“The gut is the seat of all feeling. Polluting the gut not only cripples your immune system, but also destroys your sense of empathy, the ability to identify with other humans.”

Suzy Kaseem 

Hippocrates taught us that, ‘All diseases begin in the gut’. As I believe this to be so true, I am not going to apologise for already quoting this twice. I know there is a lot to comprehend in this book, so if I was asked to draw your attention to just one statistic, it is the following: scientific research now suggests that up to 90% of all known illnesses can be traced back to an unhealthy gut.

Wow! Doesn’t that suggest we need to knuckle down and learn a little more about this extremely complex organ? Grab a black coffee or a cup of green tea and let’s begin...

Our bodies are not just single living individuals, but thriving ecosystems comprised of 100 trillion microscopic creatures living and working in and on us. As we discovered in chapter 1, we are less likely to inherit diseases or illnesses that runs in our family than we probably fear, and one of the reasons for this is that only 10% of our cells contain any human DNA! The other 90% is made up of bacteria, fungi and microflora, all of which can’t pass on anything genetically.

In 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness, author Dr Alanna Collen writes, “Over your lifetime, you will play host to bugs the equivalent weight of five African elephants. Your skin is crawling with them. There are more on your fingertip than there are people in Britain”. Our 100 trillion microbes can be divided into more than 10,000 different species. This array of vastly different creatures living on and in our body are collectively referred to as our microbiome.

gut health care

As Dr Martin J. Blaser explains in Missing Microbes, “In ecology, biome refers to the set of plants and animals in a community such as a jungle, forest or coral reef. An enormous diversity of species, large and small, interact to form complex webs of mutual support. When a keystone species disappears or goes extinct the ecology suffers. It can even collapse”.

A lot of today’s research into the human body and how it functions is now focusing on the importance of our microbiome. While these tiny creatures exist all over our body, inside and out, it is primarily their accumulation in our gut that has the biggest impact on our health. Getting the varieties of microbes in our gut balanced is now believed by cutting-edge science to have positive effects on all aspects of our health. From weight control to a healthy heart, food metabolism to a good memory, these creatures need to be respected and controlled.

They say a picture paints a thousand words, and when I am trying to create an image of what’s happening in my gut - where many creatures are so tiny you wouldn’t even see them under a normal microscope - I close my eyes and visualise ants! Just like ants working in a colony to perform tasks beyond our imagination, the bacterial army in our gut affect not just our health, but also our mood, emotions and behaviour. In 10% Human, Dr Collen writes, “Imagine, for example, one strain of bacterium that feeds on a particular compound found in our food. If we eat that food, thus feeding these bacteria, and they are able to ‘reward’ us with a dose of happiness through the chemicals they produce, so much better for them. The chemicals they produce could cause us to crave the food they feed on, and even to remember where we found it”.

Dr Aseem Malhotra

Dr Aseem Malhotra

We are now beginning to understand that these microbes are essential for brain development, as well as being heavily involved in the regulation of the immune system and metabolism. The microbiota are also involved in the production of the hormone serotonin, which, when depleted, can lead to depression. Environmental and processed food chemicals that wipe out the good bacteria from our gut and reduce diversity have been linked to the development of many disorders including obesity, depression, allergies, autoimmune diseases and the metabolic syndrome. Artificial sweeteners, antibiotics and the lack of fibre appear to have a negative effect on the gut microbiome.


It will come as no surprise to you that one of the best ways to get our microbiome under control is to follow the principles laid out at Health Results– avoiding CARBS and other sugars, eating protein, fibre and lots of berries and nuts. If possible, we should try to avoid taking any antibiotics and, if we do take a course, then make sure we immediately rebuild our microbiome by taking a quality course of probiotics.


Our guts are a bit like a coral reef. While coral reefs can be devastated by a rapid rise in sea temperature, the colonies living in our microbiome can be eradicated by either a strong virus or antibiotics, and of course sometimes both. Just like the physical coral is still intact after bleaching, our intestines remain in place too, but they become barren. For months, maybe years afterwards, the gut’s environment rests on a knife-edge. While some species are completely wiped out, one strand (firmicutes) seems to feed on disaster - and either avoid being exterminated or are very quick to regroup after a big environmental event.


