pillar  08

Gut Health and Digestive
Function.

Why the World Living Inside You Is One of the Most Important Parts of Your Health
Pillar 08 of 12 | Reading Time: 18 minutes
 
 
Content last reviewed: January 2026.
Based on peer-reviewed research available at time of publication. Medical science advances continuously. Always consult a qualified healthcare provider for personalised medical advice.

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the world living inside you

 

There is an entire world living inside your digestive system.
Not a small one.
A vast, complex, teeming world.
Approximately 38 trillion microorganisms live there.
Microorganisms are tiny living things so small they can only be seen through a microscope.
They include bacteria, which are single-celled living organisms, as well as fungi, viruses, and other microscopic creatures.
All of them living together inside your gut.
Their total number exceeds the number of cells in your entire body.
Together they are called the gut microbiome.
Micro means very small.
Biome means a community of living things sharing the same environment.
So the gut microbiome simply means the community of microscopic living things inside your gut.
And what they do is extraordinary.
They train your immune system, which is your body’s defence system against illness, from the moment you are born.
They produce more than 90 per cent of your body’s serotonin.
Serotonin is a chemical messenger produced in the body that plays a central role in regulating mood, emotional stability, and a sense of wellbeing.
They manufacture vitamins your body cannot make by itself.
They digest fibre that your own digestive system cannot break down alone.
Fibre is the part of plant food that the human body cannot fully digest.
They regulate inflammation, which is the body’s natural response to injury or infection, throughout the body.
And they communicate directly with your brain through a network scientists call the gut-brain axis, which is the two-way communication system connecting the gut and the brain.
They influence your risk of developing conditions as varied as depression, obesity, type 2 diabetes, autoimmune disease, and even dementia.
Autoimmune disease is a condition where the immune system mistakenly attacks the body’s own tissues.
For most of human history nobody knew this world existed.
In the last two decades, science has revealed it.
And what it has revealed has changed the way researchers think about almost every aspect of health.
Your gut is not just a digestive organ.
It is one of the most important regulatory systems in your body.
And what you eat every day either nourishes that world or slowly destroys it.

a story about two brothers

Picture two brothers.
Same family.
Same childhood.
Same city.

 

Daniel is 36.
He eats mostly packaged food.
He rarely eats vegetables.
He takes antibiotics, which are medicines used to treat bacterial infections, whenever he gets sick, which is often.
He is bloated after most meals.
Bloated means the stomach feels uncomfortably full, swollen, and gassy.
He gets diarrhoea when he travels.
He feels anxious more days than not.
He catches colds and other infections frequently.
He has been told his cholesterol is slightly elevated, which means higher than the healthy range.
He has accepted all of this as simply the way he is.
He has no idea that much of it traces back to one common source.
His gut.

 

His brother Thomas is also 36.
He eats a wide variety of vegetables every week.
He eats fermented foods several times a week.
Fermented foods are foods that have been prepared using a natural process that produces beneficial living bacteria.
He takes antibiotics only when genuinely necessary.
He rarely has digestive discomfort.
He travels without his gut misbehaving.
His mood is generally stable.
He gets ill once or twice a year at most.
His cholesterol is healthy.
Neither brother was born with a fundamentally different gut.

 

They were born with similar microbiomes.
But decades of different food choices, different habits, and different approaches to their health have produced two very different gut environments.
And those environments are producing two very different bodies.

what the gut microbiome actually is

The gut microbiome is the collective name for the community of microorganisms living primarily in the large intestine.
The large intestine is the final section of the digestive system, where water is absorbed from food and waste is formed before leaving the body.
This microbiome is unique to each person.
Like a fingerprint.
No two people on earth have exactly the same microbiome.
It is shaped by how you were born, whether you were breastfed as a baby, the environment you grew up in, the antibiotics you have taken, the food you eat, the stress you carry, and the sleep you get.
Think of the microbiome like a garden.
A garden with thousands of different species of plants.
Some species are beneficial.
They produce nutrients, regulate inflammation, and support the immune system.
Some species are neutral.
They neither help nor harm significantly.
A small number are potentially harmful.
They produce toxic compounds and promote inflammation if they grow unchecked.
In a healthy microbiome, the beneficial species dominate.
They crowd out the harmful ones.
They keep the garden in balance.
In a disrupted microbiome, the balance shifts.
Beneficial species decline.
Less beneficial or actively harmful species grow.
The garden becomes less productive.
More chaotic.
And the body feels it.
Scientists measure microbiome health primarily through two things.
Diversity, which means the number of different species present.
And composition, which means which specific species are present and in what proportions.
Higher diversity is consistently linked to better health outcomes across almost every measure studied.
The American Gut Project, one of the largest microbiome studies ever conducted, found that people who ate 30 or more different plant foods per week had significantly more diverse microbiomes than those who ate fewer than 10.
30 different plant foods.
Not 30 servings of the same foods.
30 different types.
Because every different plant feeds a different species of bacteria.

why the gut is called the second brain

The gut contains approximately 500 million neurons.
Neurons are the nerve cells that make up the brain and nervous system.
The nervous system is the network of nerves that carries signals between the brain and the rest of the body.
500 million neurons lining the digestive tract.
This network of neurons is called the enteric nervous system.
 
