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  • Writer's pictureLuke Stephan

The ultimate guide to gut health

Updated: Jan 20, 2023

Introduction & where things go wrong

In general, three things can go wrong with the gut:

1. Dysbiosis - An imbalance in the microbiome from too many pathogenic (bad) bacteria and/or too few beneficial (good) bacteria.

2. Increased intestinal permeability (leaky gut) - The gut lining is only one cell thick. Entry to circulation is controlled by tight junctions. When this is impaired, tight junctions open too much allowing debris, toxins and other material into circulation and activating immune responses.

3. Inflammation - Inflammation from the immune response destroys the guts defensive layers, including mucus. Inflammation from the gut can easily become systemic, affecting other organs and the brain, sometimes described as “brain fog”.

Keys to keeping these three vital factors in balance are the microbiome, the small intestine, bile and

The Microbiome

The microbiome is comprised of approximately 39 trillion organisms. It produces as many nutrients as we get from diet and contains far more cells than “you”. 90% of serotonin and 50% of dopamine is made in gut.

Fun fact: Scientists have found that give a shy mouse the microbiome from a curious mouse and the shy mouse will become curious. But that’s not all - give an anxious mouse the microbiome from a chill human, the anxious mouse will become chill.

Dysbiosis results in leaky gut, inflammation and ultimately insufficient nutrients, neurotransmitters and hormones. There is no system of the body this does not affect.

Another impact from dysbiosis is LPS, an inflammatory toxin. LPS is a component of the cell walls of gram negative bacteria. Most pathogenic species such as e-coli are gram negative. When these bacteria die and the cell wall is broken down LPS is released.

This is a two-way relationship. What you eat determines your microbiome and your microbiome influences what you eat. For example, the sugar cravings that arise after you’ve been eating a diet high in sugar come from sugar-loving bacteria releasing signals telling your brain to eat more.

Your microbiome changes rapidly in response to diet. Wholesale changes are seen in as little as 24-48 hours after a change to diet. A healthy microbiome is far more potent than the most broad-spectrum multivitamins on the market.

Short Chain Fatty Acids (SCFAs) are one of the keys to health. You can consume SCFAs but most are made when your good bacteria break down fibre. Excessive sugar in the diet will replace the beneficial species which break down SCFAs with sugar-loving species that release inflammatory LPS. Dietary fat can also reduce the number of SCFA-producing bacteria and should not be consumed in excess.

Why are SCFAs (and therefore fibre) so good? SCFAs:

  • Massively boost numbers of mitochondria throughout the body, increasing energy supply and muscle production

  • Are the preferred energy source for all gut cells

  • Are highly anti-inflammatory

  • Reduce leaky gut

  • Increase mucus production (which both protects the gut and provides a home for good bacteria)

The downstream impacts of the above include resolution of imbalances such as inflammatory bowel disease, cancer, diabetes, weight gain and depression.

Fun fact: Gorilla’s, the strongest of the primates, obtain 57% of their energy needs from microbiome generated SCFAs. Our digestive systems are not that different to Gorillas, suggesting fibre and SCFAs should be a major source of energy for humans.

Herbal and lifestyle support

The single greatest modification one can make is to mindset. When you are eating, you are eating just as much for your gut microbiome as you are for yourself.

Probiotics can, and do, help many. But on the question of prebiotics Vs probiotics… the science is settled.

Prebiotics (fiber) are far more important. Boosting prebiotics can completely change the microbiome in 48 hours. Vegetables, grains and nuts are all good natural sources. Very simple (and very cheap) prebiotics are resistant potato starch or raw banana flour. These can both be added to normal cooking flours or smoothies.

Particularly potent herbs that reduce leaky gut and bad bacteria whilst increasing beneficial bacteria include:

· Ginseng

· Gynostemma

· Turmeric (curcumin)

· Goldenseal (berberine)

The small intestine

The small intestine is where we absorb most of our nutrients. Because of this, the protective mucosal layer cannot be as thick as it is in the stomach and colon.

