The Gut Instinct on Gut Health 3/3

The third and most important part provides information on how to protect and maintain gut health

Internal Health = Eternal Health

Many people living in the present day are becoming well aware that our current way of life is fast evolving. The industrialised modern lifestyle and food system is changing at such a rate, experts agree – our way of life (including the way we eat) has changed more in the past 60 years, than in history of the entire human civilisation.

When joining some of the dots, the rise in symptoms associated with poor health and disease are the result of an un-evolved and often damaged immune system. This plagues a growing percentage of todays society.

Our way of life has changed so much in recent history that the immune system struggles to evolve with this rapidly changing environment

 Our inner microbial immune system is facing an evolving barrage of modern day toxic obstacles and have had no time to adapt – therefore microbial survival and the important role they play are either becoming altered or even obsolete.
Unfortunately this toxicity we face is only on the increase as lifestyle continues to change and become further distant from past years of much slower evolution.

On a positive note, there are ways you can reduce the impact to soften the blow.
This is what section three is all about. Read on to educate yourself for what is best to avoid and what you can do to heal and keep your guts healthy.


Science has shown us that bacteria can evolve to thrive in their environment, as they have done since the dawn of time. It is no different to the bacteria that resides in our gut. The rise in gut associated problems will tell you that the bacterial flora in many people are clearly having a hard time evolving to this rapid changing, modern lifestyle – Here are some of the main offenders


Environmental pollutants:

Many of these are becoming almost impossible to avoid as the world further modernises, the types of toxicity from our environment are so extensive, to list every single one would be tiresome.
Compounds in the fumes emitted from car and trucks are suspended in the air we breathe, things like aerosols and air fresheners, cigarette smoke and other airborne compounds, when accumulated in our bodies, have disastrous effects and attack the gut micro-biome.
Trace amounts of certain heavy metals, found in processed foods, tap water, even in some tooth fillings also have an ability to affect gut health and impair functionality throughout your brain and nervous system.
Plastics, non stick frypans, new house furnishings, chemical cosmetics, skin and hair products and antibacterial soaps will add to this chemical load.
Possibly the most unavoidable and largest assault on our gut flora, believe it or not is our tap water. Tap water in Australia will almost always will contain fluoride, chlorine and other sanitising agents. While these sanitising chemicals are great at sanitising water and are necessary for providing germ free H2O, the sanitation chemicals have their problems, caused in part by disinfection byproducts (DPB’s)
While our body has detoxifying pathways, effects of DBP’s and the other environmental junk are only now, just being understood, but it is shown that DBP’s produce carcinogenic compounds and induce inflammation markers in the gut. 

Learn how really get tap water pure… Here



Antibiotics definitely have there place and are often necessary in some cases. Overuse and indiscriminate prescription of antibiotics are creating a problem that few are wanting to address. Antibiotics can cause total gut flora destruction by wiping out entire species, lending itself to gut imbalances and dysbiosis of all kinds.
Nature is again proving that it will always ‘find a way’…. as the rise of antibiotic resistant ‘superbugs’ evolved to become immune against antibiotic medication.

Studies will show that even a single course of antibiotics can permanently alter the gut flora

Roughly 70-80% of total Antibiotics used in Australia are used in animal farming. This to combat the diseased and stressed cattle, many of which finish their life in concentrated feed operations, or (C.F.O). Here they are fed inflammatory inducing GMO grain diets – otherwise known in the shop as ‘Grain Fed’ to fatten them up for higher profits.
The growing salmon farming industry is also linked heavily with antibiotic usage.
As a result, antibiotic residues are found in many animal products… That means meat, milk and even…. you guessed it – WHEY PROTEIN.
These antibiotic residues have the ability to affect our gut ecosystem in the same way as antibiotic medication can cause havoc. As a further consequence, antibiotic residues impact the planet’s own ecosystem in many destructive ways.   


Stress is a rather broad term, with both mental and physical forms of stress having the ability to affect intestinal health…
With the ‘two way street’ between our gut and brain, bad food and lifestyle choices produce inflammation on the digestive system, placing stress on areas of the gut.
When you’re anxious sad or scared, the butterflies you feel or the cramps and loss of appetite you may get, is actually your brain communicating with your gut with mood altering endorphins.  
Although stress is something our ancestors would have encountered, it would be like comparing apples to oranges to the modern-day stresses that often plague our bodies today.

