The Miracles of the Gut Microbiome in Health and Disease

The latest research indicates that the microbes that live on us and in us may dictate up to 90% of our genetic capability.

This may be partly due to the fact there are over 3.5 millions microbial genes within us, compared to just 22,000 human genes.

 It’s hard to ignore the gut microbiome news these days, and that is partly due to some of the over 70,000 gut microbiome papers that have been published in the last ten years that have shown the modulation of the gut microbiome in health and disease.

For example, incidences of IBD may be partly due to low diversity at the gut microbial level. We may even be able to connect the diversity and landscape of our gut microbiome related to type 2 diabetes, obesity, ageing and longevity.

Low levels of keystone strains such as Akkermansia may indicate the prevalence of disease. Akkermansia is made of only one organism, it’s unique and lives deeper than any other organism. It has a special role in mucin production and metabolic syndrome, (PCOS, heart disease, dementia). The common cause could be disrupted by dysfunction which causes a loss of resilience.

The lining of our gut is coated in an epithelial barrier (gut lining) which functions better when we have optimal levels of keystone strains. Epithelial barrier dysfunction may be implicated in autoimmune conditions, IBD and systemic strains of secondary chronic illnesses such as Lupus, Hashimoto’s and eczema, and so getting to the root cause is always essential, as there are now 60-70 more immune diseases than a few decades ago.

A keystone bacteria called Faecalibacterium prausnitzii, for example, produces high levels of short-chain fatty acids (SCFA’s), which are essential for the health of our colon. Studies show that F.Prausnitzii is capable of initiating an immune response which can protect against Chrones, IBD and in some cases colon cancers and many other gut related diseases.

A 2021 review stated that there may even be a direct link between the composition of the gut microbiota and the pathogenesis of obesity and diabetes. The study observed an obesity-induced diet which can lead to increased gut permeability and microbial dysbiosis, leading to chronic inflammation and insulin resistance. In this review, F.prausnitzii was cited as a potential treatment due to its production of anti-inflammatory metabolites.

In conclusion to this review, obesity is a metabolic disorder that can be caused by many factors such as genetics, hormones, environment and lifestyle, and it also predisposes an individual to other diseases such as type 2 diabetes, heart disease and some cancers. A major factor of obesity is gut health, in particular intestinal permeability and gut microbial dysbiosis. F.prausnitzii not only produces high amounts of butyrate (a short-chain fatty acid), but it has an anti-inflammatory response, which together may have a powerful impact on the above issues. Increasing F.prausnitzii can be done by increasing prebiotic fibre from fibre rich foods, antioxidants and prebiotic supplementation powder.

So why does the immune system and gut bacteria have such a close link?

We all have what’s called an innate and an adaptive immune response. The innate response goes straight to the site of infection very quickly and the adaptive response can target specific issues. In the case of the intestines, the gut microbiome is the first system to be presented with an incoming virus, and then the immune system (cytokines) activate the innate system which sets off mast cells, granulation and inflammation.

These innate reactions can all cause us to feel lethargy, fever and swelling due to tissue damage. Debris is present in the area and so the immune macrophages and dendritic cells clear up the debris, but this is not targeted, so our immune system may ‘attack’ some of our own cells, which are being presented to the adaptive immune system, and so this is how autoimmune conditions may arise.

The ‘bystander effect’ is when our tissue becomes an innocent bystander, and so you can see how the immune response is highly influenced by the gut microbiome, as T regulatory cells make ‘decisions’ upon what is deemed a pathogen, poison or problem and needs a diverse and beneficial microbiome to make the correct calls. ‘Molecular mimicry’ can happen whereby the immune system mistakes a food or pathogen for ‘self’ and autoimmune and IBD diseases are then driven, which can also cause secondary conditions such as depression.

So you can see how this is all connected and that resilience against these conditions are rooted in the gut microbiome. Taking a look at reflux disease and  depression, for example, they have the same pathology, in that they are driven by a loss of resilience, due to low key strains of beneficial gut microbiome species.

