🌿 The Microbiome in Medicine

The microbiome is a fascinating and rapidly expanding field. My interest in reading research and publications about the microbiome was eye-opening and became one of the main reasons I pursued nutritional science for over a decade, in fact now 15 years! 

Once you begin to understand the microbiome, many symptoms that previously felt unexplained — such as weight fluctuations, inflammatory problems, digestive discomfort, skin issues or difficulties with metabolic health — suddenly begin to make more sense. For many people, there is far more that can be done to support health than they realise. 

I realised that prescription drugs had become far too easy to rely on. When I started to focus my attention on the microbiome remarkable things happened not only for me but my family too! For me it was a break through. I started to discover that microbiome was linked to autism. Majority of the diseases like diabetes, hypertension, cardiovascular which I see as the epidemic of today, they all had links to the microbiome. 

The mindset changed. Our eating habits evolved. What began as a love for food became 'eat to live,' and eventually 'eat for the microbiome.'

What began as a love for food became 'eat to live,' and eventually 'eat for the microbiome.'

🧬 What Is the Microbiome?

The term microbiome refers to the collective genomes of the microorganisms that occupy a particular environment. In simple terms, it describes the world of microbes that live inside us and on us — and how they behave as a community of organisms. 

The human microbiome includes bacteria, viruses, fungi and even tiny parasites, and these communities colonise many parts of the body including the skin, mouth, airways, reproductive tract and gut.

The gut contains the largest concentration of these microbes, with trillions inhabiting the digestive tract, particularly the large intestine. 

These microbes are not passive passengers. They interact with our gut lining, immune system and metabolism in ways we are only beginning to understand.

A healthy mucus layer keeps microbes at a safe distance from the intestinal wall, reduces inflammation, and prevents unwanted substances from leaking into the bloodstream. When the microbiome is disrupted or fibre intake is low, mucus production can fall, the barrier thins, and the gut becomes more vulnerable. 

The mucus barrier plays a crucial role in immune function and helps defend against pathogens, toxins, chemicals and undigested food particles.

When the microbiome is in balance — known as symbiosis — the gut environment functions harmoniously. Symbiosis describes the mutually beneficial relationship between the gut microbiome and the human body. We provide microbes with a habitat and nutrients, and in return they support immunity, metabolism, digestion and inflammation control. In a balanced state, this partnership helps maintain the mucus barrier, produce essential metabolites and protect against pathogens. 

When symbiosis is disrupted known as dysbiosis, the relationship shifts toward imbalance, inflammation and disease. The dysbiosis occurs if there is an overgrowth of less favourable species, or the 'good microbes' are not enough, the good microbes have totally been wiped out or there is a lack of microbial diversity. Dysbiosis is now known to be a reason for inflammation in the gut and a cascade of inflammatory events, which can futher cause other inflammatory and metabolic diseases.

🌱 Why the Microbiome Matters - the role of Microbiome in Digestion & Metabolism

Gut microbes break down food that we cannot digest on our own. The macronutrients like proteins, carbohydrates and fats need to be broken down. Furthermore, all the micronutrients need a stable microbiome and help from the microbiome to be absorbed. There function is more than just digestion. For example:

• they break down proteins into amino acids which are essential for tissue repair, metabolism and various physiological functions. 
• they ferment dietary fibre into short-chain fatty acids (SCFAs) such as acetate, propionate and butyrate which makes the gut barrier stronger - a defence mechanism against pathogens. 
• they utilise phytonutrients (polyphenols) from plants which are important as anti-oxidant, anti-inflammatory, immune modulation and DNA repair.
• they produce postbiotics and metabolites including neurotransmitters, enzymes, vitamins and signalling molecules.
• These metabolites influence metabolism, satiety, inflammation, immunity, lipid metabolism, glucose regulation and gut health. 

In recent years, microbiome research has revealed that our microbial diversity is declining. Ultra-processed diets, low fibre intake and a lack of plant diversity mean many people are no longer feeding the microbes that once thrived in the human gut. Some species have become rare, and others have disappeared entirely from certain populations. This loss of diversity matters — a richer microbiome is linked to stronger immunity, better metabolic health and lower inflammation.

This loss of diversity matters — a richer microbiome is linked to stronger immunity, better metabolic health and lower inflammation.

When dysbiosis develops, the protective gut barrier can become compromised — often referred to as 'leaky gut'. This allows unwanted particles (toxins, bacterial fragments, lipopolysaccharides and other microbial metabolites) to cross the gut lining and activate the immune system. The result is low-grade inflammation that can influence multiple organs and pathways.