Firmicutes are the bacteria that make us fat by rinsing every last calorie out of the food we eat. While firmicutes survive, overall diversity is greatly reduced, and some species never return. This imbalance is known as dysbiosis (sometimes referred to as dysbacteriosis). While antibiotics and major infections can cause complete wipe-outs, medicines, poor diets and mild illnesses can all knock our microbiome ecosystem off balance.


While there are several things we can do to reconstruct our microbiome, the most important thing is to avoid CARBS and other sugars and to eat a diet rich in fermented foods and fibre.


How important is the state of our microbiome? In truth, we don’t fully know yet. After all, with 100 trillion microscopic creatures in our body across 10,000 different species, it is an area of science that we will probably never fully understand. But logic suggests that, as the bacteria in our gut is ultimately responsible for our immune system, then we should do everything we can to nurture them and keep them on our side. And talking of our immune system, did you know that 80% of it is located in our gut? What’s your gut reaction to that fact? Hopefully it is to start taking better care of it!

Gut pain

With such a diverse range of tasks and skills, many scientists regard the gut as the second most complex engine in our body, only surpassed by the brain. It is now believed that a lot of the feelings that we can’t always easily explain, such as depression, anxiety and stress, are driven from the gut and not from the brain. It is becoming increasingly evident that there is a connection between gut health and mental illness.


Many medical journals go as far as claiming that the gut is, in fact, our second brain. Think back to the small intestine, with its sensors the size of a tennis court. Compare it to all of our other sensors, such as our eyes, nose, ears and touch. It is vastly larger. It monitors way more than all of our other sensors put together, but we never give iit credit or apportion blame for our feelings. Science is now discovering that we absolutely should. The ‘gut feeling’ is something we should not ignore any longer. In her book Gut, with the apt subtitle, ‘The inside story of our body’s most under-rated organ’ author Giulia Enders says, “Cooperation between the gut and the brain begins very early in life. Together, they are responsible for a large proportion of our emotional world when we are babies”.


Author Patrick Holford

Author Patrick Holford

The undesirable organisms that reside in the guts of many people are called pathogens. We all have approximately 1.3kg (3lb) of about 300 different strains of bacteria living within our gut. Some can be classified as good and others as bad. However, the potentially ‘bad’ guys are not a hindrance as long as there are enough of the good guys around. These bacteria help us to digest food and fight off bad bacteria that enter the body, and they even make some vitamins. But the presence of the wrong kind of bacteria can cause ill health – especially if the gut wall is permeable and they enter the bloodstream.


Where Did Our Bacteria Originate?

First things first, this planet that we inhabit is really their domain and not ours. Earth formed some 4.5 billion years ago and, while us humans have only inhabited it for less than one thousandth of that time, it’s been the home to single-celled bacteria for some 3.8 billion years! As you will read over the next few pages, we would be wise to view Earth as their planet and not ours.

Bacteria, plankton and single-celled organisms are far more shatterproof than us fragile humans. They can withstand temperatures so low that we would freeze to death in seconds. They can thrive, and indeed multiply, in temperatures so high that our skin would melt instantly. They have survived our planet’s hostile environment through toxic periods, caused by mass volcanic activities and colliding tectonic plates, that would wipe us out in a heartbeat. Compared to us Homo Sapiens, some species of bacteria are virtually indestructible. They were the first living life form on planet Earth and, in my mind, will ultimately be the last. To picture how long they have been on Earth, if you imagine a 24-hour clock, bacteria have thrived on our planet for the whole 24 hours - and us humans have only cohabited with them for the last two seconds!

In The Diet Myth, author Tim Spector writes, “These microbes are the true and permanent inhabitants on Earth; we humans are just passing through”. I love this quote because it really makes me think hard about how important it is that we create harmony between our body and our microbiome.