Some of the major causes of mortality, such as diabetes, obesity and heart disease are also related to severe mucosal dysfunction. To give an example of the mechanisms of action, when the HIV virus was able to proliferate the host and become AIDS it used gut lining mucosal dysfunction to accelerate the progression of the illness, and in more recent times, these pathways may also be why individuals with severe diabetes and chronic inflammation may have had more severe COVID related issues.

But, It’s never too late to optimise your gut microbiome. Did you know that your gut lining has a ‘gut barrier’ which has an inner mucin layer and an outer layer. Immune cells live just under the barrier and the trillions of gut organisms live just above the barrier.
This very delicate balance between the immune system and the gut microbiome can sometimes go wrong, and the effects can be extreme. Sepsis, for example, occurs when bacterial organisms are able to break through the gut barrier and enter the blood.
So the strength of this system and any bacterial dysbiosis may impact the levels of what is also known as ‘leaky gut’. A gut dysbiosis, for example, is simply the difference between microbes that build and replenish our gut versus those that destroy it as well the levels of key beneficial species.
For example, low levels of beneficial microbes such as Akkermansia, Faecalibacterium, Bifidobacterium longum and Bifidobacterium adolescentis may lead to food sensitivities, allergies, immune dysregulation and further damage of the gut barrier.

It’s so important that we focus on the ecology of our gut microbiome by taking any small steps that we can to keep unwanted bacteria at bay and increasing beneficial species where possible.

This is because pathogenic, or unbeneficial gut bacterial species produce lipopolysaccharides (LPS) which are toxic and can travel to other parts of the body. LPS may activate an immune response in any part of the body that it ends up in causing an immune reaction.

Even serious and chronic conditions such as metabolic syndrome may be  related to LSP leaking through the system. This is because obesity and insulin resistance are linked to the presence of ‘leaky gut’. LPS may also cause an inflammatory response in the brain, leading to Alzhiemers disease, dementia and Parkinson. Some cancers are also related to certain bacteria that may cause high levels of LSP, leaky gut and an imbalanced microbiome.

‘Sickness behaviour’ has been hard wired into us by our ancient ancestors as a way to ‘protect the herd’, as if we’re carrying a virus or bacteria we do not want to spread it around the herd and so inflammatory messages to the brain make us feel depressed and antisocial and so we want to retreat to the cave.

This kind of short-term depression makes us feel physically and emotionally unwell. Located in our gut, these bacteria are sending messages to our immune system generating feelings in our bra

Psychobiotics are beneficial bacteria (probiotics) or support for such bacteria (prebiotics) that influence bacteria–brain relationships. And there is undoubtedly a strong psychobiotics need in the case of inflammation of the enteric nervous system (nerves in the gut), because issues relating to this have a very strong gut-brain reaction.

Here are some issues that may arise and some tips for supporting this area of our system:

➡️The vagus nervous to enteric nervous system (dorsal nervous system) may have LSP ‘leaking in’ which may cause constipation, which may then cause a build up of microbes, leading to issues such as SIBO (small intestinal bacterial overgrowth)

➡️Bile flow malabsorption may also cause gas to move back up the digestive system, causing acid reflux, and so bile acid support may help, such as increasing bile with supplements such as Megaguard (with artichoke, licorice) post-biotics and enzymes containing HCL, while supplements such as butyrate (prebiotic) may reduce any inflammation

➡️It’s also important to look at the root causes of SIBO, as bloating is a symptom, as a healthy small bowel should be populated with only gram positive bacteria. Negative bacteria release LSP, which may leak, causing liver dysfunction, more SIBO, lower bile acid pool.

➡️Bacillus (a spore gram positive bacteria) can be used to establish the correct balance in the gut, and while prebiotics can make the bloating worse to begin with, they essentially help to feed the good bacteria and re-balance the flora.

H. pylori is a bacteria that can cause peptic ulcer disease and gastritis. Only 20% of those infected have symptoms. Symptoms include dull or burning stomach pain, unexplained weight loss and bloody vomit. H. pylori causes ulcers which are commonly treated with combinations of antibiotics and proton pump inhibitors.

