The Business of Changing Minds — When it comes to health, the CEO of AMILI trusts his gut

There's one particularly striking study that examined the effects of microbiome transplants. Researchers introduced stool samples from children with autism into germ-free mice, noting that the mice developed autistic-like behaviours. 'This discovery challenges traditional classifications of autism as a non-communicable disorder,' says Dr Jeremy Lim, co-founder of AMILI. He wonders, 'If microbiome transplants can induce these traits, could we also develop treatments based on microbiome health?'

Still, for all its promise, the idea of microbial transplants — or "poop transplants" as they are often irreverently called — still meets resistance. Some of it is due to the "ew" factor, but much is due to conservatism within medical communities. "In Singapore, microbial transplants aren't used for children with autism spectrum disorder," Lim says. "We've had discussions with the professional community, but let's just say they've been progressing slowly."

That reluctance to engage with emerging, non-traditional therapies isn't unique to Singapore — it reflects a broader issue within medicine. Lim describes that the field has often been slow to integrate new knowledge when it challenges established norms. "Microbial transplants won't be a cure," he concedes, "but the data has shown encouraging results in a significant proportion of patients."

The idea of exploring uncharted territories in medicine is at the core of AMILI's mission. Lim acknowledges that pushing the boundaries of traditional medical practices comes with its own challenges, but he believes in the importance of innovation. The microbiome is still an unfamiliar concept for many people, but its potential to revolutionise healthcare is vast. It's not just about curing diseases — it changes how we view health from a reactive approach to a proactive one.

"We're not trying to fix what's broken," Lim demurs; “we're trying to prevent people from breaking in the first place."

Learning from history

Reflecting on the history of microbiome science, Lim shares, 'The microbiome connects past practices with future possibilities.' Ancient Chinese treatments involving probiotics demonstrate a longstanding understanding of gut health, now validated by modern science. "The Chinese were actually the first to perform microbiome — or 'food' transplants. In an ancient Chinese medical text, often referred to as the Yellow Book, there's documentation of medicinal practices, including one rather unique treatment for the emperor's health."

Lim describes how this process involved taking stool from healthy 12-year-old boys, sealing it in a golden container, burying it for two years, and retrieving it as a concoction known as 'yellow soup,' (human fecal slurry, to be more specific) which the emperor would drink. "It sounds unappealing," he admits, "but it produced a nutrient-rich broth full of beneficial microbes — an ancient, thermally charged probiotic, in a sense."

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Recently, Lim explains leaning in closer and slightly more animatedly, scientists in China revisited this process, recreating it under similar conditions of pressure and temperature. "In this controlled environment, beneficial microbes thrive, consuming harmful bacteria and undigested food, resulting in a potent probiotic broth," he notes.

Forgotten for centuries, this practice eventually resurfaced in the Western world around the 1950s and only entered mainstream use around 2010, when American doctors began employing microbiome transplants to treat bacterial overgrowth syndrome. 

This condition, marked by an overpopulation of harmful bacteria, can cause severe gastrointestinal issues that are otherwise hard to treat. By introducing healthy bacteria from a donor, doctors were able to repopulate the patient's gut with beneficial microbes, restoring balance and alleviating symptoms.

A library of life

Today, from a nondescript office at Science Park, Dr Jeremy Lim is on a mission to change how we think about health. AMILI, just five years old, is Asia's first and only gut microbiome transplant bank and is building up the world’s largest multi-ethnic Asia gut microbiome database, aiming to explore how these invisible ecosystems shape our bodies, our cultures, and our futures. His journey into this complex world of microbes didn't begin as an academic interest; rather, it emerged from an existential question that many high-level executives eventually grapple with — what do you do after a successful career when your heart craves something more?

"At the end of 2018, I'd actually decided to retire," Lim confesses, his voice hinting at a kind of wistful relief. He had spent years building a flourishing healthcare consulting practice. It was thriving, he was thriving, but he knew consulting was "a young person's game." After decades of late nights and frequent travel, Lim wondered, "Do I really want to keep doing this for the rest of my life?" The answer, ultimately, was no.

After initially considering retirement or a quiet academic position at NUS, Lim's conversation with his future co-founders led him to a new calling. Their message resonated: 'If we don't do this, no one else will.' Today, Lim and his team at AMILI maintain Asia's largest multi-ethnic microbiome database, aimed at understanding the unique needs of Southeast Asia's diverse populations.