Dr Martin J. Blaser says in Missing Microbes, “If you were to gather them all up, not only would they outnumber all the mice, whales, humans, birds, insects, worms and trees combined – indeed all of the visible life forms we are familiar with on Earth – they would outweigh them as well ... Without microbes, we could not eat or breathe. Without us, nearly all microbes would be just fine”. Whether we realise it or not, the bacteria in and on our body has played a huge part in the evolution of our species, and how we look after them and treat them today is very different to the way we have partnered with them since our evolution as a species. For more than 2 million years, we did nothing out of the norm to upset our bacteria. Every aspect of human life, until the agricultural revolution some 12,000 years ago, saw us living in harmony with our microscopic inhabitants. Our bacteria felt safe and unchallenged. After all, they greatly outnumbered the cells in the humans they became attached to. But fast-forward to today, and they are at constant war with a barrage of unhealthy, highly engineered and chemically enhanced foods that they are as estranged to, as we humans are.

Here is another fantastic quote from The Diet Myth, “Over millions of years we have evolved together with microbes for mutual survival, yet recently this fine-tuning and selection has gone wrong”.

What Role Do Bacteria Play In Our Body?

It’s important to point out that not everyone will agree with what comes next, but what you will read is both highly researched and backed by lots of up-to-date independent data. Whenever you participate in an activity, say a game of football, golf, tennis or a netball match, there is always a result. Put simply, the activity leads to a conclusion. Similarly, the bacteria in our microbiome participates in a whole host of activities, which in turn eventually lead to a whole host of different results.

Let’s look at just some of the activities the bacteria in our body’s microbiome play a part in; detoxification, inflammation, the functions of our immune system, neurotransmitter production, nutrient absorption, the control of many hormones and how we utilise or store our macronutrients. Those activities in which our bacteria play an attacking role may lead to the following conditions (to name but a few); ADHD, Alzheimer’s, asthma, autism, cancer, depression, diabetes, gum disease, high blood pressure, multiple sclerosis, obesity and Parkinson’s disease.

To highlight how important our microbiome is to our health and wellbeing, let me start by asking you another question. The bacteria inhabiting our body are microscopic little things, containing just one cell each. If you could remove them all in one go and place them on your bathroom scales, what weight would you predict they would be? How about if I told you the bacteria inside our body weighs about the same as our brain? I hope that shocked you, because it certainly caused me a mild panic.

Why Do Microbiomes Collapse?

Before I scare you half to death with what I am about to say, even if our microbiome is currently completely shot, broken beyond what you might believe repairable, I am pleased to announce that it is a graceful ecosystem, and with the right nurturing and conditioning we can return our intestines back to the positive working bacterial environment that nature designed. As Dr David Perlmutter reminds us, “Thankfully, the gut’s microbiotic community is wonderfully receptive to rehabilitation”.

It is now believed that, while in the womb, we don’t have any bacteria in our body. But as we travel through the birth canal, a female organ rich with friendly bacteria, our skin acts like a magnet attracting billions of wonderful bacteria to climb on board. Those born by C-section never benefit from this microbiotic kick-start. What’s more, most caesarean births (and according to recent research over a third of births now include major surgery) are conducted simultaneously with a course of antibiotics. As their name suggests, antibiotics are ‘anti’ our body’s ‘biotics’, a.k.a. our bacteria. Sadly, they are not all that good at isolating and attacking just the bad bacteria, but often cause complete genocide, mass-murdering the good bacteria too. If you were born by C-section with antibiotics, and then didn’t benefit from bacterial-rich breast milk, then your microbiome really did get off to a poor start (even though, of course, this was neither you nor your mother’s fault).

There is also mounting evidence that people in built-up cities experience more immune diseases than those living rurally. Why is that? Because those of us living in built-up environments are living in a clinical, overly sterilised bubble. Our kids no longer bring muddy boots into the house, and at the first sight of a bit of muck, antibacterial wipes are whipped out! My daughter Lili screams at me every time I leave the toilet, “Wash your hands daddy!” The whole world seems obsessed with cleanliness, when the reality is that we are mass-murdering our friendly bacteria. As I am writing this sentence, Lili is sitting next to me on the sofa, still insisting that I need to wash my hands - and while she might be right when it comes to toilet visits, there are many other instances where we would be better off just being a little bit grubby!


Many scientists now believe that our obsession with hand sanitisers and bacterial wipes is not only killing off the bad bacteria, but the good bacteria too. Dr David Perlmutter in Brain Maker says, “There’s immense value in being unhygienic. Astonishingly new studies show a relationship between our increasingly sterile living environments and incidence of chronic illness, from heart disease and autoimmune disorders to cancer and dementia”.