The inability to counteract these stresses on our bodies, through lifestyle or therapies, can seriously affect our E.N.S (gut brain) leading to the symptoms of depression, anxiety and adrenal problems we see so much of today.


Pesticides Herbicides & Fungicides

A recent discovery of harmful effects on herbicide residues, found on our commercially grown fruits and veggies is alarming to say the least.
It really should come as no surprise, these highly toxic chemicals are designed to eliminate all bacteria and fungus, even killing insects by destroying the bugs stomach when treated food crops are eaten.
Herbicides work by destroying enzymes to kill weeds – although we are not plants, these chemicals, do affect on our own enzymatic processes and cell membranes. Whats more unfortunate is that young children are the most susceptible to the effects.

Detectable pesticide levels in humans have been found to reduce the numbers of disease-fighting ‘white blood cells’ as they impair their ability to function.
According to The Global Healing Center, as much as 85 to 90 percent of pesticides applied to agriculture never reach their targets,
these chemicals penetrate the produce, leaching into soil and waterways gaining unprecedented access to the food chain – all this in the name of higher yields and untainted produce.

Pasteurisation and Irradiation

This process kills anything living by essentially heating or zapping fresh foods with radiation. This helps eliminate food spoiling bacteria in order to preserve and make it look fresh after long range transport and storage.
While this process is needed in food preservation, it often changes properties of the food itself. Before probiotic supplementation, food was our number one source of replenishing intestinal flora. Processed foods have enough problems associated with them, therefore a diet full of them will also give zero chance of any probiotic replenishment.

Drugs and excessive Alcohol

As discussed in Part 2 in detail, recreational drugs often produce an explosion of inflammation in our gut – Could that explain the mad urge for the toilet after indulging?
Drugs will often come with come alcohol and with alcohol comes additional inflammation from sugars that feed non beneficial bacteria within the gut.

-All these challenges of our modern world toxicity place a heavy footprint on our gut health – it’s this footprint that has a firm influence of the rise of health issues of all kinds.


Rebuilding your gut health and nurture the gut brain. 

The verdict on the role of our gut is in.  With more discoveries and understanding of our ancestral eating, better interpretation of intestinal issues now being understood, symptom management and the restoration gut health is happening.
Successful clients and patients aboard of mine who have implemented an effective gut protocol will always
 require a dynamic and often individual approach;



This literally means “infecting,” or ‘re-inoculating’ your large intestine with synergistic bacterial strains. Re-establishing gut flora is paramount and the addition of beneficial bacteria is a great way of doing this.  Probiotic supplements are various strains of beneficial bacteria in a capsule that can commonly be used for conditions like yeast infections, Irritable bowel syndrome and used in the management of autoimmune disease like Crohn’s Disease and Ulcerative Colitis, or just general health maintenance.

With pronunciation challenging names such Lactobacillus, Bifidobacteria, acidophilus and many more, it makes it be easy to become confused.
Believe it or not, even popular expensive brands are often failing manufacturer’s claims in 3rd party testing, as viability of these supplements will come down to manufacture techniques and storage.

I do recommend a number of reputable probiotic brands having a great diversity of species, numbers of bacterial strains with modern manufacturing processes.
The science behind the leading therapeutic manufacturing tells us that the capsules should coated with an inert cellulose. This process prevents disintegration in the stomach and protects the microorganisms from stomach‘s acidity to insure effective bacterial survival and colonisation within the large intestine.

Remember – just as planting seedlings will struggle to rejuvenate a deforested old-growth rainforest overnight, probiotics shouldn’t be relied on as a quick-fix for gut dysbiosis and a gut-destroying lifestyle.

Traditional Foods

With a better understanding, many health professionals will agree that the evolutionary and ancestral way our gut was populated is now considered a highly effective way of maintaining and improving gut health in todays world.

