WHAT YOUR DOCTOR IS NOT TELLING YOU ABOUT ACID REFLUX

What if everything you thought you knew about acid reflux is backwards?  This blog may surprise you because for millions of people, reflux isn’t caused by too much stomach acid at all.  What if your acid-suppressing medication was actually causing more harm than good in the long-term? Read on to find out the real reasons behind acid reflux and what you can do about it…

Reflux is incredibly common - and rising

If you are one of the 30-40% of adults in the UK who regularly experiences symptoms of heartburn, acid reflux, GERD, silent reflux - the chances are you have been told that it’s something you need to “manage for life,” often with daily acid-suppressing medication.  

But if medications like Omeprazole and Gaviscon were fixing the real problem, why do symptoms so often return, worsen or morph into new digestive issues?

The big assumption that’s rarely questioned

Most reflux treatment is built on one core belief:

“Stomach acid is the problem - so we must suppress it.”

While these drugs can reduce symptoms in the short term, they don’t explain why the reflux started in the first place.

Here’s the part many people are never told:

Most people are told reflux is too much acid. In reality, low stomach acid is a very common cause.

Your stomach is designed to be very acidic. That acidity is the signal that tells the valve at the top of the stomach (the Lower Oesophageal/Esophageal sphincter or LES) to close tightly.  When stomach acid is too low, food doesn’t break down properly, the stomach empties more slowly, food ferments instead of digesting, and gas pressure builds up. That pressure forces the LES to open. Acid, enzymes, and partially digested food are pushed upward, causing:

*Burning

*Regurgitation

*Chest tightness

*Throat irritation

So the problem isn’t excess acid - it’s poor digestion and pressure from below.

When stomach acid really is too high - and how to tell the difference

True excess acid is less common - but it does happen.

Causes of genuinely high acid:

*Severe acute stress/trauma

*Helicobacter pylori stomach infection in early stages

*Certain medications (NSAIDS or steroids)

*Zollinger-Ellison syndrome (rare)

Clues acid is too low:

*Bloating shortly after meals

*Feeling overly full after short meals

*Reflux 1-3 hours after eating

*Burping, gas, or food sitting “like a rock”

*Undigested food in stool

*Symptoms improve with apple cider vinegar or bitters

Clues acid is too high:

*Burning in an empty stomach

*Pain relieved by eating

*Symptoms worsen with vinegar or lemon

*Night pain that wakes you from sleep

*History of gastric ulcers

How dental occlusion, airway, vagal tone, and histamine connect to reflux

This is the missing piece most people never get to hear.

Dental occlusion and airway

Poor bite alignment (malocclusion) can:

*Shift jaw position

*Narrow the airway

*Increase mouth breathing - leads to low CO2 - leads to nervous system stress, leads to reduced vagal tone.

Vagus nerve (the digestion nerve)

The vagus nerve controls:

*Stomach acid production

*LES tone

*Stomach emptying

When vagal tone is low:

*Acid production drops

*LES weakens

*Reflux risk increases

Histamine’s role

Histamine:

*Stimulates acid release

*Is released during stress, inflammation, and poor sleep

Poor airway + nervous system stress triggers:

*Higher histamine

*Erratic acid signaling

*More reflux sensitivity

That is why reflux over overlaps with:

*Allergies

*Sinus issues

*Anxiety

*MCAS (Mast Cell Activation Syndrome) /histamine intolerance

Therefore, reflux is often a neuro-airway-immune issue, not just a stomach problem.

Why your doctor will prescribe Omeprazole regardless

Modern medicine treats reflux as a chemical burn problem when it is more often a coordination, signaling, and digestion problem. This is because it fits the standardized, symptom-based model of pharmaceutical care.  Acid is easy to block with drugs and acid suppression reliably reduces pain in the short-term, which reinforces the approach. 

What this model doesn’t account for is why acid is dysfunctional in the first place - whether it’s low signaling, impaired digestion, nervous system dysregulation, airway compromise, or inflammation.

The root causes take time to evaluate, don’t fit neatly into a prescription, and aren’t emphasised in medical training. So treatment defaults to the simplest intervention that quietens symptoms rather than restoring normal gut function.   And GPs are not rewarded—financially, legally, or professionally—for addressing that level of complexity.

Why acid suppression can backfire

Long-term acid suppression may:

*Worsen digestion and nutrient absorption (B12, magnesium, iron, zinc)

*Increase bacterial overgrowth (SIBO) and yeast in the small intestine (which should be bug free). The toxins and inflammation from SIBO have been linked to pancreatic cancer.

