The Ultimate Guide to Gut Health

How To Improve Gut Health Naturally: The Ultimate Guide

The past decade has seen a huge scientific effort unfold in order to measure the gut microbiome. Findings of the gut’s composition, function and influence are showing we are genetically more microbe than human. And excitingly, by simply understanding our microbial inhabitants we can change our gut health for the better.

And naturally too. 

One of the easiest approaches to naturally supporting your gut health lies not in what you do; but what you don’t do. 

Because majority rules.

Choosing to NOT eat foods that encourage unfavourable microbes or NOT follow harmful lifestyle practices are an important part of natural gut healing.

Your microbial millions can then do the hard work for you, weeding out the trouble-makers and restoring balance and harmony.

Leaving you healthier, happier and glowing. 

From the inside out.

The Ultimate Guide to Gut Health

Why is Gut Health so Important?

There is a huge (and growing) body of evidence to suggest your trillions of resident microbes are not only calling the shots and driving your physical, mental and emotional wellbeing, they also influence your habits, your behaviour and your happiness.

Isn’t this what we all strive for?

The Ultimate Guide to Gut Health

The trillions of bacteria, fungi and viruses living in your gut, flourish within their own ecosystems. Creating vitamins, metabolites and energy not only for each other but symbiotically for you too.

All without your conscious input.

The balance and diversity of your gut microbiome drive processes we traditionally believed were due to organ systems and cellular functions; such as inflammation, immunity and cellular integrity.

The Ultimate Guide to Gut Health

Diseases Associated with Gut Health

States of dis-ease are quickly being recognised to be largely rooted in microbial pathways and managed by microbiome diversity, composition and influence. Making our daily choices (or avoidances) far more important than we previously understood.

Obesity: The microbiomes of those that are obese or overweight are known to be less diverse than the population within a ‘healthy’ weight range. It appears not only food and lifestyle choices play a crucial role in our fat metabolism but also our gut bacteria. Animal studies support this. One study showing mice who received antibiotics in their first month of life developed 60% more fat than those not exposed to antimicrobial drugs.

Tip: Choose to avoid unnecessary antibiotic interventions to maintain microbial balance.

Autism: Autistic spectrum disorder (ASD) children have vastly different microbiomes to neurotypical children. In a 2013 study, Italian researchers showed that ASD children’s gut microbiota composition (types of bacteria present) is very different to ‘healthy children’. Meaning the ecosystem of affected children is higher in ‘unfavourable’ bacterial groups and produces vastly different metabolites. Additionally, it is estimated that 50% of ASD children suffer from GI issues such as indigestion, malabsorption and allergies.

Tip: A microbiome test offers unparalleled insight into your microbiome providing invaluable information to empower you to make appropriate choices for your family.

Mental Wellbeing: 90% of your feel-good hormone, serotonin, is manufactured in your gut. The interaction of microbes with specialised EC (enterochromaffin) intestinal cells help modulate the production of this critical hormone. EC cells are stimulated by bacteria to produce this vital neurotransmitter. Similarly, some bacteria themselves produce brain chemicals.

Tip: Happiness is definitely an inside job!

The Ultimate Guide to Gut Health

This all begs the question, which came first?

Does an unhealthy microbiome develop as a result of a disease or do your dietary and lifestyle choices combine with your genetics to determine your microbiome?

Research is pointing to all of the above. A lot like the chicken and the egg.

Good news is the choices we make today can positively change or even correct imbalances in our microbiome to influence many conditions associated with an unhealthy gut. Such as:

  • Autoimmune conditions
  • Alzheimer’s disease
  • Acne
  • Allergies
  • Asthma
  • Cancer
  • Dental cavities
  • Eczema
  • Gastric ulcers
  • Atherosclerosis
  • Irritable Bowel Syndrome
  • Malnutrition
The Ultimate Guide to Gut Health

Making it so important to be mindful of what you are feeding your ecosystem, but also what you avoid in order to allow this natural and fascinating process to function optimally.

In order to come to this awareness, we need to understand it a little more.

