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The Microbiome - the Missing Organ?

The gut microbiome is the hottest new topic in medicine today. Some call the latest discoveries revolutionary; some even call it a game-changer. It certainly seems to be the missing part of a huge puzzle. So, what's the microbiome all about?

For the last 50 years or so, we've been in a world where one size fits all. We get a diagnosis, and we're given a drug. Of course, this is fine when we have no other options, but diagnoses tend to be generic.

Conventional medicine is based on labelling symptoms. Is it in the stomach? In the head ? The diagnosis is then categorised according to these symptoms, and not necessarily according to the causes or the mechanisms. So, more often than not we end up spinning our wheels because there may be one symptom that can cause dozens of diseases; there may also be one disease that's caused by dozens of symptoms - just because we've got the name of the disease doesn't always mean we know what's wrong.

In human health, let's take depression as an example. It's a common name given to people who are sad, feel hopeless, feel helpless, can't sleep, have no appetite, and feel suicidal. Six different symptoms there, but sufferers are given one label - "You have depression." They’re then given one drug, an anti-depressant, aka an SSRI (Selective Seratonin Reuptake Inhibitor), because the general medical thinking is that it’s all due to a lack of serotonin, the happy hormone.

Yet ‘depression’ isn't the cause of the symptoms - it's the name of the collective symptoms, and, somewhat worryingly, very often the cause isn’t a lack of serotonin. For sure, lack of seratonin being made (in the gut by the microbiota, not the brain, as we're brainwashed to believe) will be a symptom, but the causes could be many.

It could be that a course of antibiotics have altered the gut flora, so now there’s dysbiosis that's led to inflammation in the brain. It could be low thyroid function, or gluten that's triggered neuroinflammation. It could be acid blockers taken for years after every curry and now vit,B12’s no longer being absorbed because of this, so now there’s a B12 deficiency. Or there’s been prolonged lack of skin exposure to UVA sun rays so there's a vit.D deficiency. Or maybe it's due to loving sushi and now there’s mercury poisoning, or maybe it’s too much sugar in the diet and there’s pre-diabetes in the brain …

Phew! All these can cause ‘depression’. But instead of being advised to take probiotics to compensate for the antibiotics, or get out in the sunshine, or give up curries, or sushi, or sugar, we end up hooked on highly potent and dangerously addictive SSRIs, which brings with them their own very damaging physiological effects. Or worse, when they no longer work, antipsychotics and benzos start creeping in to the drug buffet, and now we're not just sad and hopeless and helpless; we've got chronic brain-fog with it.

Ultimately, the current model of diagnosing doesn’t help us get to the real causes. The medical profession needs a different GPS system to look at disease - maybe disease shouldn't be thought of as labels, i.e. depression or diabetes or cancer, but more as a series of altered processes, where disease is not a label but a different biochemical process or pathway.

The good news is that the science out there is now seriously thinking that fixing the gut microbiome might be the answer.

The gut microbiome

We now have powerful information coming out of the top labs worldwide that’s changing the way we look at medicine, with the most comprehensive exploration of the microbiome that’s ever been done. Worldwide, people are beginning to heal lifelong ailments by fixing their guts and supporting their friendly bacteria ... and this is just the beginning.

Ultimately, the microbiome is all about the complex colonies of microbial life within us all - we could think of it as a new organ just discovered in the body, one that literally interconnects with all the other organs. It’s basically the body’s very own ecosystem of beneficial bacteria, fungi and viruses, all working together to fight disease and keep the body healthy.

It's fast becoming thought of as the missing piece in health and longevity. Studies have shown that the microbiome regulates everything - immunity, health and mental state – the best part is, science is now learning to understand how.

It's showing that the organisms in the gut are the body’s first line of defence against foreign invaders. They’re also the gateway to fighting chronic disease and inflammation. The proof is in the worldwide case-studies in human health already showing that chronic conditions such as autoimmunity, obesity, diabetes, IBS, Crohns, autism, Parkinson’s, chronic fatigue syndrome, the list goes on – real people with these very real syndromes are now being completely cured by fixing their microbiome and addressing diet.

Getting to know the microbiome

The term 'microbiome' refers to all the organisms that live in and on the body – they cover the skin and they’re in the gut. Most of us think it’s just bacteria but there’s so much more – we’re talking viruses, fungal organisms, tiny one-cell protozoa. There are literally trillions of microscopic bugs that inhabit the body, more than 1-billion in just one drop of fluid in the human colon alone.