Enteric means relating to the intestine.
Think of the enteric nervous system as a brain that lives in your belly.
It can operate completely independently of the brain in your head.
It manages digestion, controls the movement of food through the gut, and coordinates the release of digestive chemicals without waiting for instructions from the brain above.
Have you ever felt a knot in your stomach before a difficult conversation?
Or felt your gut drop when you received bad news?
That is not a figure of speech.
That is your enteric nervous system responding to emotional signals sent down from the brain.
And the communication goes both ways.

 

The gut sends as many signals up to the brain as the brain sends down to the gut.
This two-way communication highway is called the gut-brain axis.
Think of it as a motorway connecting two cities.
Traffic flows in both directions.
When things go wrong in the gut, signals travel up this motorway and affect the brain.
When things go wrong in the brain, signals travel down and affect the gut.
This is why anxiety often produces digestive symptoms.
And why digestive problems often produce anxiety.
They are not separate issues.
They are two ends of the same conversation.

what a healthy gut does for you

Trains and regulates the immune system:


Approximately 70 per cent of your immune system, which is the body’s defence system against illness, lives in or around your gut.
Think of the gut lining, which is the inner surface of the digestive tract, as the border between you and everything you eat.
Everything you swallow passes this border.
The immune cells stationed along the gut lining must constantly decide what to accept and what to reject.
The gut microbiome trains these immune cells from birth.
It teaches them the difference between harmless food particles and genuine threats.
Without a healthy, diverse microbiome, this training is incomplete.
The immune system can become either too reactive, which means it attacks things it should not, or too weak, which means it fails to respond to genuine threats.

Produces serotonin:


More than 90 per cent of the body’s serotonin, which is the chemical messenger most strongly linked to mood and emotional stability, is produced in the gut.
Most people believe serotonin is purely a brain chemical.
It is a brain chemical.
But the gut produces far more of it than the brain does.
And the gut microbiome directly influences how much is produced and how effectively it reaches the brain.

Produces short-chain fatty acids:


When beneficial gut bacteria break down dietary fibre, the indigestible part of plant foods, they produce compounds called short-chain fatty acids.
Think of short-chain fatty acids as the food that nourishes the cells lining the gut wall.
They maintain the integrity, which means the strength and health, of the gut lining.
They reduce inflammation throughout the body.
They improve insulin sensitivity, which means they help the body respond better to insulin.
They support brain health.
A diet low in fibre means less of this process happens.
And the gut lining gradually becomes less healthy without it.

Manufactures vitamins:


Certain gut bacteria produce vitamin K and several B vitamins.
These vitamins are absorbed through the gut wall and used throughout the body.
A disrupted microbiome produces less of them.

what an unhealthy gut does to you

When the balance of the gut microbiome shifts in an unfavourable direction, the consequences spread throughout the body.

Leaky gut:


The gut lining is designed to be selectively permeable, which means it allows certain things through while blocking others.
Think of it like a carefully maintained fence.
It lets the right things through, such as nutrients, vitamins, and water.
And keeps the wrong things out, such as pathogens, which are harmful microorganisms, undigested food particles, and bacterial toxins, which are harmful substances produced by bacteria.
When the gut lining is damaged by poor diet, chronic stress, antibiotics, or alcohol, tiny gaps can form in this fence.
Things that should stay in the gut begin to leak through into the bloodstream.
This triggers an immune response, which means the immune system activates to deal with the threat.
Inflammation rises throughout the body.
This condition is called increased intestinal permeability.
Intestinal means relating to the intestine.
Permeability means the ability to be passed through.
So increased intestinal permeability simply means the gut wall has become more leaky than it should be.
Research published in Gut has linked increased intestinal permeability to autoimmune conditions, inflammatory bowel disease, obesity, and mental health disorders.