What is Your Gut Microbiome?

Your gut, specifically your colon, is home to the largest concentration of microbes in your body. Current estimates suggest around 38 trillion (3.8 x 10^13 ) microbes thrive in the 400g of material waiting in your colon.

And within this 400g of future faeces, your microbes make up approximately 200g.

When we talk about microbes we describe all microbial life, not only bacterial life. Like a rainforest is far more diverse than ‘just trees’, our trillions of microbes are far more diverse than ‘just bacteria’. 

The Ultimate Guide to Gut Health

The scores of bacteria in your gut coexist with:

  • Archaea. Bacteria-like single-celled organisms.
  • Fungi. Mostly yeasts and collectively referred to as the mycobiome.
  • Microbial eukaryotes. Parasites, they’re not all bad.
  • And viruses. There are many, often called the virome.

This eclectic collection of microbes is called the microbiota. And the genetic material they represent (their genes) is commonly referred to as the microbiome. 

So in short, the gut microbiome is a 200g predominantly bacterial (archaea, fungi, parasites and viruses make up less than 0.1%) vast community living in your large intestine, eating what you eat and contributing a significant volume of DNA. 

From here, we can look closer to understand the contribution of the different types (phyla) of bacteria within your gut microbiome. The most predominant gut bacteria fall into five phyla although many others may be present, these represent the majority for most people.

  1. Bacteroidetes
  2. Firmicutes
  3. Actinobacteria
  4. Proteobacteria
  5. Verrucomicrobia

And as these large groups are examined further, the abundance of various bacterial genera and species are revealed. For example, the presence (and abundance) of Akkermansia muciniphila (a member of the Verrucomicrobia phylum) can be a positive finding as it has a key role in maintaining gut integrity and mucus production.

Your gut microbiome reads like a menu of what you eat every day. 

Skilled practitioners and scientists can interpret microbiome test results to provide invaluable insight into not only what you eat but importantly what you don’t eat. 

Providing you with informed dietary recommendations and support on your healing journey.

All by using a simple microbiome test.

The Ultimate Guide to Gut Health

Why Take a Gut Microbiome Test?

Knowledge is power. And we know that different bacteria consume different foods and produce different by-products.  

So it follows that their relative abundance and balance can be controlled by you, through diet.

Naturally. You can choose who to feed.

Knowing precisely who is thriving (or not) in your gut allows you to really target the source of your issue, and correct it. Quite the opposite of symptom spotting.

If you’ve been living with chronic health issues you’ll know how much energy can be spent on finding someone who understands you and your individual health concerns.

Microbiome testing removes the guesswork and gives you a snapshot of exactly what’s going on in your gut.

Combined with appropriate and individual dietary/lifestyle advice, microbiome testing can allow you to take back control of your health. 

It can change your life. 

And your resident microbes’ too.

After all, your wellbeing supports their lives. Your body is their home.

The Ultimate Guide to Gut Health

Gut Health and Your Body

One of the most empowering outcomes of microbiome awareness is rooted in the intrinsic ability of the body to heal.

We now know that simple changes, like taking a probiotic or incorporating gut healing foods can improve debilitating diseases.

  • Digestive disorders. Irritable bowel syndrome (IBS), Crohn’s Disease, chronic constipation, leaky gut, SIBO, bloating, diarrhoea …
  • Skin conditions. Eczema, psoriasis, rosacea and acne …
  • Autoimmune diseases. Fibromyalgia, Hashimoto’s, multiple sclerosis (MS), coeliac, lupus, rheumatoid arthritis …

As you begin to understand how your digestion and microbes work you’ll begin to make choices based on their wellbeing. Which will, in turn, influence your own.

The Ultimate Guide to Gut Health

We are a superorganism.

A collection of many, all with a common goal. Our bodies do not set out to work against us (although it may feel like it at times). Our bodies want to be well and disease is simply a symptom of an imbalance and a call for help.

Understanding the source of our symptoms is the key to wellbeing.

And when we remove foods and practices that harm us, our body (and our microbes) restore balance. That innate intelligence within all life works towards health.