The role of the microbiome cannot possibly be summarised in one sentence. When I first began researching it, many of my colleagues had not heard much about it — and it certainly wasn't something we were taught at medical school. Today, the science has moved forward rapidly, yet I still feel there isn't enough awareness of how crucial this ecosystem is to our health.

The microbiome has a wider function than most of us realise! It contributes to:

• digestion of fibre and complex carbohydrates (we do not have the enzymes to break those down)

• production of short-chain fatty acids (SCFAs) such as butyrate, acetate and propionate important for mucus  barrier and gut motility

• stimulation of mucus production and reinforcement of tight junction integrity therefore preventing a leaky gut

• modulation of inflammatory pathways and immune tolerance
  

• regulation of inflammation due to the intact mucus barrier as a defence mechanism

• nutrient absorption and vitamin synthesis (e.g., B vitamins and vitamin K)

• immune system development and function

• regulation of metabolic and insulin pathways therefore regulating insulin sensitivity

• maintenance of the gut barrier and mucus layer

• communication with the brain through the gut–brain axis via neural, hormonal and immune signaling

• bile acid metabolism
  

• and much more we are only beginning to understand

When these interactions remain in balance — in symbiosis — the microbiome supports health.

When the balance is disturbed — dysbiosis — symptoms and disease can begin to emerge.

👶 How We Develop Our Microbiome

We aren't born with a microbiome — we acquire it. 

We begin life without a microbiome. Colonisation starts at birth, when the mother's microbes seed the infant's gut — particularly during vaginal delivery. Breastfeeding, skin contact, early nutrition and everyday microbial exposure continue to shape the developing microbiome in the first months of life.

As children grow, their microbiome is influenced by:

• environment

• diet

• exposure to pets, soil and the outdoors

• family members and household microbes

This early microbial education plays a fundamental role in immune development, metabolism, neurodevelopment and protection against pathogens. Remarkably, the microbiome remains essential throughout life and even contributes to natural decomposition after death.

Human survival without microbes would not be possible. While genetics contribute, the microbiome is highly individual — even between identical twins — reflecting lifestyle, environment and diet more than DNA alone.

We aren't born with a microbiome — we acquire it at birth during a normal delivery when the mother's microbes seeds the infant's gut.

🔄 What Can Disrupt the Microbiome?

The microbiome is dynamic and responds to many factors, including:

• diet

• medications (including antibiotics)

• stress

• sleep quality

• infections

• pesticides & environmental exposures

• ageing

• lifestyle

• chronic illness

Antibiotics remain essential in clinical care, but they can reduce beneficial microbes because many are broad-spectrum. Recovery may take months, and side effects such as diarrhoea or thrush are not uncommon. Increasingly, clinicians consider microbiome impacts when prescribing.

My focus remains on our nutrition. If we have a diet free of ultra-processed foods, more whole foods and a fully clean diet, the microbiome will be balanced. A balanced microbiome will help improve stress hormones, sleep quality, ability to fight infections, other metabolism, neuro-modulation, less inflammation, less likely to develop inflammatory diseases (and less likely to need medications needed for inflammatory/chronic diseases). A good nutrition, healthy microbiome and a healthy gut is the missing key!

🧠 The Gut–Brain and Gut–Immune Connection

The gut and brain are in constant communication through a complex network known as the gut–brain axis. This network involves the vagus nerve, hormones, neurotransmitters, immune signalling and microbial metabolites. It's a two-way conversation — how we think and feel can influence gut function, and changes in the gut can influence mood, cognition and behaviour.

This communication helps explain why stress, anxiety or emotional triggers can worsen digestive symptoms such as bloating, cramps or bowel urgency. It also explains why gut disorders like IBS are often linked with stress and why psychological therapies such as CBT or gut-directed hypnotherapy can be effective for some people. It isn't "all in the head" — it's physiology.

The microbiome plays a key role in this system. Gut bacteria ferment dietary fibres to produce short-chain fatty acids (SCFAs) such as butyrate, acetate and propionate. SCFAs help to:

• nourish the colon lining

• strengthen the mucus barrier

• tighten the epithelial junctions

• modulate inflammation

• support immune tolerance

• influence metabolic pathways

• and communicate with the nervous system

SCFAs can travel through the bloodstream and even influence brain chemistry. Some gut microbes synthesise neurotransmitters or their precursors (such as serotonin, GABA and dopamine), while others modulate vagal signalling — illustrating how deeply connected the gut and brain truly are. 

When the gut barrier becomes compromised and inflammatory molecules such as lipopolysaccharides (LPS) leak into circulation, the immune system responds. This low-grade inflammation can contribute to fatigue, brain fog, mood changes and systemic metabolic effects. In this way, chronic inflammation can begin in the gut but affect distant organs — including the brain.