Chronic low-grade inflammation:


A disrupted microbiome produces more inflammatory compounds and fewer anti-inflammatory ones.
Inflammatory compounds are substances that trigger and sustain inflammation in the body.
This creates a state of chronic low-grade inflammation throughout the body.
Chronic means long-lasting.
Low-grade means mild but persistent rather than intense.
So chronic low-grade inflammation means mild inflammation that persists throughout the body for a long time.
Think of it like a small fire that is never quite put out.
It never blazes.
But it never stops smouldering either.
Over years it quietly damages blood vessels, brain tissue, and metabolic function.
It is one of the driving forces behind cardiovascular disease, type 2 diabetes, Alzheimer’s disease, and certain cancers.

Poor mental health:


Because the gut produces most of the body’s serotonin and communicates directly with the brain, a disrupted microbiome is linked to higher rates of depression and anxiety.
Research published in Psychiatry Research found significant links between gut microbiome composition and both depression and anxiety.
The gut is not just affected by how you feel.
It contributes to how you feel.

how the gut talks to your brain

The gut-brain axis, which is the two-way communication system between the gut and the brain, works through three main channels.

 

The vagus nerve:

 

The vagus nerve is the longest nerve in the body.
A nerve is a bundle of fibres that carries signals between the brain and other parts of the body.
The vagus nerve runs from the brain all the way down through the chest and into the abdomen.
Think of it as the main telephone cable running between the gut and the brain.
It carries signals in both directions.
Approximately 80 per cent of the fibres in the vagus nerve carry signals from the gut up to the brain.
Only 20 per cent carry signals from the brain down to the gut.
The gut is doing most of the talking.

 

Hormones and chemical messengers:

 

The gut produces dozens of hormones, which are chemical messengers the body uses to send instructions from one area to another, that travel through the bloodstream to the brain.
These include serotonin, dopamine precursors, which are the raw materials the brain uses to make dopamine, and GABA.
GABA stands for gamma-aminobutyric acid.
That is a complicated name for a simple idea.
GABA is the brain’s primary calming chemical.
Think of it as the volume dial for anxiety.
The gut produces a significant amount of GABA.
A disrupted microbiome produces less of it.
The volume dial turns up.
Anxiety increases.

 

The immune system:

 

The immune cells in the gut communicate with immune cells throughout the body, including in the brain.
Inflammatory signals from a disrupted gut microbiome can reach the brain and influence mood, thinking ability, and behaviour.
 

what damages the gut microbiome

Ultra-processed food:


Ultra-processed food is food manufactured with artificial ingredients, emulsifiers, which are substances added to food to keep ingredients mixed together, and preservatives, which are substances added to extend shelf life.
It is very low in fibre and high in added sugar, salt, and industrial fats.
Many of these additives directly damage the gut lining and disrupt the microbiome.
Research published in Cell found that commonly used food emulsifiers disrupted the gut microbiome and promoted inflammatory conditions in the gut.

Low fibre intake:


Fibre, which is the indigestible part of plant foods, is the primary food source for beneficial gut bacteria.
Without sufficient fibre, beneficial bacteria starve.
Their populations decline.
Less beneficial or potentially harmful species fill the space left behind.
The garden becomes less balanced.

Antibiotics:


Antibiotics are essential and life-saving medicines.
They are drugs that kill or stop the growth of bacteria.
But they are not targeted.
Think of an antibiotic as a powerful pesticide applied to the entire garden.
It kills the harmful species it is aimed at.
But it also kills a significant proportion of the beneficial species.
Recovery of the microbiome after antibiotics can take months.
Sometimes longer.
Repeated courses of antibiotics cause cumulative disruption.
Cumulative means building up over time.

This does not mean avoiding antibiotics when they are genuinely needed.
It means using them thoughtfully.
And supporting microbiome recovery afterwards with probiotic-rich fermented foods.
Probiotic means containing live beneficial bacteria.

Chronic stress:


When cortisol, which is the main stress hormone, is elevated for a long time, it alters how quickly food moves through the digestive tract.
It changes the composition, which means the makeup, of the microbiome.
It increases gut permeability, which means it makes the gut wall more leaky.
It suppresses the beneficial bacteria that produce short-chain fatty acids.
The physical consequences of stress are felt directly in the gut.

Poor sleep:


Research has shown that even two days of disrupted sleep measurably changes the composition of the gut microbiome.
Sleep and the microbiome share a relationship that works in both directions.
Poor sleep disrupts the microbiome.
And a disrupted microbiome produces less melatonin, which is the sleep hormone, and less serotonin, which worsens sleep quality.
Each makes the other worse.