The microbiome adjusts. The body heals.

And the mind comes along for the ride.

The Ultimate Guide to Gut Health (Naturally)

Gut Health and Your Mind

We are so fortunate to bear witness to the plethora of amazing research linking gut health to mental health. 

It is now common knowledge that the gut is home to millions on millions of neurons and produces neurotransmitters, messengers for sending and receiving messages to AND from the brain. 

It’s little wonder we used phrases like gut feeling, gut instinct and food for thought, describing this connection long before science ‘discovered’ it.

Consequently, people all over the world are healing from mental illness through diet with the right support and lifestyle changes.

New fields are emerging like nutritional psychiatry, exploring the gut-brain connection (also called the gut-brain axis) and finally acknowledging food can treat psychological conditions.

It was never ‘all in your head’.

The Ultimate Guide to Gut Health

The Gut-Brain Connection

It is all also in your gut.

The gut is home to your Enteric Nervous System (or ENS) an intricate network of neurons deeply connected with your gastrointestinal (GI) tract. This includes the vagus nerve, the largest pathway connecting your brain to your gut. And it’s a two-way street. Signals have been shown to go BOTH ways

Not surprisingly, stress has been found to inhibit the vagal nerve and has negative effects on the GI tract and microbiota and is involved in the disease processes of many illnesses including IBS and IBD (inflammatory bowel disease – a similar condition presenting with intestinal dysbiosis).

The role of stress in disease is widespread and stress reduction is an important consideration for everyone, especially those of us looking to heal gut issues.

Stress is hugely significant in the development and chronic nature of many gut-related conditions but unfortunately, it is one of many potential causes of an unhealthy gut.

The Ultimate Guide to Gut Health

What Causes an Unhealthy Gut

Building a better microbiome isn’t just about what you feed your body, but what you keep out. Modern life has introduced many microbiome polluters, substances that critically change the composition of your microbiome.

Sadly they are often hidden in your daily routine.

If you are looking for an easy place to start with gut-healing eliminating microbiome polluters is a great place to start. 

  1. Antibiotics. Antibiotics have been designed to be anti-biotic, biotic meaning relating to or resulting from living organisms. And rather than being targeted they are wide acting chemicals whose effects have been likened to a ‘bomb going off’ in your gut. Antibiotics undeniably save lives but should be used only when absolutely necessary. Every time you take antibiotics, not only are you wiping out the ‘bad’ bacteria, you’re also destroying most of your beneficial gut bacteria. It can take years for your body to rebalance your gut bacteria without additional help.

    Tip: Supplementing with a high-quality probiotic and eating fermented foods after taking antibiotics will help re-seed and support your microbiome balance.

  2. Processed Foods. Ultra-processed foods common in the Western diet are a relatively recent addition to the human menu and are often high in refined carbohydrates, harmful sugars and devoid of any real nutritional benefit. It follows that diets rich in these food-like-substances are not supportive of the bacterial friends that the human pre-fast food diet nurtured. Dr Mercola suggests these foods select for and feed ‘bad’ bacteria. Additionally, many of the artificial additives found in processed foods, like Polysorbate 80, also have a detrimental effect on your microbiome.

    Tip: If it’s in a packet and you can’t pronounce it, don’t eat it.

  3. Tap Water. The water you receive when you turn on the tap is far from pure. Although it may be free of bacterial and protozoan infectious organisms (due to heavy chlorination) it contains a multitude of other harmful substances. Municipal water is treated with numerous chemicals that are toxic in high doses. The Australian Drinking Water Guidelines describes a number of buffering agents that are used in addition to the well-known chlorine and fluoride. They are chemicals who mimic the action of important thyroid hormones, substances collectively termed endocrine disruptors.

    Tip: Use water filters in your kitchen and install a shower filter to reduce your family’s exposure. Heated water increases both vaporisation of the chemicals and your skin’s permeability.