Sadly, as of yet there is little publicity about how protecting our microbiome is as crucial for our health and longevity as preserving our rainforests, oceans and corals are to the survival of our planet.

Author Patrick Holford

Author Patrick Holford

Fifty thousand tons of antibiotics are used each year throughout the world on humans, animals or plants. In the UK alone, doctors write over 50 million prescriptions for antibiotics annually – roughly one per person per year. Not only are antibiotics intestinal irritants, wiping out healthy intestinal bacteria that can take over six months to be restored, but their widespread use is leading to the development of drug-resistant strains of life-threatening bacteria, from staphylococci to mycobacterium tuberculosis and streptococci; which are responsible for most sore throats.

How To Recolonise Our Microbiome

Under a separate topic we discuss fermented foods and discover which are rich in positive bacteria. After being missing in action from supermarket shelves for decades, these probiotics foods - which were the norm - are mounting a resurgence. Regularly eating fermented foods (probiotics) such as yoghurts, kefir, sauerkraut and certain pickles will undoubtedly help rebuild most lacklustre immune systems.

Getting the gut back in good working order is actually a two-step process. We need to eat foods that are rich in healthy bacteria, as well as foods that the bacteria themselves like to feed on. These are known as prebiotics, and they are insoluble fibrous foods that cannot be absorbed or broken down by the gut, and as a result they remain there long enough to feed and fertilise our legions of healthy bacteria. While we can take prebiotics as a supplement, artichokes, raw garlic, chicory, onions (raw or cooked), raw asparagus and raw leeks are all natural sources.

Another way to take care of our microbiome is to regularly put our body into a ketogenic metabolic state. Research has shown that this increases the healthy variety of bacteria known as bacteroidetes and decreases the undesirable firmicutes. Let’s remind ourselves what this means. Among other things, firmicutes are able to extract the most energy out of food, effectively stripping out maximum calories and leading to us putting on weight, getting fatter and eventually obese. Being ketogenic is effectively a spiral of upward health benefits. Our body not only consumes its own fat for fuel, but also removes the bacteria that over-extracts calories from food too.

A ketogenic diet is a positively healthy double dose of goodness, where in collaboration we burn our own body fat as our primary fuel source and the good bacteria redirect any excessive incoming energy straight to the exit!

keto diet

The Bacteria That Makes Us Fat and That Which Keeps Us Lean

I mentioned earlier that it’s all too easy to criticise fat and obese people for overindulgence and being too lazy to exercise. It’s a natural conclusion for those unaware of the effects of our bacteria. But knowledge is power, and I am hopeful that these next few sentences will help you understand one of the hidden secrets of why some people eat rubbish food and almost instantly get fat, while others seem to be naturally fat-defiant without any real effort. You see, even though there are thousands of different bacteria in our gut, much of it is killed off in the Western human, leaving just two to dominate the entire digestive system. I have mentioned them a few times already, their names are firmicutes and bacteroidetes. It is believed that, together, they might account for more than three-quarters of the bacteria in our body - the combined weight of their armed forces being in excess of 0.9kg (2lbs)! If we want to lose weight, we need to work out how to reduce the volume of firmicutes in our gut. These clever creatures are superefficient at extracting maximum calories from the food that we eat. Bacteroidetes just aren’t as qualified at unbundling energy.

Remember the saying ‘we are what we eat’ or when it comes to meat, ‘we are what we eat – eats’? In our gut, our bacteria are forced to eat what we eat. Different bacteria thrive and survive on different foods. This is one of the key reasons why we all have very different ecosystems. Is your diet encouraging the right bacteria? Is it providing a safe harbour for firmicutes? If it is, then you’re most likely overweight. But don’t take it the wrong way, because getting our weight down might be as simple as working out how to balance our microbiome. Once we have balanced our firmicutes and bacteroidetes, the next thing is to encourage the widest variety of gut bacteria possible.