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Unlike many health technologies imported from the West, AMILI's research focuses on people living in Southeast Asia — multi-ethnic populations whose microbiomes differ vastly from those in the West. As Lim points out, "Across regions, microbiomes differ significantly, which makes sense — people in tropical, rice-eating areas have different microbes compared to those in temperate, wheat-eating regions. Microbes evolve and adapt to the environment they're in."

The uniqueness of our microbiomes is shaped by our diet, climate, and lifestyle, meaning that findings from Europe or America don't necessarily apply here. Instead of asking, "Does Bulgarian yoghurt work for us?" Lim and his team focus on finding, "What is the equivalent of Bulgarian yoghurt for multi-ethnic Asia?" This kind of specificity — this precision — is what AMILI aims to offer.

AMILI's work can potentially bridge the gap and connections between cultural practices and modern health. What Lim and his team of researchers seek to do is to understand these relationships better and provide more effective and culturally appropriate healthcare solutions. 

The ability to know how different populations respond to different treatments could, in no small way, reshape global healthcare and reduce disparities in medical outcomes.

A change in approach

Lim's story of embracing the microbiome's potential is a poignant one that feels, at its core, existential, challenging the very boundaries of what it means to be well.

"The microbiome literally encompasses the microbes that live in and around us," he says — saying "us" in a way that blurs the lines between human and microscopic life. "There are many different microbiomes: the gut microbiome, which is the most complex and the one we primarily focus on, as well as microbiomes on the skin, in the lungs, and in the vaginal area, among others."

Yet, this attention to detail was not commonplace thirty years ago when Lim was a medical student. He was part of a cohort that was taught to view these microbes as passive hitchhikers, creatures best left undisturbed as long as they didn't cause trouble.

"The idea was: don't disturb them, and they won't disturb you." Back then, he explains, it made sense; without the tools to see the microbiome's impact on human health, the best approach was a hands-off one. Today, however, with advances in sequencing and computing, this understanding seems almost laughably simplistic.

The contrast he draws is striking. "The Human Genome Project, completed in 2000, cost around a billion dollars and mapped about 23,000 human genes," Lim says, eyebrows raised with understated gravity. "In contrast, a typical gut microbiome contains two to three million genes, making it vastly more complex. A single microbiome analysis generates about one terabyte of data — the equivalent of around 2000 movies in Netflix terms."

It makes our genome look almost primitive by comparison.

On equity

Lim also passionately discusses how inequalities in healthcare can profoundly impact an individual's microbiome and, ultimately, their health. He reflects on his visits to Indonesia and the Philippines, where stunting affects a significant proportion of children. "Physical stunting is visible, yes, but the brain is also developing during that time. So, have we lost untapped potential in Indonesia and the Philippines due to stunting and poor nutrition? I think the answer is clearly yes."

There’s a direct relation, Lim posits, between poor nutrition and the quality of the microbiome in the body. Ergo, without access to diverse and nutritious foods, children in underprivileged communities may not develop a robust microbiome, leaving them more vulnerable to diseases and less able to thrive cognitively and physically.

It’s why AMILI's research on how different ethnicities across Asia process and react to various diets is crucial. "If we can help humans digest food more efficiently, we could need less food overall," Lim suggests, echoing ideas championed by Bill Gates, who has called the microbiome a key to solving malnutrition. 

The impact this could have on third-world countries is massive, potentially reducing the need for food imports and easing the strain on limited resources while giving children a stronger foundation for lifelong health.

The forgotten diversity of our diets

"Do you think older generations had healthier diets because they ate fewer processed foods?" I ask, reflecting a time when meals were simpler, sourced locally, and free from chemical additives more readily found in food today. It's a question that, for me, as a child growing up in the 90s, stirs memories of kitchens unmarked by labels and ingredient lists, where food was fresh by necessity rather than choice, where people went to the market at the crack of dawn every day, without fail, to feed a household of growing minds. 