  4. Low-fibre, high-fat diet. Low-carb is all the rage right now with bacon and butter being promoted as health foods. In moderation, these foods can be a balanced part of any diet, but problems can arise when we prioritize fat and reduce health-supportive fibres. Helpful bacteria eat fibre and harmful bacteria love fat, so a fibre-deficient high-fat diet can be the instigator for an unhealthy microbiome.

    Tip: Take Michael Pollan’s sage advice. “Eat food. Not too much. Mostly plants.” And you’ll be well on your way to getting enough fibre, think soluble, insoluble and resistant starch.

The Ultimate Guide to Gut Health

Gut Microbiome Case Study

An intriguing case study into the effects of a pre-modern-era diet was conducted by Jeff Leach, an anthropologist studying the microbiomes of the Hadza. A central-Tanzanian hunter-gatherer tribe whose existence has remained largely unchanged for 10,000 years. 

No antibiotics, no processed anything (they don’t even cultivate crops), seasonal rainwater and a very primal high-fibre diet.

He mapped his own microbiome on both the Standard American Diet (with the apt acronym – SAD) and after following the Hadza fibre-rich diet. 

Gut bacteria image graph

The results show a striking shift in the predominance of Firmicutes (a fat-loving phylum known to contribute to obesity) and Bacteroidetes (a phylum associated with leanness and overall health).

On the left, the SAD diet results are dominated by the red coloured Firmicutes. The graph on the right shows a dramatic shift to the blue coloured Bacteroidetes flourishing in response to his increased consumption of fibre, only 2-3 weeks later.

This undoubtedly illustrates the importance of both microbiome testing but also the rapid response of the microbiome. Bacteria replicate in response to food availability and they decrease in response to food scarcity. Exponentially.

It’s the balance of health-promoting microbes and the less favourable species which determines how you feel and how your body responds to their metabolites.

Signs and Symptoms of an Unhealthy Gut

We often don’t realise how unwell we were until we feel better. The dis-ease becomes a constant companion and our frame of reference. We learn to tolerate and live with all the niggly symptoms of disturbed health.

We miss the signs.

It’s only when we look back that we see how far we’ve come. 

If you are struggling with one or more of the following symptoms, gut microbiome testing might be a helpful tool for you.

  1. Digestive Signs
    Typical upset stomach symptoms like chronic diarrhoea, constipation, bloating and flatulence can all point to an unbalanced microbiome or dysbiosis. These can be caused by bacterial, fungal or parasitic disturbances resulting in inflammation, excessive gas production and irritation or leaky gut. Other symptoms include bad breath or halitosis and heartburn.

  2. Skin Signs
    Our skin is said to be a mirror of our gut. Dark circles under the eyes, acne, blotches, rashes and rosacea can all be associated with gut troubles. Of particular note is eczema, a chronic inflammatory skin condition that is as unsightly as it is debilitating. Elimination diets can be very effective in relieving skin conditions as they are easily visually monitored.

  3. Mood Signs
    Significant mood changes can indicate poor gut health. Seemingly harmless symptoms like moodiness, headaches and brain fog can mean the beginning of more concerning poor gut health symptoms like anxiety, depression and memory loss. ADD, ADHD and other behavioural and psychological syndromes have been shown to respond favourably to improvements in gut health.

  4. Body Signs
    Your body will try to alert you to your hidden gut issues with symptoms such as sleep disturbances, rapid weight change and fatigue. More serious symptoms like autoimmune conditions (lupus, rheumatoid arthritis, Crohn’s disease, coeliac) are also heavily involved in unhealthy gut processes. Suffering from low immunity, joint pain or arthritis can also point to the gut.

  5. Food Signs
    If you battle with food cravings or food intolerances and sensitivities chances are your gut is the culprit. Eating a diet high in sugar or suffering with nutritional deficiencies are also indicators of a gut out of balance.

Sound all too familiar? Take our online Gut Health Quiz to discover if you have any of the hidden warning signs of an unhealthy gut.

And remember, if you suffer any of the symptoms mentioned above it is important to get assessed by your healthcare provider or a qualified practitioner. While these symptoms are typical of gut health issues and related conditions there may be other underlying causes. 

