbes can produce or influence compounds involved in brain function, including serotonin, gamma-aminobutyric acid (GABA), and dopamine-related molecules. These findings suggest that the gut microbiome may play a role in mood, cognition, and neurological health.
Research in animal models has demonstrated that transferring gut microbes from individuals with certain neurological conditions can influence behaviour and symptoms in recipient animals. While such findings do not prove causation in humans, they have sparked growing interest in exploring microbiome-based therapies for conditions such as autism spectrum disorder and other neurodevelopmental disorders.
Human studies are ongoing, and while results are promising, you should always consult your doctor first.
For years, nutrition advice has largely focused on what people eat. Increasingly, scientists are discovering that who is eating the food may be just as important.
Studies have shown that two individuals consuming the same meal can experience very different blood sugar and blood lipid responses. One possible explanation lies in differences in their gut microbiomes.
"For example, we can tell our patients that eating sourdough is good for you," Dr. Lim shares. "However, sourdough is good for you if you have the right type of microbes.”
This growing understanding has fuelled interest in personalised nutrition, which combines microbiome data, lifestyle factors and metabolic measurements to develop individualised dietary recommendations.
"The key message is that one size doesn't fit all," he concludes.
According to Dr. Lim, the goal is to move beyond generic dietary advice and help individuals make food choices that are better suited to their unique biology.
The digestive tract is home to approximately 70% of the body's immune cells, making the gut a critical hub for immune regulation.
"The gut is where we are most exposed to foreign materials through the foods we eat and the beverages we drink," Dr. Lim explains. "It's therefore not surprising that the microbiome plays such an important role in immune regulation."
Every day, the immune system encounters substances from food, beverages, and the external environment. The microbiome helps train and regulate these immune responses.
Researchers are investigating the microbiome's role in a variety of immune-mediated conditions, including:
While evidence continues to evolve, studies suggest that modifying the microbiome may help influence immune function and inflammation in certain individuals.
However, microbiome-based therapies are still an emerging field, and treatment decisions should always be made under the guidance of qualified healthcare professionals.
One of the most well-known microbiome treatments is fecal microbiota transplantation (FMT), which involves transferring beneficial microbes from a healthy donor to a recipient.
However, Dr. Lim notes that the field has evolved significantly.
"We don't really use the term fecal microbiota transplant with patients anymore," he says. "We prefer the term microbiome restoration therapy because that's really what we're trying to achieve—restoring a healthy microbial balance."
The procedure has also become far less invasive than many people imagine.
He adds, “Twenty years ago, colonoscopy was the primary method. Today, microbiome restoration can often be delivered through oral formulations, making it much simpler and more accessible for patients."
FMT is already an established treatment for recurrent Clostridioides difficile infections, while researchers continue to investigate its potential role in other conditions.
While microbiome restoration therapy has shown promise in certain medical conditions, researchers are also investigating its broader implications for health and longevity. Studies of healthy centenarians have found that their microbiomes often resemble those of much younger individuals.
"Every study of healthy centenarians points to one interesting observation — their microbiomes look much younger than their chronological age," Dr. Lim states. “Their microbiomes are much closer to people half their age, 50 to 60 years old.”
Researchers believe the microbiome may influence aging through its effects on inflammation, metabolism and immune function. As chronic low-grade inflammation is increasingly recognized as a driver of age-related diseases, maintaining a healthy microbiome could become an important part of future healthy aging strategies.
The microbiome is helping to reshape how scientists think about health and disease.
Rather than viewing illnesses solely through the lens of genetics or environmental factors, researchers are beginning to recognize the microbiome as another important piece of the puzzle.
Advances in artificial intelligence, microbiome sequencing, continuous health monitoring, and personalised nutrition are creating new opportunities to better understand individual health risks and responses to treatment.
While many microbiome-based therapies remain under investigation, one message is already clear: our microbial partners play a far greater role in health than previously imagined.
As research continues to unfold, the microbiome may become one of the most important frontiers in preventive medicine, personalised healthcare, and healthy aging.
