My deep dive into gut health and nutrition

The gut brain axis is a phrase used to describe the interaction between the gut and the brain. This communication occurs via something called the Vagal nerve.

So, Serotonin 90-95% manufactured by the microbiome! Don’t let it get robbed though….

As the vagal nerve is the interface between gut brain communication the health of the vagal nerve will influence the gut brain axis.

“The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease”. This is commonly called the microbiome.

The health of the gut microbiome can influence behaviour, mood and thought patterns. For example, germ free mice exhibit more confident and curious behaviour patterns, when compared to those with normal pathogens. Germ free mice are bred without any microbiome….

As well as influencing mood and behaviour the gut microbiome can influence metabolic health and blood glucose metabolism.

Metabolic disease states, like obesity, can alter the gut microbiota to promote more energy extraction from food (Bäckhed et al. 2007). The gut microbiota can also influence blood glucose. Lower bacterial diversity correlates with insulin resistance and higher adiposity (reviewed in Zhu & Goodarzi 2020).

The imbalance of the microbiome is referred to as dysbiosis.

A healthy microbiome can directly influence inflammation.

Inflammation is the body’s defence and repair mechanism. A transport mechanism for immune system function. Needed acutely, bad when switched on chronically.

Inflammation pulls on the body’s tryptophan reserves; this is called the tryptophan “steal” this is how inflammation can worsen mood state and cause depression. This is also sometimes called cytokine (an immune cell responsible for the inflammatory response) sickness.

Dysbiosis and excessive inflammation can lead to intestinal permeability, or “leaky gut” barriers also exist between the blood and the brain, this is another type of mucosal barrier. This is called the blood brain barrier or BBB.

A leaky gut and gut inflammation can lead to a leaky BBB. This in turn can lead to something called neuroinflammation.

Chronic Stress = compromises gut integrity. Compromised BBB integrity and can cause Neuroinflammation.

A leaky gut can also lead to particles of food entering into the blood stream triggering an immune reaction. Sometimes proteins mimic body structures. This is called molecular mimicry. If these proteins e.g., from gluten or dairy trigger an immune reaction the body can attack its own tissues. This is how intestinal permeability is linked to autoimmune diseases and excessive inflammation.

An over reactive immune system can be calmed via using anti-inflammation protocols.

A yeast called candida can cause leaky gut if it becomes too strong.


Red apple skin feeds Akkermansia a probiotics with far reaching health benefits, it help gut integrity and is inversely associated with better metabolic health. Guess what it loves red apple skins, thrives off them.

“Collectively, the increasing body of evidence from animal and human studies suggest that A. muciniphila is a highly promising probiotic, especially its potential for the prevention and treatment of diabetes, obesity, and their associated metabolic disorders, which is of great interest for future research and development”.

An apple or 4 a day, really might keep the Dr away.

Healing a compromised gut lining can take time, the lining has a fast cellular turnover and is built primarily from glutamine and amino acid. The 4R approach to gut function and healing involves removing the culprits which might be compromising gut health. Repopulating beneficial bacteria, healing the gut lining. More can be read about the 4R approach here.

The microbiome is built from giving birth vaginally which gives the baby more of the mother’s microbiome. Breast feeding continues to build the babies immune function via transfer factor and special mothers milk sugars called oligosaccharides.

The majority of the body’s immune defences and cells are housed in the gut.

Looking after the health of the gut will directly influence immune system function.

A healthy microbiome is a diverse microbiome. Research suggests that having a wide array of microbes in our gut makes our microbiome more capable and resilient.

How can I make my microbiome diverse?

Eating foods such as yogurt, kefir, fermented cottage cheese, kimchi and other fermented vegetables, vegetable brine drinks, and kombucha tea led to an increase in overall microbial diversity, with stronger effects from larger servings.

A low bacterial diversity is linked to allergic diseases in childhood including asthma, eczema and other allergies.

A high sugar, low fibre diet is associated with low bacterial diversity.

Eating a large variety in fibres from consuming different vegetables and plants can contribute to a healthy microbiome and microbiome diversity.

Some fibre rich foods are called resistant starches, these are good to include in the diet for gut health. They include things like unripe bananas and cooked then cooled potatoes, beans and oat bran.

Polyphenols, including pigment plant-based chemicals also help with microbiome health and diversity.

Polyphenols include:

Herbs, spices, berries, dark chocolate, coffee, green tea, vegetables, olives, nuts (with skin on) beans, olive oil, flaxseeds…….

Gut microbiome diversity decreases as we age. Long lived populations tend to have a good level of microbiome diversity

This is not surprising when we consider the link of gut health and neuroinflammation, cognition and cognitive decline.

When the gut bacteria process fibres they produce fats called short chain fatty acids.

SCFA’s. These are extremely good for gut health, barrier integrity and can also influence brain neurotransmitters, like serotonin and dopamine.