Instead the small intestine relies on additional layers of defence, all associated with the villi.

1. Half-way down the villi, goblet cells release mucus

2. Paneth cells at the base of the villi release anti-microbial peptides that kill bacteria

3. The villi produce alkaline phosphatase

Alkaline phosphatas hase has three main functions:

1. detoxifying LPS

2. preventing LPS entering circulation

3. reducing inflammation

The key to a health small intestine is healthy villi. Villi damage accrues from dysbiosis, leaky gut and inflammation. A loss of defences caused by damage to villi results in endotoxemia, chronic inflammation, malnutrition and downstream impacts such as chronic stress, fatigue and insomnia.

Herbal and lifestyle support

Focus areas to boost the health of the small intestine include addressing mucus, inflammation, and leaky gut.

Mucus: Slippery elm, marshmallow root and aloe vera all have high mucilage content, are anti-inflammatory and support the health of beneficial bacteria.

Inflammation: Turmeric, ginger, garlic and most spices are potent anti-inflammatories. Turmeric should always be taken with black pepper and a fat source (such as ghee) as the curcumin has poor bio-availability on its own.

Leaky gut: Berberine and licorice root are highly beneficial for leaky gut.

For gut health generally, glutamine powder can be beneficial in instances of significant tissue damage. Glutamine is the primary raw ingredient gut cells use to replenish themselves and regrow.

A quick go-to gut shake when things go wrong:

  • Flesh from one aloe vera leaf

  • 1 tsp glutamine

  • 1 tsp turmeric

  • Black pepper

  • 1 tsp ghee


Bile is a magical substance responsible for much of your digestion.

It is best known for emusifying (breaking apart) fats. This enables fat digestion but it also helps control bad bacteria. The cell membranes of bacteria are made of fat – bile breaks this down. Not much bile makes it to the large intestine (only 5%) and the beneficial species living here are bile resistant.

But bile does much more:

1. It reduces leaky gut and increases detoxification through activation of the PXR enzyme. A main ingredient of bile is bilirubin.

2. Bilirubin is what turns stools brown, urine yellow and bruises green. It is also one of the body’s most important anti-oxidants. Bilirubin is the fat-soluble partner to glutathione, the bodies major water-soluble antioxidant. This bilirubin antioxidant function appears to be a key reason the body flushes the entire gastro-intestinal system with bile 7-10 times per day.

3. In the digestive system the body binds bile to the amino acid taurine to prevent tissue damage. Taurine is the most abundant amino acid in the body with many critical roles including:

a) Turning on the gut inflammasome (when bile is broken down in the colon)

b) Protecting the body against LPS toxins

c) Upregulating GABA to reduce stress and anxiety & help you socialise and sleep.

d) Counteracting histamine to dampen allergic and IBS responses

Note that taurine is found mainly in meat. Dry cooking destroys approximately 52% of taurine while 79% is lost in boiling.

Whilst bile is stored in the gall-bladder, bile itself is made in the liver. Bile production is constrained by the liver’s other functions, particularly detoxification of toxins (especially LPS) and hormones (especially cortisol). So more stress and inflammation result in less capacity to make bile.

Herbal and lifestyle support

Bitters, leafy greens, beetroot, and dandelion all support the liver and boost bile production.

Ginger tea and herbal bitters are well known pre-meal boosts to bile. Deep breathing is a less well-known life hack for more bile. When breathing deeply the diaphragm massages the liver, stimulating bile production. Stress does the opposite of this, encouraging shallow breathing.

Vegetarians or those who eat purely cooked meat should consider taurine supplementation. Taurine can often benefit those with IBS, SIBO, GERD or fat malabsorption etc.

The migrating motor complex

When you eat can be just as important as what you eat. This is largely because of the migrating motor complex.

The migrating motor complex (MMC) is a 90minute pulsing process that sweeps undigested food, debris, bacteria and toxins from the gut down to the colon. Bile is the mop. MMC is the broom.