Taking a look back through history you’ll find that modern food storage ‘refrigeration’ has only been mainstream for half a century.
Evidence shows that the thousands of years before refrigeration, food preservation relied heavily on bacteria – yes, many of the same microbes in our gut, also preserved food.
Traditional food preservation was a complex yet simple natural process that in short, fed humans in times when fresh food was scarce. Bacteria have been ‘co-evolutionary’ throughout our living existence and should continue to be.

Traditional foods included various cultured and fermented vegetables much like todays sauerkraut and kimchi.  Milk was often cultured into Kefir (similar to yogurt) and fermented drinks such as kombucha, beet kvass even traditional beers were all essential ways of long term food storage with the bonus of beneficial bacteria and compounds these foods possess. Picturing these foods as your probiotic pill and you will be on track to receive health benefits, with many beyond the scope of modern pharmaceutical.

– I do urge caution in some fermented food in particular with kombucha vinegar’s etc as they can contain a compounds of hystimines and aldehydes. These compounds can in some cases cause reactions of itchiness, swelling, congestion, heart rate increases and can be counter-productive in some people with preexisting severe gut issues

Before we had the fridges and pasteurisation that kept things looking fresh, and large scale food operations that processed the life out of once living foods, these traditional ways of storing and processing food, essentially feed us in times of foods shortages – and helped with the repopulation and balance of our inner microbes

As the shift from ancestral eating differs more every day  It appears majority of the western population today have little need, even forgetting about these traditional techniques..


Fibre Feasting

While microbes and probiotics receive all the attention, Its actually fibre in its correct forms that are the ‘life support’ of a healthy gut. The trillions of living organisms inside us need to feed and more and more research supports the concept that allowing them to feed on their meal of choice helps beneficial strains thrive.
It is known that beneficial microbes feed on fermentable fibre’s that come from various vegetables, certain whole grains and other foods that resist digestion once eaten.
In contrast excess carbohydrates or notable sugars are consumed, the rise in pathogenic bacteria, fungi and yeasts like candida become a real issues.

‘Many people’s diet today, is arguably fibre-poor by historical standards, population estimates it at 15 grams of fibre daily. This amount is a far cry from earlier hunter-gatherers were likely eating close to 10 times that amount of fibre each day,

Imagine the effect that has on our microbiota over the course of our evolution.

-The Scientific American tells us that a recent study when beneficial microbes are starved of fibre, they can start to feed on the protective mucus lining of the gut, causing inflammation.

Reducing Intestinal Inflammation

Inflammation in our gut can be quite common in even the healthiest of people, as it’s your body’s natural and helpful immune response to tissue damage.

Inflammation is contributed by gluten grains and genetically modified foods that can promote intestinal permeability along with changes in our intestinal flora that facilitate growth of pathogenic bacteria, yeast, and fungus.
These bad guys produce their own nasty bi-products as a result of metabolism, damaging intestinal lining while keeping our immune system in a state of alarm. This constant inflammation causes not just uncomfortable symptoms but chronic inflammation of the gut can trigger autoimmune disorders like Crohn’s Disease, Ulcerative Colitis, Intestinal and Bowel Cancers and more.

Negative or unpleasant reactions to foods are really the best way for you to tell that the gut is stressing out. Everybody reacts differently to different foods, so in reality there is no set rule book to follow. Keeping note of any reactions to foods will help identify inflammatory triggers.
It’s common for people to be somewhat conditioned to symptoms of inflammation of the gut. Bloating, acid reflux, strange poo’s, skin reactions that could have been developing for years may seem a part of daily life. Those with great gut health and digestion, symptoms will be far from common.

Functional Treatment

Looking to the future, we are finding we might just be able to combat major health issues by influencing and manipulating our bacteria. With the improved testing/diagnosis and alternative treatments such as Fecal transplants (the inserting of a healthy person’s poo and microbes for people with crippling gut infections) – is already happening in countries including Australia.
The functional medicine approach is continually improving with pioneering science as diagnosis. Testing and treatment protocols are shown to improve symptoms and heal compromised and damaged digestive systems  

Going to a doctor in the future, you may find a gut test will be as routine as a blood test.

