Advanced Functional Medicine

You have reflux. Your GP gave you a PPI. The reflux improved a bit, then came back worse.

Here's what most people don't know: reflux is often caused by too little stomach acid, not too much.

Low stomach acid means food sits in the stomach longer, fermenting and producing gas. That pressure pushes stomach contents back up through the lower oesophageal sphincter, which itself loses tone when acid is low.

PPIs lower stomach acid further. They suppress the symptom in the short term while making the underlying problem worse. Long-term PPI use also reduces absorption of B12, magnesium, iron, calcium and protein, raises infection risk, and changes the gut microbiome.

How to tell if you're actually low in stomach acid: reflux that gets worse after big meals or coffee, bloating in the upper stomach within 30 minutes of eating, undigested food in stool, iron and B12 deficiency despite a good diet, and a positive baking soda test in the morning.

This is one of the most common patterns I see, and one of the most reversible once it's identified correctly.

Most gut protocols fail for the same reasons. No testing. Wrong order. Wrong target.
If you have tried everything and nothing has held, this is why.

https://advancedfunctionalmedicine.com.au/why-gut-protocol-not-working/

You can do every gut protocol perfectly. Eat clean. Take the supplements. And your gut still won't heal.

Here's why.

The vagus nerve controls digestion. It tells your stomach to produce acid, your pancreas to release enzymes, your gallbladder to release bile, and your intestines to move properly.

Low vagal tone shuts all of that down.

Chronic stress, trauma, and sympathetic nervous system dominance flatten vagal tone. The body stays in fight-or-flight, where digestion is not a priority. You can be eating perfectly but absorbing nothing.

This is why we work on vagal tone in every gut protocol: Slow nasal breathing (especially long exhales) Gargling, humming, singing Cold water exposure (face splash works) Stress management and sleep Movement, especially walking after meals

These aren't "extras." They are the foundation. Without restoring nervous system function, the supplements and the diet only do half their job.

Learn more about how we work: advancedfunctionalmedicine.com.au/how-we-work

If you've been told everything is normal but you feel anything but normal, this book is for you.

The Healing Hierarchy is the framework I have used for over a decade to help patients with chronic fatigue, autoimmune disease, gut dysfunction, hormonal imbalance and unexplained chronic illness recover.

It is not another protocol book. It is the order, the sequence, the framework that makes every protocol work.

Inside you will find: The four levels of recovery and which markers tell you where to start Why most chronic illness protocols fail (and how to avoid the same trap) The three tests that change everything How to read your bloodwork through an optimal lens, not a disease one

Grab your copy:

AUSTRALIA: amazon.com.au/dp/176457110X

USA: amazon.com/dp/176457110X

Chronic fatigue is never one problem. It is always a stack of overlapping dysfunctions.

Underneath chronic fatigue we typically find: Gut dysbiosis or pathogen overgrowth Mitochondrial dysfunction on the OAT Low ferritin or B12 Suboptimal thyroid (often Hashimoto's) HPA axis dysregulation Sometimes mould exposure or chronic viral reactivation

Treating one of these in isolation never works. You can give someone thyroid hormone, iron, and adrenal support, and if the gut and mitochondria are still broken, none of it holds.

This is why we test comprehensively before treating. Blood panel, stool, OAT. Three tests give us the full picture. Then we treat in the correct sequence using the Healing Hierarchy.

Learn more: advancedfunctionalmedicine.com.au/how-we-work

Most people with gut issues end up on increasingly restrictive elimination diets. Gluten out. Then dairy. Then FODMAPs. Then nightshades. Then eggs.

Six months later, they can only eat about 15 foods. And they still don't feel well.

Elimination diets work in the short term because they reduce immune load. But they don't fix what made you reactive in the first place. The underlying gut barrier dysfunction, the overgrowth, the inflammation. Those are still there.

Real recovery is about widening the diet back out, not narrowing it further. That only happens when you fix the gut, not just avoid the foods.

advancedfunctionalmedicine.com.au

Chronic fatigue, brain fog, joint pain, sensitivity to everything. Specialists keep saying nothing is wrong. Have you been tested for mould?

Mould exposure produces mycotoxins. These bind to mitochondria, disrupt the immune system, and drive systemic inflammation. They can take years to leave the body once exposure stops.

Common signs: Symptoms that started after moving house Water damage in the home or workplace Multiple chemical sensitivity Recurrent sinus infections Unexplained weight gain

Mycotoxins are tested through urine, looking at specific metabolites. This is not a routine test. But for the right patient, it changes the entire treatment plan.

Learn more about how we work: advancedfunctionalmedicine.com.au/how-we-work