These trillions of bugs are dynamically interacting with biology every second. They're controlling levels of inflammation; they're controlling the permeability of the gut; they're controlling brain chemistry, hormones, metabolism, nutrient levels and what’s absorbed/what’s not absorbed.

Incredible! You’d think ... However, not all the bugs are friendly - there are also negative bacteria which can become pathogenic if they get out of control. These bad microbes feed on - you've guessed it - sugar! And can cause real harm to the body, creating red-raw inflammation, but usually they’re outnumbered by the friendly bugs and they're kept in check.

I say usually – trouble is, if there’s excess sugar in the diet, there'll be more of the bad microbes - their job becomes all about world-domination, to proliferate their own type by the gazillions and kill off the good bugs, and here's where the bad news starts. When a beneficial microbe is killed off by the bad microbes, the death process releases a dangerous endotoxin straight into the gut environment.

This is known as dysbiosis, aka an imbalance in the gut microbiome, and a term now becoming all too familiar these days, certainly in the horse world. If there are more of the bad bugs than good bugs, they literally eat their way through the small intestinal wall and cause Leaky Gut, through which the undigested toxic matter in the small intestine leaks into the bloodstream. And so begins the cascade of inflammatory disease with the immune system on hyper-overdrive.

And how does the gut environment become altered and out of balance? By food! It all starts with what goes in the mouth, and this applies to both human and horse. If us, or our horse, is experiencing any kind of health imbalance, the first priority it to look at what feed regime we’ve adopted to nurture our, or our horse’s, gut microbiome.


For most of modern medical history, there's never been any connection on how dysbiosis could be related to disease - the gut flora/microbiota, call it what you will, and the gut microbiome, the host of it all, has been basically ignored. Until now.

Just to acknowledge how impressive the microbiome is, there are literally thousands of different species. In us humans alone, there are an astonishing10-times as many bacterial cells as our own body cells - think about that for a second. It gets more eye-opening - there are a whopping100-times as much bacterial DNA than our own DNA! We're literally only about 1% human (!), and science is discovering that these bugs aren't just waste matter waiting to be eliminated.

The undeniable discovery is that they’re the most important beings in mammalian life - they control All Health, and they’ve been completely ignored until the last decade or so, when research labs worldwide started focusing on understanding the structure and function of the microorganisms that live in the GI tract. There’s still so much more to learn about the microbiome, but at the very least so far, it's recognised that these microbes are critically important in health and disease.

What's also recognised is that the microbiome plays a part in just about all the chronic diseases that have risen dramatically since WWII. Since the widespread use of antibiotics, which is the one underlying factor in diseases that have risen dramatically since then, all relate to a changed microbiome. It really is a game changer – everything that we put into the gut has a direct effect on the microbiome.

There’s no hype about this - thousands of research papers are being published on this. There isn't a field in medicine that isn't impacted by the gut microbiome. Science is discovering that the gut microbiome impacts all disease.

It’s too important for us not to recognise that when we look at health, we need to look at all the factors. Having pathogenic bacteria in the gut definitely creates the risk of disease, but there are a whole range of other factors we also need to consider to determine what kind of microbiome 'type' each organism has.

The fuel (food) will determine the microbiome type, as in a diverse range created by a diverse diet, or not, and here's a top tip - diversity is key. However, there are other really important factors we need to consider, i.e. exposure to environmental toxins, and topical treatments that contain parabens/SLS being absorbed through the skin. Significantly, prescribed drugs - in the case of our horses, we're usually talking antibiotics, bute, chemical wormers - all producing a really unhealthy, altered microbiome in the body. It really is a whole-picture scenario.

Profound intelligence

The microbiome is the body’s scaffolding – it literally affects - and holds up - the whole body, with multiple messages concurrently working towards health. It heals the brain, it heals the other organs, it heals the immune system, in one broad stroke. There's no drug that can possibly do this - it's profound intelligence.

Then there’s the gut-brain connection, a whole other huge and fascinating story; how events in the gut, specifically microbial events, affect everything from mood and emotion to neurodegeneration.

Then there’s the central nervous system, in both the brain and in the intestines. These two nervous systems talk to each other, communicating directly through the vagus nerve. This is a whole new area that scientists are working on, understanding what the basis is of that communication - how the microbes mediate this interaction between gut and brain.