Healing of serious gut issues can be fairly complex and sometimes drawn out, lesser issues can be helped with only little nutritional and lifestyle ‘tweaking’. Custom protocols that I provide clients are aimed at improving the gut environment or as I like to put ‘terrain remodelling’ to allow the gut to heal, this can often work to improve symptoms.
More serious and prolonged case’s where dysbiosis and autoimmune disease is suspected, I utilise functional pathology testing with a single or sometime combination of tests.
It’s important to understand that dysbiosis is not detected by routine tests that your conventional doctor may order. That’s why it’s important to be aware of the type of testing that’s available to you.

I.P Testing (intestinal permeability)
The Intestinal Permeability (IP) test, also referred to as a “leaky gut” test, is a precise and non-invasive method for assessing gastrointestinal mucosal integrity. Involving simple urinary testing with basic patient preparation the IP test will help determine the level impact of chronic stress from the common person with food sensitivity and food allergy, irritable bowel syndrome, Crohn’s disease, Arthritis, Coeliac disease and dermatological conditions such as eczema, psoriasis and acne. All of which affect the permeability of the gut wall.

Complete Digestive Stool Analysis (CDSA)
The CDSA combines a large number of tests that evaluate the function of the gastrointestinal tract and gives comprehensive picture of a patients gut health can be obtained. The analysis investigates digestion, metabolism, pancreatic function, balance and estimation of beneficial bacteria, pathological bacteria presence, yeast overgrowth and parasites, with several different CDSA panels available,

  • Macroscopic & microscopic description
  • Digestive, absorption & metabolic markers
  • Inflammation markers
  • Tumour/Ulcer markers
  • Beneficial & other bacteria
  • Yeasts
  • Parasites (visual detection & chemical EIA detection) & sensitivities)

As the name suggests, samples of your poo are needed with fairly precise patient preparation protocols needed will collection of samples taken over 3 days. The CDSA will allow to better evaluate and document the medical necessity for protocols or further analysis.

Secretory IgA – Saliva test
Simple saliva testing with minimal patient preparation, secretory immunoglobulin A or (SigA) is biomarker that I will assess for adrenal deregulation and decreased immune function. SIgA is the main immune defence of your gastrointestinal tract against foreign bacteria, parasites, viruses, and yeast. It can be measured in your blood and stool, but now more recently, an non-invasive saliva test.
Low SIgA makes you more likely to have infections and other problems in your gut and identifying this will lead to greater precision in treatment.

While, there are many ways to prevent or successfully reverse symptoms of leaky gut, dysbiosis and autoimmunity, functional medicine help to identify the root cause along with possible food and lifestyle triggers.
The solution is never as simple as a pill or special elixir, instead a multi facet or holistic approach of nutrient-dense and healing foods, and lifestyle refinement.

Known as the ‘5Rs’ we must;
Remove, Replace, Reinoculate, Repair, Rebalance

Whether it’s monitoring and abstaining from known foods triggers and chemical pollutants , helping soothe and maintaining integrity of the the intestinal tract, getting the right balance of fibre to feed our bacteria, populating the gut with a diverse bacterial profile to help eliminate parasites and pathogenic fungus, even going as far as to supporting gastric acid P.H levels, these all need to be addressed to a degree to allow proper gut function.

A long and drawn out gut rehab protocol is probably not what most might want to hear, in not setting a ‘quick fix’ expectation like people often do, it will help you to stick to a consistent approach long enough for it to work.  

If you or anyone you know are suffering gut health issues, the process is enhanced when positive changes are made, stuck to consistently and made as part of everyday lifestyle.
Many clients in my experience often experience noticeable improvements after a only a few weeks on a personalised Gut Restoration Program.
Please go to the services menu or send us an email to find out more information on how I can help to improve gut health, manage symptoms and more importantly how healing can be better integrated it into your lifestyle.

I do hope you got something out of it this article, as having an understanding of this intricate subject can help you make more informed decisions and hopefully uplift perspective and improve lifestyle as it has with my clients and loved ones.

If you have anything to add or any questions, I would love you to leave a comment and give your thoughts.

Love your Guts      

Author: Jake

Bringing you this article, Jake combines his 15 years of expertise in integrated nutrition and fitness to provide his insights on matters of substance.