The gut–brain–immune axis is still an evolving field, but the direction of research is clear: our microbiome influences far more than digestion. It shapes immunity, stress responses, mental health and overall resilience.

The gut communicates constantly with the brain and the immune system. This helps explain why stress or emotions can worsen gut symptoms, and why chronic inflammation can arise from disruptions in the gut barrier.

📉 Dysbiosis & Chronic Health Conditions

In the beginning sections, we define dysbiosis. Dysbiosis occurs in microbiome imbalance - if there is an overgrowth of less favourable species, or the 'good microbes' are not enough, the good microbes have totally been wiped out or there is a lack of microbial diversity. This causes inflammation in the gut and a cascade of inflammatory events, which can futher cause other inflammatory and metabolic diseases and various chronic health conditions. 

At a physiological level dysbiosis can:

• increase baseline inflammation

• impair immune tolerance

• disrupt metabolic regulation

• disturb the gut–brain axis

• alter barrier integrity ("leaky gut")

• shift hormonal/metabolic signalling

These changes don't always cause disease directly, but they can push physiology toward risk.

While scientists don't claim that dysbiosis causes every disease, there is growing recognition that an imbalanced microbiome can influence inflammation, immunity and metabolism — the same pathways involved in many modern chronic conditions. 

Dysbiosis associations (with varying strengths) exist for:

• autoimmune diseases (IBD, psoriasis, rheumatoid arthritis)

• metabolic + cardiometabolic diseases (type 2 diabetes, obesity, insulin resistance, NAFLD, PCOS)

• neurodevelopmental + neuropsychiatric (ASD, anxiety, depression)

• GI disorders (IBS, SIBO, IBD, celiac)

• allergic + atopic conditions (asthma, eczema, food allergies)

• women's health (endometriosis, dysmenorrhea, menopause metabolism)

• cancer (colorectal + emerging links to others)

• chronic inflammation and ageing ("inflammaging")

Research is ongoing, and while no single "microbiome signature" defines disease, the patterns are compelling. We are beginning to get microbial mapping patterns where we can predict glucose and fat responses of individuals after eating. More on this in my upcoming blog!

Instead of viewing diseases as separate organs with separate problems, microbiome research shows they often share upstream drivers — particularly inflammation, immune dysregulation and dysbiosis.

🥗 Food, Fibre, Metabolites & the Microbiome

Diet is one of the most powerful influences on the microbiome. A pattern rich in whole foods, fibre, polyphenols and plant diversity tends to support microbial diversity and the production of beneficial metabolites, including short-chain fatty acids. In contrast, diets dominated by refined sugars, emulsifiers, additives and ultra-processed foods can reduce diversity, weaken the gut barrier and promote dysbiosis.

Emerging research suggests that aiming for 30+ different plants per week and around 30g of fibre per day helps nourish a broader range of microbial species. This diversity matters, because different microbes "prefer" different substrates — the more variety we provide, the more resilient the ecosystem becomes.

The microbiome appears to influence key metabolic pathways, including:

• insulin sensitivity

• glucose regulation and post-prandial glucose spikes

• fat metabolism and energy extraction

• appetite and satiety signalling

• inflammatory and immune pathways

This helps explain why weight regulation is not simply a matter of "calories in vs calories out." Dysbiosis may make weight loss more difficult by altering metabolic flexibility, inflammation and hunger signals. Interestingly, some individuals with obesity display higher rates of SIBO (Small Intestinal Bacterial Overgrowth), suggesting the gut microbiome and weight are more intertwined than we previously believed.

Metabolites

When gut microbes ferment dietary fibres and resistant starches, they produce metabolites known as Short-Chain Fatty Acids (SCFAs). These include:

• Butyrate — fuels colonocytes, supports gut barrier integrity, and has anti-inflammatory and immunomodulatory effects

• Propionate — influences satiety signals, hepatic glucose regulation and lipid metabolism

• Acetate — the most abundant SCFA; involved in cholesterol and lipid metabolism and can serve as a substrate for peripheral tissues

Higher SCFA production nourishes the gut lining, strengthens the mucus barrier, enhances immune tolerance and may support metabolic flexibility. SCFAs are one of the key ways in which dietary fibre translates into physiological benefit — illustrating how we "feed the microbiome," and in turn, how the microbiome feeds us.

SCFAs are not the only metabolites of interest. Microbial metabolism can also generate compounds from dietary fats, proteins and choline-containing foods. For example, certain microbial pathways convert choline, phosphatidylcholine and L-carnitine from animal-based foods into trimethylamine (TMA), which is then converted by the liver into TMAO (trimethylamine-N-oxide). TMAO has been studied in relation to cardiovascular risk and atherosclerosis, although research remains ongoing and findings are not entirely uniform. What TMAO research does highlight is the bidirectional relationship between diet, microbiome and host metabolism.