In Brain Maker, Dr David Perlmutter writes, “It’s now firmly established that the gut community of lean people resembles a rainforest filled with many species and that of obese people is much less diverse”.

healthy diet

At the University of Gothenburg in Sweden, Professor Fredrik Bäckhed, an award- winning expert in cellular microbiology, has performed numerous clinical studies with mice to uncover more about the critical role that microbes play in our gut. In 2004, he took a selection of skinny mice that were all born by C-section, and who had lived in a sterile environment to ensure that they didn’t have any bacteria in their guts and began his experiment. He took bacteria from the caecum (the pouch located between the small and large intestine) of normal mice and placed it in the fur of the sterile mice. So, as they licked their fur, the microbes started to arrive in their guts. Within weeks, even without changing their diets, these mice - which had been lean for their entire life - became fat. Seriously fat. Within just weeks, on average they put on 60% more weight.

The professor then reduced the amount of food the mice were eating and they still put on weight. So, without doubt, when it comes to mice, certain varieties of microbes make them put on weight. You might now question if there is any relevance to what goes on in the stomach of a mouse and that of us humans, but let me just remind you that while the vessel might be different, i.e. mouse vs human, the crew is exactly the same! Certain microbes are able to extract more energy out of food than the body can on its own. Whether they reside in mice or humans, a microbe is a microbe. If they are experts at extracting energy from food then they will perform their tasks regardless of their host.

So, if we are fat or obese, the fault might not lie in just our food choices, but the state of our microbiome. In fact, the microbiome can also affect how good our body is at producing the hormone leptin, which informs our brain when our stomachs are full and therefore when we should stop eating. If we have damaged our body’s ability to produce sufficient leptin, and we have too many microbes that are experts in extracting energy, then we could lay the blame of every excess pound of body weight at their door!

In 10% Human, Alanna Collen describes another mice experiment, this time carried out by microbiologist Ruth Ley in America, where she studied the DNA of a variety of supersized mice that are known as ob/ob (their name appropriately derived from their obesity). These mice are almost round in shape, and because they just won’t stop eating, they are three times heavier than normal mice. Alanna writes, “Although they appear to be a completely different species of mouse, they actually have just a single mutation in their DNA that makes them eat non-stop and become profoundly fat. That mutation is in the gene that makes leptin, a hormone which dampens the appetite of both men and mice if they have a decent supply of stored fat”.

Hang on a minute, if it’s as simple as the satiety hormone leptin controlling our hunger, why can’t we take leptin tablets or have leptin injections? Sadly, it’s not so much a lack of the ability to produce leptin, but also the brain becoming insensitive to it. Just as type 2 diabetes can occur when cells stop accepting insulin (insulin resistance) due a long period of overwhelming abundance, the brain ignores the cries of leptin to stop eating if it has sustained periods where we have over-eaten when we were already full. To the brain, leptin’s performance is viewed as a cry wolf scenario.

More Gut Facts


If you take antidepressant tablets, their role is to simulate the brain’s happiness neurotransmitter serotonin. However, some scientists suggest that as much as 90% of serotonin is not, as you might assume, created in the brain, but in our intestines. When we feel depressed, my recommendation would be not just to pop a pill and create temporary relief, but to spend time figuring out how to get our gut in order. Did you know that serotonin is synthesised from tryptophan, and foods rich in tryptophan include eggs, cheese, pineapple, salmon, turkey, pork, nuts and seeds?


I know I have already covered the negative effect to our health caused by stress, and some of what I am about to say you have already read, but it’s so important to our wellbeing that it’s worth repeating. Stress plays havoc with our microbiome. It can send our bacteria into a frenzy. Short sharp moments of stress, such as what we experience during sprinting and weightlifting, don’t set alarms bells off in our internal bacterial network. But persistent stress – caused by endurance sports and horrible bosses, for example – does. Our microbiome sees prolonged stress as a potential threat to the body and summons the support of both steroids and adrenaline. Together, this mighty taskforce summons the help of a built-in safety device called inflammation. However, nature invented inflammation to protect injured joints, to isolate snakebites and other such dangers. Summoning inflammation when it’s not really needed can lead to a whole host of diseases, from cancer to Alzheimer’s, from MS to depression. It is therefore important to avoid stress at all costs.

avoiding stress

If we don’t avoid stress, the Guy Fawkes in our microbiome is going to start setting fire to many of our internal systems, leading to mass-inflammation. If we have a lot of healthy fire-fighting bacteria protecting our corner, then we should be okay at dealing with short exposure to stress. But if they have already left the building due to our diet or sedentary lifestyle, we could be in for big trouble. It’s for this reason that many people who suffer from stress also suffer from a myriad of gut-related illnesses. For those that have never got to the root cause of their irritable bowel syndrome, reducing stress levels and rebuilding the health of their microbiome may resolve the issue.