Alcohol:


Alcohol damages the gut lining directly.
It disrupts the balance of the microbiome.
It increases gut permeability.
It promotes the growth of less beneficial bacterial species.
Regular alcohol consumption is one of the most consistent predictors of a less diverse and less healthy microbiome.

what restores and strengthens the gut microbiome

Fermented foods contain live beneficial bacteria.
Think of them as direct reinforcements sent into the garden.
Natural yoghurt, kefir, which is a fermented milk drink, kimchi, which is a Korean fermented vegetable dish, sauerkraut, which is fermented cabbage, miso, which is a fermented paste made from soya beans, and kombucha, which is a fermented tea drink, all contain live cultures, meaning live beneficial bacteria.

 

Research published in Cell found that a diet high in fermented foods increased microbiome diversity and reduced inflammatory markers more effectively than a high-fibre diet alone.
Including both fermented foods and a wide variety of plant foods is the most powerful approach.

 

Eat prebiotic foods:

 

Prebiotics are foods that specifically feed the beneficial bacteria already living in the gut.
Prebiotic means before life, referring to substances that nourish life rather than containing it directly.
Think of prebiotic foods as targeted fertiliser for the most valuable plants in the garden.
The best prebiotic foods include garlic, onions, leeks, asparagus, oats, bananas, and Jerusalem artichokes, which are a root vegetable with a similar appearance to ginger.
 

Reduce ultra-processed food:

 

Every reduction in ultra-processed food reduces the exposure of the microbiome to the additives and emulsifiers that disrupt it.

 

Manage stress:

 

Lower cortisol, the stress hormone, means a healthier gut environment.
Every tool for stress management is also a tool for gut health.

 

Sleep adequately:

 

Protecting sleep protects the microbiome.
The two are deeply connected.

 

Use antibiotics thoughtfully:

 

Take them when genuinely needed.
Finish the prescribed course.
Support microbiome recovery afterwards with fermented and prebiotic foods.

 

 

common digestive conditions explained simply

Irritable Bowel Syndrome, also known as IBS:

 

IBS is one of the most common digestive conditions in the world.
It causes recurring abdominal, which means stomach and belly, pain, bloating, and changes in bowel habits, meaning either diarrhoea, which is frequent loose stools, or constipation, which is difficulty passing stools, or both.
Think of IBS as a gut that has become hypersensitive, which means oversensitive, reacting more strongly to things that would not trouble most people.
Stress, certain foods, and disrupted sleep are common triggers for IBS.
A trigger is something that sets off a reaction.
The NHS notes that dietary changes, stress management, and in some cases medication can all help manage symptoms.
If you suspect IBS, speak to your doctor for diagnosis and guidance.

 

Inflammatory Bowel Disease, also known as IBD:

 

IBD is a different and more serious condition from IBS, despite the similar name.
It includes two specific conditions called Crohn’s disease and ulcerative colitis.
Both involve chronic, which means long-lasting, inflammation of the digestive tract.
Inflammation of the digestive tract means the inner lining of the gut becomes swollen, sore, and damaged.
These conditions require medical diagnosis and ongoing professional management.
If you experience persistent rectal bleeding, which means blood coming from the back passage, significant unintentional weight loss, severe abdominal pain, or persistent diarrhoea, see your doctor promptly.

 

Gastro-oesophageal Reflux Disease, also known as GORD:

 

GORD occurs when stomach acid regularly flows back up into the oesophagus, which is the tube connecting the mouth to the stomach.
Think of the valve between the oesophagus and stomach as a trapdoor.
In GORD, that trapdoor does not close properly.
Acid escapes upward.
Symptoms include heartburn, which is a burning feeling in the chest, regurgitation, which means food or liquid coming back up into the throat, and a sour taste in the mouth.
Dietary changes, managing body weight, and avoiding triggers are the first approaches.
The NHS provides guidance on managing GORD.

a simple daily framework for your gut

Eat widely across the plant kingdom:


Choose a different vegetable each time you shop.
Add herbs and spices to every meal.
Try a legume you have not eaten before.
Every new plant feeds a new set of bacteria.

Add one fermented food to your daily diet:


A spoonful of natural yoghurt.
A small serving of kimchi or sauerkraut.
A glass of kefir.
These are simple, affordable, and powerful.

Eat enough fibre every day:


The NHS recommends 30 grams of fibre per day for adults.
Most people eat significantly less than this.
Whole grains, vegetables, fruits, and legumes are the richest sources.

Manage stress actively:


Every tool for stress management is a direct investment in gut health.

Sleep seven to nine hours:


Protecting sleep protects the microbiome.

Reduce ultra-processed food:


Not perfectly.
Simply as a daily default.
The more whole food you eat, the better your gut garden grows.

key yakeaways

✓ The gut microbiome contains approximately 38 trillion microorganisms, which are tiny living things invisible to the naked eye, that train the immune system, produce serotonin, manufacture vitamins, and regulate inflammation throughout the body.
 