Lim's response is unequivocal. "Yes, exactly — this pattern is seen across all cultures in Asia. I have a presentation with a fascinating chart on microbiome diversity that I'll send you. It shows that the more diverse your microbiome, the better your health tends to be. Researchers examined various populations, from Tanzanian hunter-gatherers to urban residents in San Francisco, and found a clear decline in microbiome diversity as societies shift from traditional agrarian lifestyles to urban, especially in the U.S."

This loss of diversity isn't a small issue; it is directly correlated with health outcomes. As societies have shifted towards more urban, processed, and convenience-focused diets, they have also seen sharp rises in chronic conditions.

"We've unknowingly damaged our diets and microbiomes, and it shows in the rise of various diseases. For example, with autism — just last week, a headline in Singapore reported a rate of 1 in 100; in the U.S., it's 1 in 15. Thirty years ago, it was 1 in 500." He continues, "Similarly, immune diseases and allergies have skyrocketed over one or two generations. Our genes don't change that quickly, so this spike points to environmental factors, and many scientists believe it's at least partly mediated through the microbiome. That's why there's so much excitement around modifying the microbiome to treat conditions like alopecia areata, Autism Spectrum Disorder, Parkinson's, and more."

In Parkinson’s, fecal microbiota transplant (FMT) has demonstrated potential in alleviating motor symptoms by restoring balance to the gut microbiome. Patients receiving FMT from healthy donors have shown modest yet encouraging improvements in movement, likely due to reduced inflammation and enhanced gut-brain communication. By targeting gut dysbiosis — a suspected contributor to Parkinson’s symptoms — FMT offers a new, non-invasive avenue for managing this complex disease. 

The promise of FMT extends to autoimmune conditions like alopecia areata (AA) and alopecia universalis (AU), where inflammation and immune misfires lead to hair loss. In some cases, patients undergoing FMT for unrelated gut issues experienced unexpected hair regrowth, hinting at the gut-skin axis’s powerful influence. This treatment may modulate immune responses that trigger alopecia, paving the way for a therapy that addresses hair loss at its roots and bringing hope to those seeking a scientifically sound and holistic solution

Eating for the Microbiome

Lim's personal journey into microbiome health with AMILI has led to significant changes in his own diet. He shares candidly about his daily routine: "My typical day starts with a cup of black coffee — no milk, no sugar. That's for myself. Then I eat something for my microbiome, usually oats or a loose granola mix. Do I actually enjoy it? Not really," he says with a laugh, "but it's good for my microbiome, and it keeps me energised throughout the day."

Lim believes in being very deliberate about what goes into his body, both for his own health and for the health of his microbiome. "These days, I eat far less meat, focusing more on plants and vegetables. It's not that you can't eat meat — your microbiome is actually quite forgiving. I just avoid overdoing it, so an occasional steak or burger is fine; I just don't make it a daily habit."

Lim's philosophy on food is something he's eager to instil in his children. "Thankfully, yes, it didn't take a very long time (for them to change their mind about the food they eat), but I do think the kids are much more aware now. Over dinner, we discuss findings, and I send them articles, so I think the behaviour is slowly shifting." 

Still, he takes pains to emphasise that the aim isn't to impose strict limits. "I'm not saying everyone needs to be Spartan or live a monastic lifestyle — no, life is meant to be enjoyed. We just need to eat our vegetables and make sensible choices."

Lim acknowledges that for his family, creating lasting dietary habits comes down to balance and sustainability. "What I've described works for me. When I start the day focusing on my microbiome, I find there's less room to indulge in unhealthy things," he explains. And while Lim admits he still enjoys desserts, he approaches indulgences with a new mindset. "As I get older, I'm a bit more realistic. I'll look at a big slice of cake and think, 'That's too much for me,' and that's okay."

As a family, they've even embraced a practical approach to reduce waste, opting to bring containers along when dining out. Lim reflects on his childhood, where finishing every bite was encouraged. "Growing up, our parents would insist on finishing everything to avoid waste, and in hindsight, that wasn't the best advice," he shares. "We shouldn't waste food, but it doesn't mean we need to overeat. Now, we're much more disciplined about that."

A better future through fibre

One of the simplest yet most profound changes Lim advocates for people concerned (especially after reading this article, you're welcome) about their body's microbiome is the most practical. "The data is clear — over 90% of people in developed countries don't get enough fibre. This is largely because most commercially available foods are designed to give us an immediate dopamine kick and feel-good factor."