The immune system has been mentioned several times throughout this book. It is effectively the body’s inbuilt self-defence system, which is activated when potential trouble arises. Highlighting the importance of our gut, the Gut Associated Lymphatic Tissue (GALT) represents approximately three-quarters of our entire immune system. Why does the immune system deploy the vast majority of its army in our gut? Because this is where our body needs its defence bolstered in order to stop the enemy breaching the delicate lining of our intestinal wall, which is only one cell thick. Yes, the only thing that stands between all of the nasty stuff that we swallow, that keeps harmful ingredients inside our gut, is just one cell wide. When the bad guys penetrate the immune system’s defences, it is referred to as a leaky gut.

Irritable Bowel Syndrome

Irritable Bowel Syndrome (IBS) is rife, with around 10% of the adult population suffering from it, and two out of three people affected by it are female. This common disorder affects the large intestine and causes, among other things; cramping, abdominal pain, gas, bloating, diarrhoea and constipation. While it tends to be used as a catch-all diagnosis when doctors can’t pinpoint the exact cause of a patient’s discomfort, I believe that, for many sufferers, the cause is an imbalanced microbiome. However, with thousands of varieties of microbes in our gut, where should sufferers turn for a solution? I am a big believer in the Pareto Principle, named after the Italian engineer, sociologist and economist Vilfredo Pareto (1848 - 1923), where 80% of an effect comes from 20% of the causes (also known as the ‘law of the vital few’). Therefore, with firmicutes and bacteroidetes occupying around three-quarters of our gut bacteria by volume, weighing in at about 0.9kg (2lbs), more than three times heavier than the human heart, I am confident to recommend to IBS sufferers that they try two things – firstly commit to a diet that creates an environment that firmicutes do not like, and secondly, do everything possible to reduce stress in their life.


Like I previously stated, I have to be careful not to oversimplify something that is regarded as a complex matter. In all walks of life, I often feel sorry for professionals where too much knowledge can cloud their vision and make it difficult to accept a simple solution. In business, I always ask my team to stand back from the coalface and search for a simple solution. But, could obesity in the main be caused by a negative microbiome?

I have already mentioned the brilliant research carried out by Professor Ruth Ley. In another experiment she evaluated the balance of firmicutes and bacteroidetes in both lean and obese mice, and then repeated the experiment across lean and obese humans. The result: obese mice and obese humans have a higher number of firmicutes than bacteroidetes. Lean mice and humans have higher number of bacteroidetes than firmicutes.

Microbiome Conclusion

Living in Great Britain, where antibiotics and antibacterial wipes are the norm, where packaged food is stripped of nutrients, we are in danger of developing a microbiome depleted of so many species of microbes that the human body was designed upon. To restore the very foundation on which nature created the human body, we all need to take steps to rebuild and then maintain our microbiome.

  • It will come as no surprise to you that one of the best ways to get our microbiome under control is to follow the principles in this book.
  • With such a diverse range of tasks and skills, many scientists regard the gut as the second most complex engine in our body, only surpassed by the brain.
  • Over millions of years we have evolved together with microbes for mutual survival, yet recently this fine-tuning and selection has gone wrong.
  • Eat as many organic vegetables and fermented foods as possible, and take a quality probiotic supplement.
  • There are 100 trillion microscopic creatures living on and in our body.
  • Three-quarters of the weight of our faeces is bacteria.
  • There are more than 10,000 different species in the human microbiome.
  • Our faeces are made up of more than 4,000 species.
  • Individual bacteria cells live from a few days to a few weeks.
  • Around 90% of illnesses can be traced back to the gut.
  • We are 90% bacteria, fungi and microflora and only 10% human.
  • 80% of our immune system is located in our gut.
  • Microbes have thrived on our planet for more than 3.8 billion years.
  • Firmicutes make us fat.
  • As much as 90% of serotonin is created in the gut.