✓ The American Gut Project found that 30 different plant foods per week was the single strongest predictor of microbiome diversity.

 

✓ More than 90 per cent of the body’s serotonin, the mood chemical, is produced in the gut. The microbiome directly influences mood and mental health.

 

✓ Research in Psychiatry Research found significant links between gut microbiome composition and rates of depression and anxiety.

 

✓ A diet high in fermented foods increased microbiome diversity and reduced inflammatory markers more effectively than a high-fibre diet alone according to research published in Cell.

 

✓ Commonly used food emulsifiers found in ultra-processed food disrupt the gut microbiome and promote inflammatory conditions according to research in Cell.

 

✓ Approximately 70 per cent of the immune system lives in or around the gut. Gut health and immune health are inseparable.

 

✓ Chronic stress, poor sleep, alcohol, antibiotics, and ultra-processed food all damage the microbiome. Plant variety, fermented foods, prebiotic foods, and good sleep restore it.

 

✓ The gut communicates with the brain through the vagus nerve, hormones, and the immune system. Gut health and mental health are deeply connected.

frequently asked questions

What is the gut microbiome?
The gut microbiome is the community of approximately 38 trillion microorganisms, which are tiny living things invisible to the naked eye, living primarily in the large intestine, which is the final section of the digestive system.
It includes bacteria, fungi, viruses, and other microscopic organisms.
It is unique to each person and is shaped by birth, diet, antibiotics, stress, and sleep throughout life.
It plays a central role in immune function, mental health, metabolic health, and protection against disease.
Because the gut and the brain are in constant two-way communication through the gut-brain axis, which is the network of nerves, hormones, and chemical signals connecting the two.
When the brain detects stress, it sends signals down through the vagus nerve, which is the long nerve running from the brain to the gut, and through stress hormones that directly alter gut function.
Digestion slows or speeds unpredictably.
Gut sensitivity increases.
The knot in the stomach is a real physical response to emotional signals.
And gut signals travel back up to the brain and can amplify feelings of anxiety.
Probiotics are products containing live beneficial bacteria, usually taken as supplements or found naturally in fermented foods.
The evidence for probiotic supplements is mixed and depends heavily on the specific bacterial strains and the specific condition being addressed.
A strain is a specific type of bacteria within a broader species.
For general gut health, food-based probiotics from fermented foods like natural yoghurt, kefir, kimchi, and sauerkraut have stronger evidence than most supplements.
For specific conditions such as diarrhoea caused by antibiotics, certain probiotic strains have good evidence.
If you are considering probiotics for a specific health condition, speak to your doctor about which strains are best supported by evidence for that condition.
Research suggests the microbiome can begin to shift within days of significant dietary change.
Meaningful improvements in diversity can be seen within two to four weeks of consistently eating more plant variety and fermented foods.
However, deep, sustained improvement requires sustained dietary change.
The microbiome reflects current habits, not past ones.
Occasional bloating, which means the stomach feeling uncomfortably full and gassy, after a large meal or certain foods is normal.
Persistent bloating every day, or bloating accompanied by pain, bleeding, or significant changes in bowel habits, is not normal and warrants a visit to your doctor.
Add variety.
If you ate the same three vegetables this week that you ate last week, add one new one.
Then another next week.
Variety is the most powerful single driver of gut microbiome diversity.
Add one fermented food to your daily diet.
Even a tablespoon of natural yoghurt counts.

Start there.

MEDIcal references

McDonald D et al. (2018). American Gut: An Open Platform for Citizen Science Microbiome Research. mSystems. 3(3):e00031-18.
 
Wastyk HC et al. (2021). Gut-Microbiota-Targeted Diets Modulate Human Immune Status. Cell. 184(16):4137-4153.
 
 
 
Dash S et al. (2015). The Gut Microbiome and Diet in Psychiatry. Psychiatry Research. 226(1):31-37.
 
National Health Service. (2023). Irritable Bowel Syndrome (IBS).
 
National Health Service. (2023). Acid Reflux and Heartburn (GORD).
 
National Health Service. (2023). How to Get More Fibre into Your Diet.
 
Cryan JF et al. (2019). The Microbiota-Gut-Brain Axis. Physiological Reviews. 99(4):1877-2013.
 
Liang S et al. (2015). Administration of Lactobacillus helveticus NS8 Improves Behavioural, Cognitive, and Biochemical Aberrations Caused by Chronic Restraint Stress. Neuroscience. 310:561-577.