He explains that fibre doesn't feed us in a way that it makes us feel fuller sooner — it actually feeds our microbes. However, food manufacturers often remove fibre because it attracts airborne microbes that can cause spoilage, like fungal spots. As a result, much of the modern food available on shelves has been engineered to have the fibre taken out. Fibre-less food is also more shelf-stable. 

"If you ask me, one of the simplest things we can do is increase fibre intake through fruits, vegetables, or even options like the brown rice mix promoted by the Health Promotion Board. Many noodles, for instance, are now made with up to 10% brown rice mixed in, which helps boost fibre without drastically changing our diets."

Lim underscores the importance of fibre as a key to maintaining a healthy microbiome, which in turn supports a healthy immune system, reduces inflammation, and even affects mental well-being. "Our microbiome is a living community that needs to be nurtured," he says. "And fibre is one of the most essential nutrients we can provide." He believes that even small changes — like choosing whole grains over refined ones — can make a big difference in supporting a healthy microbiome.

Lim also draws attention to the role of fibre in disease prevention. He points out that populations with high-fibre diets tend to have lower rates of chronic diseases such as cardiovascular disease, type 2 diabetes, and even certain cancers. "Fibre is the unsung hero of our diet," Lim insists, surely to the glee of health officials at Singapore's Health Promotion Board. "It's something that's been lost in our modern eating habits, but it's crucial for our health. By reintroducing fibre, we can begin to reverse some of the damage that's been done to our microbiomes and overall health."

Hope in science, not ideology

Still, Lim is careful not to position himself as a radical — he is not an anti-establishment figure. He advocates for a more expansive understanding of health, a vision that sees wellness as more than merely the absence of disease. His faith lies in data, technology, and the unshakeable belief that tomorrow can be better than today — if we're willing to challenge some of our most deeply held assumptions.

"By nature, I'm a techno-optimist," he admits, seeing his work as making improvements from within. The rise of precision health, for instance, isn't merely about treating individuals more effectively — it's also about addressing broader inequalities, ensuring that the benefits of good science reach everyone, not just the affluent.

The relationship between food and public health, especially concerning the microbiome, requires urgent, collective action from governments, food producers, and consumers. Industrialised food production and widespread processed foods, often high in sugar and low in fibre, undermine a balanced microbiome, contributing to issues like inflammation, metabolic disorders, and compromised immune health. 

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To create a positive shift, regulatory policies must encourage healthier, nutrient-dense food options and discourage misleading marketing that often promotes these highly processed options as “healthy.” This requires transparency in food labelling, accountability from food companies, and education to equip consumers with the knowledge to make microbiome-friendly choices. 

Consumers, too, play a key role in demanding accessible, healthy food options that support microbiome diversity. Choosing whole, minimally processed foods can foster a healthy gut, supporting broader health benefits that extend to mental well-being and disease prevention. 

But for these choices to be widely feasible, equitable food accessibility must become a priority. By addressing disparities in food access, empowering consumers, and prioritising the microbiome’s role in public health, we can make meaningful strides towards a healthier, more resilient population. It is at this junction that policy and science intersect, and Lim hopes that AMILI's research can help influence public policy in a way that benefits everyone.

Navigating wellness culture

Contemporaneously, while the rise in wellness culture brings gut health into the spotlight, Lim approaches this trend with both appreciation and caution. "Societal interest in gut health is great," he says, "but science and influence don't always align." 

Lim sees the rising public interest as a positive sign, especially when it sparks conversations around optimising well-being. However, he points out the complexities of translating scientific insights into mainstream appeal. "It's gratifying that society is interested in optimising gut health," he shares, but adds that this awareness can sometimes bring with it "a range of views, with some being more scientifically informed than others."

"I wish there were a stronger connection between scientific credibility and market reach, but unfortunately, those two don't always align," he notes. While doctors and scientists dedicate years to honing their craft, the skills that amass large followings on social media are vastly different. Lim suggests this disconnect is where a collaborative approach could bring expertise and outreach together.

At AMILI, Lim sees such collaboration as a crucial step forward. "We have the scientific know-how, but we don't have the same access to distribution channels or social media engagement strategies," he explains. 