The Ultimate Guide to Gut Health

How Foods Help or Hurt Your Gut

Diet is the most natural (and empowering) way to address your gut health. Choosing to eat foods that positively influence your microbiome and avoid those that do not is a crucial step in gut healing.

Consequently, there are a growing number of diets that have had wonderful results for people all over the world. 

Paleo, Keto, Plant-Based Whole Food, Low-Carb High-Fat, Gluten-Free Casein-Free and everything in between. And while all this information is wonderful, the conflicting advice can quickly become overwhelming. 

Which is why choosing to work with a qualified practitioner who has tested your microbiome can fast-track your healing and takes the guesswork out of choosing the diet that’s right for you.

In the meantime, understanding how food affects your gut is an important step forward as often simply by eliminating troublesome foods you will notice improvements.

The Ultimate Guide to Gut Health

How Wheat Affects Your Gut

Wheat has received a lot of bad press recently, and with good reason. In addition to heavy spraying and ever increasing glyphosate concentrations, modern day wheat is very high in gluten. 

The Ultimate Guide to Gut Health

Wheat gluten is comprised of different protein types called gliadins and glutenins.

And these soluble gliadin proteins act as messengers triggering your gut lining cells to produce and release another protein (called zonulin) which opens the spaces between gut cells (called tight junctions).

This increased permeability allows large molecules, including gluten, to pass through the gut lining causing an inflammation cascade of immune cells, cytokines and symptoms of what is commonly referred to as leaky gut.

On a cellular level, eating wheat causes your gut lining to leak.

The Ultimate Guide to Gut Health

What Dairy Does in Your Gut

Similarly, the dairy protein casein can negatively affect gut health. The casein proteins present in bovine dairy products are classified as A1 or A2-type bovine beta-caseins. 

A1 caseins have been shown to stimulate gastro-intestinal inflammation by the release of the opioid beta-casomorphin. A1 is also thought to interfere with the production of the enzyme lactase causing malabsorption and mimicking lactose intolerance and associated symptoms. 

Other troublesome and common foods include soy, refined sugar, caffeine and alcohol.

The Ultimate Guide to Gut Health

The Resistant Starch Pathways in Your Gut

On the other hand, consuming foods rich in resistant starch helps nourish and heal the gut. When resistant starch reaches the large intestine intact, it feeds bacteria that produce short-chain fatty acids (SCFA). 

Butyrate is one of these SCFAs and has been associated with many health benefits including reduced intestinal inflammation, increased cellular fluid transport, increased motility and reinforces gut cell defences.

All very good reasons to eat more foods rich in resistant starch.

The Ultimate Guide to Gut Health

Steps to Improve Gut Health Through Diet

While these are broad guidelines for improving gut health through diet it’s important to remember that like your microbiome is unique. It’s a complex fingerprint of all the foods, experiences and life that has gone before you.

So it’s imperative to acknowledge what works for someone else may not work for you. You need to tune into your body, understand what’s in your microbiome and go from there. Gently.

Some widely regarded great starting steps are:

  • Food. Following a whole food diet, low in processed foods and high in plants will immediately increase your fibre quota (to feed your helpful microbes) and lower your fat and sugar intake. Keeping stalks on fibrous vegetables like broccoli, cauliflower and asparagus are instant resistant starch boosters. Leeks are also wonderfully fibre-full.

    Further reading: 26 Best Foods For Gut Health

  • Fats. Increasing your intake of quality fats from fish, coconut oil, avocados and flax whilst reducing in from more unhealthy sources such as vegetable oils and saturated fats will help heal and repair your gut lining.

    Find out more: Gut Bacteria and Weight Loss, The Surprising Connection

  • Ferments. Incorporating good quality, homemade fermented foods into your daily routine such as sauerkraut, kimchi or fermented vegetables are an easy (and cost effective) way to boost probiotics naturally. A tablespoon a day can be enough to keep unfavourable microbes at bay. And if your kids are not keen on eating kraut, consider adding the juice to their cooled dinner. They won’t even know.