This is why when you eat a lot of fresh and raw vegetables you can actually feel more positive and happier.


I heard recently about a case of an “awakening” this is where someone with advanced dementia or Alzheimer’s is suddenly able to communicate, remember and interact with those around them often shortly before their death. This can occur after years of apparent loss of these senses.

Perhaps indicating an ability to tap into deeper brain reserves. This phenomenon is by no means unique, the case I heard about was also combined with IV antibiotic therapy.

Antibiotics, reduced inflammation in the gut, this affect translates to less neuroinflammation, enough perhaps to allow the brain to function…in a normal manner for a short period of time.

Unfortunately, in this case the antibiotics were withdrawn, the patient fell back into her shell and died the following week.

Intensive farming is often associated with overcrowding animals and rife use of antibiotics, this isn’t just to prevent disease, it’s also used to prevent the animals becoming depressed and anxious… of course it’s not a good idea to use medication like this when you have natural solutions, read on for more juicy information…..

How this link between the brain and the gut works is unravelled below for you…..

Gut Brain Axis - what is it? Why is it Important?

Ever wondered why you sometimes feel things in the gut? Trust your gut feeling is a phrase which used to be used more often when I was a kid… the reason tons of your neurotransmitters are manufactured in the gut. Depending on what you read 90-95% of serotonin is produced by gut bacteria and gut cells.

Your gut health and influence how you feel, communicate and behave. The gut health or microbiome health, is vital for brain health but also regulating inflammatory processes in the body and the brain.

“Recent studies have suggested that the intestinal microbiome plays an important role in modulating risk of several chronic diseases, including inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, and cancer. At the same time, it is now understood that diet plays a significant role in shaping the microbiome, with experiments showing that dietary alterations can induce large, temporary microbial shifts within 24 h.”

Serotonin is a chemical that carries messages between nerve cells in the brain and throughout your body. Serotonin plays a key role in such body functions as mood, sleep, digestion, nausea, wound healing, bone health, blood clotting and sexual desire.

Still, scientists following this line of research have become increasingly convinced that to fully understand our emotions and behaviors, we need to study the gut as much as the brain.

That Gut Feeling…… it’s a 2-way street.

The gut, the brain and the vagal nerve….. Just as your microbiome can influence brain function and neurotransmitter production, your brain in turn can alter the balance of bacteria in the colon… stress can also alter the permeability of the gut.

Chronic Stress = ¯ gut integrity. BBB. Neuroinflammation.

The microbiome can influence the production and release of neurotransmitters. Stress, worry and rumination can adversely affect gut flora, gut permeability and also the permeability of the blood brain barrier (BBB).

What are neurotransmitters? Serotonin, GABA, Dopamine, Acetyl Choline…… you can read more about them here:

Dopamine; drive, ‘get up and go’ reward, sex
Acetyl Choline; memory and muscle contraction
GABA; rhythm, relaxation, calming
Serotonin; sleep, well being, cravings, emotion
These are often an area I’ll look to biohack for clients in order to improve motivation, sleep, sex drive, memory and so on. Looking after the gut means you’ll have plenty of available neurotransmitter reservoir….

So, the brain and mood state can alter the balance in the microbiome, stress and depression alters the microbiome balance. As always, it’s a case of improving the health of the body combined with improving the health of the thought processes, stress management, personal development and planning. Regulating inflammation…..via how you think about things, now there’s a thought.

The way we can smooth the communication between the brain and the gut is via an intermediatory nerve called the vagal nerve….

Learning to breath properly, meditate, deep relaxation, massage, and getting yourself cold are a few quick ways to keep vagal nerve tone in tip top shape.

Keep you gut microbiome in good shape. The gut and brain are

intricately connected via the vagus nerve information

superhighway. Harm your gut, harm your mind. Support your gut = support your mind.

The vagal nerve is an intermediatory between the Gut Brain Axis.

The vagus nerve represents the main component of the parasympathetic nervous system, which oversees a vast array of crucial bodily functions, including control of mood, immune response, digestion, and heart rate. It establishes one of the connections between the brain and the gastrointestinal tract and sends information about the state of the inner organs to the brain viaafferent fibers.

Vagal Tone and vagal nerve supporting habits can then improve mood state, stress and PTSD via this pathway. This makes gut supporting and vagal nerve tone supporting habit vital alongside conventional therapy, CBT and other behaviour supporting therapies… You could even say goal setting might improve via this route.

The health of the gut, the health of the brain and the health of the vagal nerve are all vital for well-being.