*Slow stomach emptying which leads to gas and bloating.

*Weaken natural reflux-prevention mechanisms.

Many people notice that while PPIs dull the burn, they don’t restore comfort, resilience, or digestive strength — and coming off them can be extremely difficult with rebound worsening acid symptoms. They may end up with additional health problems like osteoporosis or dementia.   All these symptoms show that the underlying problem has not been addressed.

The COVID connection nobody warned about

Since 2020, clinicians worldwide have noticed a surge in new-onset reflux after COVID infection — even in people who never had digestive issues before.

Possible reasons include:

*Covid disrupts vagus nerve function (affecting stomach acid and valve function)

*Covid increases inflammation and histamine release

*Covid alters the gut microbiome

*The viral stress of Covid reduces stomach acid production 

For many, reflux after COVID isn’t about acid excess — it’s about disrupted signaling and impaired digestion. In many Long Covid patients, reflex is neurogenic, inflammatory and viral-driven, not acid-driven. In this case, the “one-size-fits-all” approach of simply giving acid blockers will not fix the problem.

Reflux isn’t just about the stomach

Reflux can be influenced by:

*Stress and nervous system tone

*Breathing patterns and posture

*Jaw alignment, airway restriction, and dental factors

*Meal timing, chewing, and food combinations

*Mineral status and protein intake

*Stomach infections like Helicobacter pylori

Yet these are rarely discussed in a 10-minute appointment.

The Functional Medicine approach to stomach acid: Fix the signal, not just the burn

Functional Medicine views reflux not as an excess-acid problem, but as a breakdown in digestive coordination. Instead of asking “How do we block acid?” it asks, “Why isn’t digestion working the way it’s designed to?” Rather than suppressing symptoms, the goal is to lower the inflammatory load, so acid production and sensitivity can normalise by doing the following:

1.Thorough case history - explore digestive symptoms, assess for low stomach acid, no stomach acid, ulcer history, home “burp test.” 

2.Identify inflammatory and histamine triggers -

*Food sensitivities

*Gut infections (H. pylori, SIBO, Coxsackie etc.)

*Mould exposure

*Histamine intolerance (two tests to check for gut breakdown of histamine and whole body clearance of histamine)

3.Look upstream: airway, jaw, and posture

*Dental occlusion, TMJ and jaw tension

*Jawbone, tooth and gum infection (H.pylori can originate in the mouth)

*Narrow airways, mouth breathing and tongue-tie.

*Forward head posture - these factors can perpetuate reflux by keeping the body in a continual stress state disrupting digestive reflexes.

4.Restore proper digestion gently

Instead of forcing acid suppression, functional strategies focus on:

*Improving chewing and meal timing

*Using bitters, or mild acid support when appropriate

*Correcting nutritional deficiencies

*Addressing infections if present

*Rebuilding stomach signaling over time

5. Individualise the plan

There is no “one-size-fits-all” protocol. Functional Medicine differentiates between:

*Low vs truly high stomach acid

*Nervous system-driven reflux

*Structural or airway-related reflux

*Inflammatory or histamine-driven reflux

Bottom line

If you are suffering from acid reflux and are taking acid-suppressing medications, this might not be addressing the root cause. By continuing medication to suppress symptoms, you might even be setting yourself up for bigger digestive and health problems down the line.  By exploring why you have symptoms and addressing the findings, the goal is normal digestion, not lifelong medication. 

If you are suffering from reflux and would like to find out why, please get in touch with the Good Health Clinic on goodhealthclinic@outlook.com to request a free 30 minute Enquiry Call or book an appointment. Please note that an Enquiry call is not a consultation but an exploratory call to see if this is a clinical approach you wish to pursue.To your very good health, 

Suzanne Jeffery (Nutritional Medicine Consultant)

M.A.(Oxon), BSc.(NMed), PGCE, GNC, BSEM, MNNA, CNHC

The Good Health Clinic at The Business Centre, 2, Cattedown Road, Plymouth PL4 0EG

Tel no: 07836 552936/ Answer phone: 01752 774755 

Disclaimer:

All advice given out by Suzanne Jeffery and the Good Health Clinic is for general guidance and informational purposes only.  All advice relating to other health professionals’ advice is for general guidance and information purposes only. Readers are encouraged to confirm the information provided with other sources.  Patients and consumers should review the information carefully with their professional health care provider. The information is not intended to replace medical advice offered by other practitioners and physicians. Suzanne Jeffery and the Good Health Clinic will not be liable for any direct, indirect, consequential, special, exemplary or other damages arising therefrom.