    Read more: Fermenting Is The Food Trend You Need – For Your Gut’s Sake

  • Friends.  The importance of good friends cannot be emphasised enough. Both in your gut with the addition of a reputable multi-strain, high CFU probiotic and finding a community who understands your food goals and supports you. Gaining a community around your lifestyle choices can help when no one else seems to understand.

    Looking for support? Book your Free Discovery Call with Amanda.

If you’re looking for some guidance or an easy to follow plan our Gut Heal and Nourish Program is a great place to start. 

Learning to listen to your body and monitor how it responds to diet and lifestyle changes you make is a powerful gut-healing practice and important life skill.

The Ultimate Guide to Gut Health

How Your Lifestyle Can Heal Your Gut

In addition to feeding your microbiome for health and creating a community of like-minded health-conscious people, there are a number of gut-supportive lifestyle choices or practices you can incorporate into your week.

  1. Get outside. Numerous studies have linked dirt microbes to better gut health. Mycobacterium vaccae found in soil has been shown to fight depression and boost immune responses. And while M.vaccae can be bought as a probiotic, it lives free-of-charge in your garden. So forget the hand sanitiser and get dirty.
  2. See the sun. While sunlight is undeniably good for mental wellbeing, vitamin D deficiency has been shown to reduce the antimicrobial molecules (defensins) that are important for maintaining healthy gut flora.
  3. Toxin reduction. Reducing your exposure to xenobiotic (including antimicrobial) chemicals and pesticides will help you maintain your microbiome diversity. Commonly used chemicals such as chlorine, sanitisers and household insecticides are designed to kill microorganisms including yours.
  4. Reduce Stress. Stress comes in many forms, there’s; psychological, sleep disturbance, environmental stressors (extreme weather etc), diet, physical activity, noise and even pollutants act as stressors. Research is showing that stress impacts the function, composition and metabolic activity of the gut microbiome. Different origins of stress have different effects and can be both helpful or harmful.
  5. Intermittent Fasting. Fasting is quickly becoming a recognised beneficial practice for improving and maintaining gut health. It appears that traditional wisdom knew a thing or two about microbiome maintenance long ago. Intermittent fasting involves eating and fasting in cyclical patterns, often with up to 18 hours between meals. The health benefits are proving to be highly popular, all from skipping breakfast.
  6. Stay Hydrated. Keeping you and your gut microbes well watered is an easy way to maintain a healthy gut naturally. Did you know, around 8 litres of water per day is absorbed in digestive processes! As well as the myriad of general health benefits of consuming water, it is important to make sure your water is as pure as possible.
  7. Sleep. Sleep has long been touted a cure all, and conversely, the sleep deprivation is known to have serious consequences. And your microbiome plays a crucial role, via the gut-brain axis and also directly. Serotonin and GABA are important neurotransmitters involved in relaxation and sleep. And both are produced by gut bacteria. Streptococcus and Enterococcus produce serotonin which helps make the sleep molecule melatonin. Lactobacillus and Bifidobacteria produce GABA (gamma-aminobutyric acid) decreases beta-brainwaves and increases the calming alpha-brainwaves.
  8. Learn.  And finally, one of the most empowering things you can do for your family’s health is to educate them on the importance of gut health. Incorporating simple diet and lifestyle changes into your everyday routine (or eliminating harmful ones) can reap massive physical, emotional and environmental benefits.
The Ultimate Guide to Gut Health


Natural gut health is a lifestyle philosophy. 

Becoming aware of your daily practices, your diet and who’s in your microbiome are powerful tools to improve every aspect of your health. 

Including foods that heal, eliminating those that do not and truly understanding the dynamic and supportive role that microorganisms play in our biology can bring about massive change.

Your health is absolutely in your control.

That said however, there really are no quick-fix solutions.

When it comes to healing the gut naturally, persistence, patience and the right advice are cornerstones for gut health. Our Gut Heal and Nourish Program offers personalised support, an easy-to-follow 8-week meal plan, recipes, shopping lists, supplement advice and more.

And if you apply what you’ve learned, you’re well on your way to ultimate gut health, naturally.


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