Another molecule gaining interest is lipopolysaccharide (LPS) — a structural component of Gram-negative bacteria. When the gut barrier is compromised, LPS can translocate into circulation, triggering pattern-recognition receptors and immune activation. Persistent, low-grade LPS exposure may contribute to cardiometabolic inflammation and insulin resistance, a phenomenon sometimes referred to as "metabolic endotoxemia." Some cardiovascular researchers have noted the presence of bacterial endotoxins, including LPS fragments, within coronary plaques — a finding that has shifted attention toward the gut–vascular–immune axis.

Together, these metabolites illustrate that food is not simply calories — it is a substrate for microbial chemistry. The byproducts of this chemistry can influence inflammation, metabolism, vascular health and disease risk.

The link between what we eat, how our microbes respond and how we develop disease is becoming clearer. Food is not just calories — it is information and chemistry for the microbiome. And the science is still unfolding; what we know today is only a glimpse of what has been discovered in recent years.

🥒 Prebiotics, Probiotics & Fermented Foods

Prebiotics are the fibres and plant compounds that feed our gut microbes. Probiotics are the live microbes themselves, which can be found in certain foods or taken as supplements. Not everyone responds to probiotics in the same way, and not every strain colonises the gut, but they can still have meaningful effects for some people.

Fermented foods such as kefir, yoghurt, kimchi, sauerkraut and kombucha naturally contain live microbes and bioactive compounds. These foods have existed in traditional cultures for generations — long before we understood their microbial significance — and many people are now reintroducing them into their diets with gut health in mind.

There is growing interest in prebiotics, probiotics, postbiotics and fermented foods because each supports the microbiome differently.

• Prebiotics nourish the microbes we already have and help promote diversity.

• Probiotics can introduce new strains or species.

• Postbiotics are the metabolites produced by microbes — including short-chain fatty acids — which influence inflammation, metabolism and immunity.

• Fermented foods offer a combination of microbes and metabolites, alongside their nutritional value.

It's fascinating to see how mainstream this has become. Brands are now designing supplements, tonics and "gut shots" specifically around these concepts. To me, this shift reflects a growing recognition that food does far more than provide calories — it interacts with an ecosystem that affects our health in ways we are only just beginning to understand.

🔍 Microbiome Testing & Future Medicine

Commercial stool testing is becoming more accessible, although interpretation varies and the clinical significance is still evolving. Even so, research has already introduced the concept of personalised nutrition, and the future may include targeted metabolites, postbiotics and microbiome-based therapies. We are not there yet — but the direction of travel is unmistakable.

Modern microbiome analysis allows nutrition programs to sequence stool samples to map which microbes are present, how diverse they are, and which metabolic pathways they influence. From this, a functional "microbiome score" can be generated, reflecting the ecosystem's ability to break down fibre, produce short-chain fatty acids, regulate immune signals, modulate inflammation and support metabolic flexibility. These scores are not diagnostic, but they can offer personalised insights into why some individuals struggle with bloating, post-meal energy crashes, glucose spikes or weight loss plateaus. 

What makes this approach interesting is how it tailors recommendations to the person — suggesting specific foods, fibre types, plant diversity goals and dietary swaps to support microbial balance and metabolic health. It moves nutrition away from generic guidelines and toward something more practical, personalised and evidence-informed.

What is clear is that the microbiome represents an important bridge between nutrition, lifestyle, metabolism, inflammation and chronic disease — a bridge many of us were never taught in medical training. 

It's remarkable that stool — something we once ignored — may become key to personalising nutrition and metabolic health.

🌸 A Changing Landscape in Medicine

The microbiome was not part of traditional medical education, and like many clinicians, I initially viewed health through more conventional aetiological frameworks. As research evolves, there is increasing interest in how nutrition, lifestyle and environmental factors interact with disease pathways.

Stepping into this field transformed how I understood my own health, and how I viewed the health of my patients. It opened up a different way of thinking — more holistic, more connected, and often more empowering.

Understanding the relevance of the microbiome has opened up a different way of thinking — more holistic, more connected, and often more empowering.

🌼 Final Thoughts

We are only just beginning to understand the microbiome and its relationship with chronic disease, metabolism and immunity. The next chapter in medicine may well involve these unseen ecosystems and the foods that nourish them.

Eat healthy, Eat a plant diverse diet, Eat for the microbiome!

If you would like to explore more, see the sections on:

→ Nutrition the missing link
→ Nutrition, Gut health, Microbiome connected to Health & Disease
→ Weight & Metabolic Health
→ Perimenopause & Menopause