By merging scientific accuracy with effective communication, Lim believes health messages can achieve greater reach and impact. "The pandemic taught us that even the best science can fall short without proper outreach," he remarks, likening it to a vaccine that's only as good as its uptake.

When asked for hai view on the apparent disparity between well-informed scientific guidance and mainstream health messages, Lim takes a pragmatic stance. Rather than frustration, he feels a measured concern about the impact of economic divides on access to quality health information. 

"I wouldn't say it frustrates me. I'm old enough to be more accepting of things. Still, I worry that the best-informed are increasingly the most affluent," he reflects, adding that health should be accessible to all, not just those with resources. This widening gap, Lim warns, could lead to stark inequalities in dietary choices and long-term health outcomes. In wealthier communities, freshly prepared foods are often the norm, while others may depend on ultra-processed foods and instant meals. 

Lim recognises that the path to closing this gap is a complex one. With limited time and information, many families make choices based on what's marketed as 'good' rather than what's best for their health. "There's both an informational and a financial gap," he says, underscoring the additional cognitive load on individuals already stretched thin.

Ultimately, Lim believes this issue requires collective action but acknowledges the inherent challenges. "In a way, it's everyone's fault, which makes it even harder to address — when everyone is at fault, no one feels responsible enough to act," he explains. Singapore has made strides in addressing these issues through various Head Start programs, yet Lim sympathises with regions where even daily survival remains uncertain. 

"It's incredibly challenging," he remarks, "but perhaps collaboration and a sense of shared responsibility can start making a difference.

Not just stools

"People often think we only deal with stool, but that's just one part of it," Lim shares when I ask what people most misunderstand about his work at AMILI. "Food is really the raw material through which we extract microbes, and from those, we gain insights." He doesn't see this as a misunderstanding per se but rather an underestimation. "When people think of the microbiome, they think locally — gut health, digestion — but that's only one aspect. There are so many fascinating connections to brain health, immune function, and overall metabolism."

Lim points to groundbreaking work overseas, highlighting companies in the U.S. leveraging probiotics to manage diabetes without conventional medicine. Meanwhile, in the U.K., a large-scale study is investigating how specific probiotics might support cancer therapy. 

"Since many cancer treatments today involve immunotherapy, which essentially uses the body's own immune response to target cancer cells, the question becomes: how do you optimise the immune system before beginning cancer therapy?" Lim explains, adding that this U.K. study is testing probiotics as a way to prime the immune system.

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He draws a parallel from his surgical experience, recalling pre-operative protocols used to prepare patients for surgery. "Back when I was doing surgery pre-AMILI, we'd assess patients before any operation. If a patient was frail, still smoking, or underweight, we'd send them for pre-op optimisation — diet adjustments, chest physiotherapy, stopping smoking, and so on — to get them in the best possible condition for surgery."

This same principle, he notes, is now being applied to immunotherapy and cancer care. "It's about asking, 'Is my patient in the best possible state for immunotherapy? How can I enhance the immune system?'"

The future of health

As we inch closer to the 90-minute mark, I ask Lim what gives him hope in the current state of the world. For him, hope lies in the possibility of collective action and the transformative power of technology. He sees encouraging signs among younger generations, particularly in Singapore, where a shift towards communal and universal values is emerging. 

"There's a growing awareness, especially among younger people, that we either succeed together or struggle together," he notes, finding optimism in movements like Prime Minister Lawrence Wong's "Forward Singapore" initiative, which embraces a more community-focused vision for the country's future. Today, Lim is convinced that the right combination of technology, knowledge, and shared purpose could close the gaps that divide us.

As AMILI moves forward, the path Lim has charted is clear: a healthcare model that doesn't just react to disease but proactively supports wellness across all socioeconomic levels. His work reminds us that the future of healthcare is in building systems that serve everyone equitably. In Lim's vision, health isn't a privilege — it's a fundamental right that science and society can work hand in hand to preserve.

"The modern environment has been a mixed blessing," he tells me as our interview draws to a close. "While we're no longer facing high mortality from diseases like malaria, dengue, and tuberculosis, we're now seeing a surge in other health issues." This brings us back to where we started — "I believe the microbiome is central to understanding many of these new challenges. But that story needs to be told in a way that resonates with people and connects with the broader population."