H. Pylori may live in the digestive tract, stomach and small bowel, where it is robust and spirals in deep to the tissue. It is classed as a type 1 carcinogen, and it produces ammonia which causes lowering of the stomach acid, which causes more un-benefical microbes to grow.

Pathogenic, or unbeneficial gut bacterial species produce lipopolysaccharides (LPS) which are toxic and can travel to other parts of the body. LPS may activate an immune response in any part of the body that it ends up in causing an immune reaction.

Putrefaction byproducts in the large intestine, such as LPS, may cause inflammation, and use of PPI’s may worsen SIBO symptoms and exacerbate H Pylori proliferation, while ammonia also increases gastric pressure.

Some products that may help included PyloGuard, which is a brand new product from Microbiome Labs specifically targeted to H Pylori and also Mega Mucosa, Mega Guard, pre and probiotics, as well as magnesium for the enteric nervous system support and HCL release, and Mega Spore to restore flora heal any antibiotic use.


Did you know that anxiety may be a sign of pre-dementia due to inflammation. So what causes it and what can we do to avoid these chain reactions?

➡️A neurotransmitter called BDNF, repairs inflammation that occurs in the brain during the day, and it enhances neuroplasticity and so we need this in abundance

➡️Pathogenic, or unbeneficial gut bacterial species produce lipopolysaccharides (LPS) which are toxic and can travel to other parts of the body. LPS may activate an immune response in any part of the body that it ends up in causing an immune reaction

➡️A study found that stress can impact the microbiome just like antibiotics in something known as ‘stress induced dysbiosis in the gut’, where translocation of LPS has been postulated to be the number one killer worldwide.

➡️If someone has a gut dysbiosis then it is recommended to treat the whole household, as gut issues can be the most toxic issue for the brain

➡️The gut lining is sterile! The mucosal layer is the only sterile part of our body, yet trillions of microbes live next to it

➡️E coli and bacteroides fragilis can seep through the mucosal lining causing issues, they are commensal (beneficial) but can seep through the mucosal layer

➡️Immune cells may mistake this for sepsis and as LSP leaks through, inflammation occurs which can translocate to the brain

➡️LSP are lipid molecules so they can enter the brain easily. LSP can induce anxiety like behaviour

⭐️Central nervous system responses⭐️

➡️1 – LPS interferes with serotonin and doesn’t allow it to bind as effectively

➡️2 – It also interferes with dopamine in the brain, so dopaminergic substances may be used instead  – ‘a stoking of dopamine’

➡️3 – Inflammation in the brain increases, which triggers the hypothalamus to increase adrenaline and increases adrenal fatigue

➡️4 – LPS also interferes with tryptophan which is the precursor to melatonin and serotonin, and elevated LPS causes melatonin to be made from other substances

➡️Cortisol may get dumped in the gut, which helps blood flow and blood pressure and this is how it increases blood pressure from HPA, cortisol to the gut

➡️Cortisol may enhance gut leaky as IL-6 increases, which can activate the HPA axis,  so this is the IBS-Stress Connection

➡️The rest, digest and repair system is off

➡️The gut needs to negate the clearing of cortisol

A Final Word on Digestive Enzymes?

Dairy, for example, is inflammatory in the small intestine and can cause bloating and gas in the large intestines due to a lack of digestion and absorption in the small intestines by digestive enzymes.

And protease enzymes which break down protein, for example, may even help with CFS, ME and fibromyalgia.

In the case of SIBO, the abdominal area is blocked and enzymes work to unblock the ‘drain’, erode bacteria, lower inflammation and activate the body’s natural antimicrobial enzymes.

In the case of FODMAP reactions, it’s a brush border issue, and this is what needs healing, not the removal of the food, but the ability of the body to break down the foods and so enzymes are needed as support.

When both Candida and SIBO are present food intolerances occur as the foods aren’t breaking down properly and are being left in the intestines, and so again, enzymes are needed to break down the foods and also kill of the Candida. Products like Candisole and Candigold so this by breaking down the outer layer (beta gluten) so that the yeast is ‘visible’ to the immune system.