What’s also been discovered is the important gut-immune system connection. Recent studies are showing how the microbiome is responsible for regulating the immune system, how it can calm it down, and how a healthy microbiome can prevent the immune system become ‘autoimmune’, which is huge for better understanding what triggers autoimmune syndromes, and best of all, what we need to do to overcome these events.

The immune system is constantly communicating to the microbiome inside the gut. Imagine the immune system asking, "What's going on in there?" and the microbiome is sending messages back saying that either everything's fine, or warning that everything’s far from fine. If it's the latter, this triggers an immune system panic-attack, because this means there are high concentrations of the negative pathogenic bacteria that aren't supposed to be there.

If this is the case, eventually the microbiome will develop to such an inflammatory state that it'll start tearing the gut lining apart. The immune system will literally respond back by saying "Whoa! Way too many red-alerts coming through - we need to get rid of some of the messengers."

The immune system will then start to attack the microbiome, which, until the microbiome recolonises with good microbes, will bring on 24/7 inflammation, meaning that the immune system will remain permanently hyperactive. This is fine if there's an active infection, but if there's no infection this basically means the immune system is now attacking its own body.

Cue autoimmune syndrome. And here’s a scary fact – in our human world, autoimmune disease now affects more people than cancer, diabetes, and heart disease combined.

Let's summarise

Unlike other health fads, the focus on gut health isn’t going anywhere. Even multinational brands like Dove skincare are talking about the microbiome, making it a common household discussion around the world.

Dr. Martin J. Blaser, director of the NYU Human Microbiome Program states, “It's reasonable to propose that the composition of the microbiome and its activities are involved in most, if not all, of the biological processes that constitute human health and disease.

So let's summarise why the gut is so important...

  • The gut microbiome behaves more like an organ While scientists are hesitant to call the gut microbiome an organ due to the fact that it consists mainly of species that aren't of human origin, it does in fact behave like an organ when it comes to performing specific functions throughout the body, being a key player in the nervous system, the immune system, and the endocrine (hormone) system.
  • The microbiome affects every bodily function From digesting food, metabolising hormones and controlling circadian function - the biological rhythms and sleep cycle - the microbiome is the biggest detox organ and the biggest nutrient generator. It's also the first to metabolise all drug treatments, which means a drug will be effective or not, depending on the microbiome; this has been clearly seen in human cancer and diabetes therapy.
  • The gut microbiome acts like a second brain In the human gut alone, over 2kg of bacteria and other microbes exist at any given time. Together, these microbiota, the enteric nervous system, and the vagus nerve are responsible for 80% of the signals sent from the body to the brain. This is why the gut microbiome is referred to as the 2nd-brain because there is strong evidence it affects mood, happiness, motivation, behaviour, hunger levels, and even can contribute to suboptimal neurological performance later in life.
  • The gut microbiome has more diversity than a rainforest When we think of a rainforest, images of a rich, diverse ecosystem with many different species comes to mind. Yet a rainforest pales in comparison to the gut microbiota, which is far more diverse with over 40-trillion different species.
  • The gut microorganisms aren’t all bad guys We have been quick to name some bacteria like E.coli as “bad guys”, when in fact they actually provide a benefit to some locations within the gut. In reality, E.coli helps stimulate regeneration of the gut lining. When it comes to gut microbiome health it's about optimising the microbes and understanding how they function uniquely inside the body.
  • There are more than just bacteria in the gut Although the gut microbiome is made up mostly of bacteria, there are also all sorts of other organisms in there including archaea, fungi, yeast, and bacteriophages. Archaea are an ancient organism that have no cell nucleus, often produce methane and have the distinct ability to live in extreme environments, including an acidic gut. The gut is also full of yeast and other fungi and possibly even a few parasites too. But perhaps the most fascinating of all of the gut’s inhabitants are bacteriophages, which are tiny viruses that infect specific bacteria. Since these organisms target particular bacteria, the thinking is that in the future they can be used as a targeted antibiotic.
  • Antibiotics wreak havoc on your gut microbiome Antibiotics are like a nuclear bomb for the gut microbiota and can quickly change its composition, potentially leading to serious dysbiosis, which as we know leads to serious health-affecting leaky gut/autoimmune syndrome. Although antibiotics can be necessary to treat certain infections, they can have both short and long-term effects on health due to the fact that the microbiome is critical in many physiological processes including immune system regulation. And let's not forget that these days most bacteria are now resistant to most antibiotics - a vet once told me (when our Carmen developed joint sepsis) that antibiotics only had a pathetic 5% chance of working.
  • The microbiome is astoundingly resilient Although antibiotics aren’t great for the gut microbiome, you’ll be happy to know that your microbes have an amazing ability to recover - but only if the right foods are eaten to create the right environment.
  • The microbiome is at the epicentre of revolutionary science and research Functional metagenomics - the study of genetic material - goes beyond identifying who’s in the gut to finding out what’s actually going on inside our gut. Metatranscriptomic sequencing technology is at the forefront of this gut revolution which is able to measure the actual functions of the microbes, as in what their genes tell them to do. This science is now beginning to suggest that the function of the microbiome is more important than the composition type to overall health and disease outcomes.