Top 8 Gut Health Habits

  • Chew your food
  • Eat in a relaxed setting
  • Eat vegetables
  • Eat high fibre foods
  • Eat fermented foods
  • Eat bioactive food
  • Eat a big variety of plant-based food + polyphenols
  • Try a 30 different plant foods per day challenge, this can include spices, herbs and so on

Bad Habits for Gut Function

  • Lack of sufficient good habits listed above
  • Antibiotic use, sometime necessary always rebalance after use with probiotics + pre-biotics
  • Excessive caffeine
  • Excessive alcohol
  • Too much meat in relation to vegetables
  • Stress
  • Poor vagal nerve tone
  • Artificial sweeteners

Top Vagal Nerve health Habits

  • Deep breathing
  • Chanting, singing and humming
  • Probiotics and pre-biotics
  • Gratitude, nurturing and love
  • Yoga
  • Meditation
  • Getting cold
  • Via the gut or increasing serotonin via supplementation and deep sleep
  • Exercise
  • Lowering inflammation
  • Intermittent fasting

Top 12 good things for the brain

  • Stimulus + learning new tasks and skills
  • Relaxation
  • Interaction
  • Good fats
  • B-vitamins + other essential nutrients
  • Nootropics
  • Vitamin D / Sunshine
  • Sleep
  • Practice and making mistakes
  • Goals
  • Fitness
  • Clean food, air and water

Top 8 bad things for the brain

  • Lack of stimulus
  • Stress
  • Isolation and lack of interaction
  • Bad fats
  • Lack of good nutrients, b-vitamins and other essential nutrients
  • Lack of vitamin D / sunshine
  • Lack of goals
  • Toxins + processed food
  • So, Serotonin 90-95% manufactured by the microbiome! Don’t let it get robbed though….

How is the serotonin made? Which microbes help serotonin production?

Peripheral serotonin is produced in the digestive tract by enterochromaffin (EC) cells and also by particular types of immune cells and neurons.

The researchers found that the EC cells from germ-free mice produced approximately 60 percent less serotonin than did their peers with conventional bacterial colonies. When these germ-free mice were recolonized with normal gut microbes, the serotonin levels went back up—showing that the deficit in serotonin can be reversed.

"EC cells are rich sources of serotonin in the gut. What we saw in this experiment is that they appear to depend on microbes to make serotonin—or at least a large portion of it," says Jessica Yano, first author on the paper and a research technician working with Hsiao.

Previous work in the field indicated that some bacteria can make serotonin all by themselves. However, this new study suggests that much of the body's serotonin relies on particular bacteria that interact with the host to produce serotonin, says Yano. "Our work demonstrates that microbes normally present in the gut stimulate host intestinal cells to produce serotonin," she explains.

It’s important to choose the right probiotics which include some of these types of probiotic species.


VSL and Symprove both from Amazon, I’ve also been trying these ones which seem like they are having a positive benefit:

All that lovely serotonin can work wonders, unless you regulate inflammation though it might all get robbed via a pathway called the Kynurenine pathway…..or the tryptophan steal.

Inflammation…..tryptophan + serotonin…. Tryptophan “Steal”

If you are experiencing the tryptophan steal you can use increased levels of serotonin pre-cursors and nutrients to smooth the serotonin pathway. Also if you work on lowering inflammation this can in turn, shift the steal back towards the serotonin pathway.


Microbiome Prebiotics and Probiotics… variety is key. I heard Tim Spector talking about the gut and making it simple, he mentioned it’s a bit like a garden you need plenty of species and variety and lots of different fertiliser. One way to ensure a good diverse microbiome is to eat 30 different plants based and gut healthy foods per week. You could even aim for 20 different ones in a given day if you like.

It includes things like nuts and seeds, herbs and spices and all things nicey, so once you get going it’s not too tricky…

Fermented foods, mixed fibre foods……resistant starches and pre-biotic rich foods.


Pre-biotic rich foods include those rich in inulin, garlic, onions, leeks, beans and pulses, bananas, oats, oat bran, almonds, pecans etc. Lovely foods eat plenty of them.

Resistant starch is a type of carbohydrate that doesn't get digested in your small intestine. Instead, it ferments in your large intestine and feeds beneficial gut bacteria. This type of starch provides numerous health benefits and has fewer calories than regular starch as it’s indigestible

Plantains and green bananas (as a banana ripens the starch changes to a regular starch)
Beans, peas, and lentils (white beans and lentils are the highest in resistant starch)
Whole grains including oats and barley
Cooked and cooled rice or potatoes


Are also really an excellent addition to an all-round healthy diet. It’s no coincidence that most of the longest lived cultures around the world all include plenty of high quality fermented foods in their diets.

I like to use cider vinegar most days, along with pickles, kimchi, sauerkraut, a home-made coleslaw which I make with cider vinegar and let it stew a bit before popping in the fridge. Natto for a really punchy flavour addition and Natto kinase is one of my daily supplements…..Kefir’s an easy one as well, cold from the fridge. You can also make your own with a kefir culture.

cultured milk and yoghurt
fermented sausage.