The MMC cycles will not initiate until about 3 hours after your last meal. They are also far stronger when you are awake than when sleeping. The feeling of hunger is often a sign of the MMC at work – a good sign.

Impaired MMC cycles, for example through constant snacking, causes issues like SIBO and IBS.

Herbal and lifestyle support

Key ways to maximise MMC cycles are:

  • Eating breakfast later

  • Eating dinner earlier

  • Trying to get 4 hours between meals

  • Avoiding snacking

Note – going to bed with heavy food in your stomach is never a good idea. Melatonin blocks insulin and interferes the ability to process glucose. Eating late at night sets you up for high blood sugar and metabolic disease.


Whilst what you eat and when you eat are important, perhaps more important still is exercise. Exercise increases mitochondria in ALL cells, including the gut.

When you exercise the body creates lactate and hydrogen ions which must be quickly removed.

Mitochondria do this by burning lactate and hydrogen ions for energy. Less exercise equals less mitochondria. Glucose without sufficient mitochondria to remove lactate and hydrogen ions results in acidity and inflammatory oxidation.

Exercise also up-regulates anti-oxidant production, improves endotoxin clearance, decreases the inflammatory response to endotoxin, improves movement through the GI system and balances the sympathetic and parasympathetic nervous systems to reduce stress. Exercise also increases bile flow by up to 10x.

Finally, exercise has direct effects on the microbiome. It increases species diversity and increases the quantity of the SCFA-producing bacteria which produce energy and dampen inflammation.

A note on IBS

IBS used to be an umbrella term to describe a loose collection of symptoms – gas, bloating, pain, brain fog etc. Cause unknown. That is no longer the case. In 2018 scientists clearly established IBS was an overactivation of the enteric (gut) nervous system that occurs in a specific combination of high serotonin, histamine and elastase.

Overactivation of the gut nervous system in cells exposed to histamine, serotonin and elastase. Notice the huge response when all three are in combination.

Serotonin will always be found in huge quantities in the gut as it regulates so many functions.

Histamine is released in the gut in response to “triggers” that vary from individual to individual. Triggers can include nightshades, gluten, dairy and fat. There is no “one trigger fits all” however a key component of gut histamine release is generally fat. Fat increases the permeability of tight junctions which enables the triggers to enter circulation. This triggers a histamine response from the gut immune system.

Elastase is a protease enzyme that enables digestion of protein.

For 5000 years traditional systems of medicine such as ayurveda and TCM have advocated avoiding combining heavy quantities of proteins and fats. However humans have always been able to consume reasonable quantities of protein and fat in combination. So where is the IBS epidemic coming from?

The last piece of this puzzle comes in the form of the elastase inhibitor SERPIN-BL.

Remember it is the combination of serotonin + histamine + elastase which causes IBS. SERPIN-BL removes the elastase which stops the IBS reaction. The “BL” stands for Bifidobacteria Longum. SERPIN-BL is made by the beneficial bacteria bifidobacterial longum. It is the absence of this beneficial bacteria which predisposes to IBS.

Overactivation of the gut nervous system in gut cells with IBS compared to gut cells with IBS in the presence of SERPIN-BL.

To combat IBS:

  • Avoid combining large quantities of protein and fat in meals

  • Use a Bifidobacterial Longum probiotic to increase SERPIN-BL (widely available from many chemists)

  • Use mast cell stabilisers to reduce histamine response. Natural mast cell stabilisers include:

  1. Buckwheat (an amazing source of quercetin, luteolin & rutin)

  2. Resveratrol (grapes, wine)

  3. Vitamin C (fruits)

  4. Nettle

  5. Chamomile

  6. Nearly all spices including ginger, garlic, turmeric, black pepper, cinnamon and cardamon

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1 Comment

Sep 25, 2022

Wow!! This is amazing Luke! Thank you for your wisdom

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