To conclude

Everywhere we look, there’s something new that promises to help us - and our horses - get healthy, lose weight, feel happy and so on. Yet understanding the world going on inside us, especially what’s happening inside each and every unique microbiome, empowers us with information about our very being, instead of another fad that promises to work wonders.

From a human perspective we likely all know someone with diabetes, obesity, autoimmune disease, depression, anxiety, autism, heart disease or cancer. And here's the connecting factor - all these chronic diseases are caused by low-grade inflammation which starts inside the gut and is literally caused by the food that's consumed every single day.

Through RNA sequencing (RNA - a nucleic acid molecule essential in various biological roles / Sequencing - a technique used to reveal the presence/quantity of RNA in a biological sample at a given moment, analysing the continuously changing cellular transcript) and revolutionary artificial intelligence (AI) analysis, the science is now out there, capable of seeing everything that's happening in the gut microbiome right down to the strain level. Certainly in our human world, we can now fine-tune the function of our gut microbiome with a personalised food regime in order to restore beneficial bacteria in our gut, lower inflammation in the body, increase energy, and improve the balance inside of us. I've done this myself via Atlas BioMed so I don't have to guess anymore, or spend hours searching for answers on Dr Google, or enter the minefield of supplement companies - been there!

This field of medical research is exploding! We've all become too quick to think that we can simply take a pill to fix everything, and make problems go away without any lifestyle change. We've got to switch from the old healthcare model to a new proactive lifestyle medicine - it's totally about how we live and what we eat. It's not even all about taking probiotics because many beneficial organisms can't be grown in a lab yet, so maybe it's more about living probiotically - we need to upcycle diet and lifestyle for lasting results.

Bringing microbiome science to the masses is coming - of course there's very little research for our horses, although EquiBiome is already out there which performs faecal hindgut testing, which is a brilliant start. The real revolution is all about personalised healthcare because every DNA and gut bacteria are unique in every one of us, human, horse, or dog! So personalising it is a tough nut to crack - there's no one-size-fits-all diet for each individual's lifestyle or microbiome. We're now asking the question, what does each gut need more of, or less of, in the right balance of? With advances in microbiome studies with powerful computers crunching big data, the answers are coming.

So just who's running the show? I think we know the answer to this one - the microbiome! Which means we need a really healthy, happy microbiome. And if there's only one thing we do to keep our horses as healthy as possible, we need to nurture a healthy, happy microbiome for them.

Which means …

  • We feed biologically species-appropriate, real food, high in diverse, multi-species soluble fibre, and we choose organic to avoid toxic chemical saturation from all the growth treatments non-organic agri-crops have been sprayed with. Check out the Pre-Alpin Agrobs range - Top Tip - allow a week for delivery as they're very busy.
  • What we don't feed is the C.R.A.P.* feeds from shiny feedbags piled high in our feed merchants, which are filled with molassed-laced, poor-quality, pointless fillers (oatfeed/wheatfeed, cereals, grains, corn, soya etc etc etc - check your feedbag's ingredients list, or for the full horrible story, see our Why what we feed has to be right page in our Feeding our Horses section), all chemically treated and mostly GM. And all cheaper than a bag of shavings, so how can that be healthy? In other words, all typical feedstuffs that have shifted our equine world over the last half-century towards an exploding disease state.

Meanwhile, I'm off to have a chat with my own bugs and ask them what they'd like for breakfast - banana, anyone?

* C.R.A.P. - not me being rude - it stands for Carbs, Refined, Artificial, Processed. In other words, crap.