Beta-glucans also act as prebiotics, feeding the good bacteria in your gut and helping balance your gut microbiome. In combination with inositol and digestive enzymes, beta-glucan has been shown to help improve gas, bloating, and abdominal pain in people with IBS and IBD.

Short Chain Fatty Acids and their influence on Gut Brain Axis. SCFA’s and the brain.


The simple way to encourage the gut to ferment more fibres into SCFA’s is, to eat more fibre which the gut enjoys for this purpose. Generally, if you eat raw, fibrous vegetables this is an excellent way to encourage the gut to product more of these beneficial fats.

Oligosaccharides of which there are many types are a wonderful way to do this. They occur in all the pre-biotic foods listed above and tend to be in inulin rich foods. Inulin is actually a mixture of oligosaccharides and polysaccharides. Some of these saccharides, termed fructans, are inulin and oligofructose. They possess many physiological attributes normally associated with dietary fiber.

The positive health effects of SCFAs are myriad, including improved immunity against pathogens, blood–brain barrier integrity, provision of energy substrates, and regulation of critical functions of the intestine.

Microbiota-gut-brain-crosstalk refers to the effects of the gut microbiome on the brain and vice versa. There are several ways that SCFAs may influence brain health. They may cross the blood-brain barrier through endothelial cells that have a high number of monocarboxylate transporters (MCTs). Levels of butyrate, acetate, and proprionate are all detectable in human cerebrospinal fluid (CSF).

SCFAs may also modulate the levels of neurotransmitters. These metabolites have been shown to regulate the expression of tryptophan 5-hydroxylase 1 and tyrosine hydroxylase.


This is mainly accomplished through eating a diet high in fiber. The fiber in food is composed of chains of oligosaccharides. The oligosaccharides are not easily digestible but serve as food for gut microbes. SCFAs are the main metabolite produced by the fermentation of the indigestible fiber. High-fiber diets include vegetables and fruits including onions, beans, broccoli, apples, berries, avocados, and more.


The usage of a sodium oligomannate, with known cognition improvement effect in humans, suppressed neuroinflammation, Aβ plaque deposition, and cognition impairment (164).

Chronic Stress = gut integrity. BBB. Neuroinflammation.

To avoid Depression…..and ”tryptophan Steal”

Anxiety vs Depression. Definition.

Cabbage…..Vitamin ‘U’ excellent for healing gut…..

Bone broth…… glutamine….. leaky gut……zinc carnosine, colostrum…….


Don’t just grab any old probiotic…

Probiotics, functional fibres + resistant starches…..

SCFAs + serotonin and dopamine…..


Red apple skin…Akkermansia……. help gut integrity…….

Fibre Slide…… Fibre = lower inflammation…….How?



Omega supplements, fish oils, krill oil, cod liver, vs 3, 6, 9……



Strikingly, 90% of serotonin required for mood, behavior, sleep, and several other functions within the CNS and gastrointestinal (GI) tract is produced in the gut (87).

In addition, bacterial fermentation of indigestible dietary fibers produces among the SCFAs, butyrate, propionate, and acetate in the colon (97). SCFAs maintain gut health by promoting intestinal barrier integrity, mucus production, and supporting a tolerogenic response over inflammation (49,

Of extreme relevance, the altered microbiota of patients could transfer the disease from a human host to a mouse host (113, 116–120).

Stool microbial profile of AD patients display decreased numbers of Firmicutes and Actinobacteria, and increased Bacteroidetes compared to controls. Within the Firmicutes, the families Ruminococcaceae, Turicibacteraceae, and Clostridiaceae were all less abundant in AD patient (160).

The usage of a sodium oligomannate, with known cognition improvement effect in humans, suppressed neuroinflammation, Aβ plaque deposition, and cognition impairment (164).

Probiotics supplementation has been taken into consideration also for AD (168, 169). The human isolate Bifidobacterium longum (NK46) was orally administered in 5xFAD mice and induced anti-inflammatory effects (decrease in lipopolysaccharide (LPS) levels, NF-κB activation, and TNF-α expression), changes in the intestinal microbiota composition of the recipients (increase in Bacteroides and reduction in Firmicutes and Proteobacteria phyla), and suppression of Aβ accumulation in the hippocampus (170).

The first signal comes from pathogen- or danger-associated molecular patterns (PAMPS/DAMPS) from outside of the cell and induces the transcription of genes encoding for inflammasome components and products. The second signal comes from intracellular danger signals, such as adenosine triphosphate, uric acid, fatty substances that can induce lysosomal damage, or nicotinamide adenine dinucleotide phosphate oxidase- or mitochondria-driven reactive oxygen species production. These processes result in the assembly and activation of inflammasomes (191–193).

Tags: Gut, Gut Health