Table of contents

What is reflux?

Reflux is a common digestive issue in which stomach acid flows back into the oesophagus, irritating its lining. While nearly everyone experiences this sensation occasionally, if it occurs at least twice a week, it is classified as gastroesophageal reflux disease (GERD).

GERD is caused by a malfunction of the lower oesophageal sphincter (LES). This muscle normally prevents stomach acid from flowing backward into the oesophagus. When it fails to close properly, acidic stomach contents can easily backflow and, over time, damage the oesophageal wall. [1]

This issue is becoming increasingly prevalent worldwide. It is estimated to affect 20% of adults [2], and its incidence continues to rise due to modern lifestyles, dietary habits, and other environmental factors. Although most people manage their symptoms with lifestyle changes and medication, these measures do not address the underlying causes and may not result in long-term improvement.

Therefore, reflux is not merely an unpleasant condition—it can have serious long-term health consequences, making timely recognition and treatment essential. [3]

Symptoms of GERD – When reflux is more than just discomfort

Many people have experienced the unpleasant sensation of heartburn, especially after a heavy meal or when lying down immediately afterward. However, if these symptoms recur and worsen over time, they may signal a more serious digestive disorder, one that not only affects quality of life but may also lead to complications. [4]

The most common symptoms

  • Burning sensation in the chest or stomach

The burning pain caused by acid reflux typically starts in the middle of the chest or the pit of the stomach and may spread to the neck, jaw, shoulders, or back. This pain often worsens after meals, particularly when bending over, lifting heavy objects, or lying down.

  • Sour or bitter taste in the mouth

A hallmark of reflux is the backflow of stomach acid into the throat or mouth, producing a burning, unpleasant taste. This occurs most frequently in the morning or after meals and may damage teeth over time.

  • Regurgitation or backflow of stomach contents

People with GERD often feel not only acid but also partially digested food coming back into the mouth. This is not only unpleasant but may lead to nausea and aversion to eating.

  • Difficulty swallowing and a lump-in-the-throat sensation

Chronic acid irritation may cause inflammation and mild narrowing of the oesophagus, resulting in the sensation that food is moving slowly or that something is constantly stuck in the throat.

  • Chronic cough and hoarseness

Acid can irritate the airways as well as the oesophagus. This often leads to a persistent dry cough, frequent throat clearing, and hoarseness. These symptoms are often mistaken for respiratory issues, though they may be reflux-related. [5]

  • Shortness of breath and asthma-like symptoms

Reflux can impact the respiratory tract, especially if acid vapours reach the windpipe and lungs. This can cause shortness of breath, wheezing, or even asthma attacks, particularly at night when lying down facilitates acid backflow.

  • Bloating and frequent belching

Reflux sufferers often feel bloated, as though their digestion isn’t functioning properly. Accumulated stomach acids and gases create a feeling of fullness and lead to increased belching.

  • Tooth enamel damage

Constant exposure to acid can erode tooth enamel, increasing sensitivity and the risk of decay. A sour taste in the mouth in the morning is a sign that warrants regular dental check-ups. [2]

Symptoms of reflux

Figure 1. Symptoms of reflux

Types of reflux

Classic acid reflux (GERD)

Reflux varies depending on where the digestive fluids cause irritation. GERD primarily affects the lower oesophagus due to backflow of stomach contents. It typically results in heartburn, particularly after meals or while lying down. GERD is often caused by a weak lower oesophageal sphincter. Symptoms include chest pain, throat burning, sour or bitter taste, nausea, vomiting, regurgitation (backflow of acid or food), and difficulty swallowing, particularly in the chest where food seems to get stuck. [6]

Silent reflux – Laryngopharyngeal reflux (LPR)

Laryngopharyngeal reflux (LPR) is a lesser-known yet common form of reflux. Here, stomach acid travels past the oesophagus to the throat and vocal cords, causing different symptoms from classic GERD, which is why LPR is often referred to as ‘silent reflux’.

This condition affects areas beyond the oesophagus—especially the pharynx and larynx—thus falling under extraoesophageal reflux. Typical symptoms include hoarseness, throat clearing, laryngitis, chronic cough, and difficulty initiating swallowing.

Diagnosing LPR is difficult, because classic heartburn is often absent so its symptoms are frequently misattributed to colds or allergies. Yet medical findings show that more than half of patients with chronic hoarseness may have LPR.

Both GERD and LPR can cause difficulty swallowing, but in different ways: GERD causes pharyngoesophageal dysphagia (a sensation of food being stuck in the lower throat or chest), while LPR results in oropharyngeal dysphagia (discomfort at the start of swallowing). LPR often presents with red, irritated vocal cords, while GERD can cause mucosal damage, which over time may lead to ulcers, oesophageal stricture, and, rarely, oesophageal cancer. [7]

Bile reflux – When acid is not the culprit

The third type, bile reflux, is not caused by acid but by the backflow of bile produced during digestion. Bile is normally produced in the liver, stored in the gallbladder, and released into the small intestine to aid in fat digestion. However, if the sphincter between the stomach and the small intestine—the pylorus—is overly relaxed or obstructed, bile can flow back into the stomach and even into the oesophagus. This backflow irritates the mucosal lining of the stomach and oesophagus, leading to inflammation, pain, and tissue damage. The symptoms of bile reflux are similar to those of GERD and often include bloating or a sensation of fullness, but more commonly involve a burning feeling in the stomach, nausea, bile vomiting, and a bitter taste in the mouth. [8]

Types of reflux

Figure 2. Types of reflux

Recognition and diagnosis of reflux disease

In many cases, reflux causes only temporary symptoms that may resolve on their own. When this happens, it is not necessarily considered a disease—this condition is known as uncomplicated, intermittent GER (gastroesophageal reflux). However, when symptoms become persistent, recurring, or worsening, it indicates a more complex digestive disorder that affects not only the oesophagus but also the entire gastrointestinal system. In such cases, we speak of reflux disease (GERD), which, without proper treatment, can cause inflammation, complications, and permanent mucosal damage over time.

Accurate and timely diagnosis is therefore essential—not only to relieve symptoms but also to prevent complications and to enable personalised, cause-based treatment.

The diagnostic process

In most cases, doctors diagnose reflux or GERD based on a patient’s symptoms and medical history. If the symptoms are typical (e.g. frequent heartburn, acid regurgitation), treatment can often begin based on this alone, involving lifestyle changes and medication. Diagnostic tests may be necessary if:

  • symptoms do not improve with treatment,
  • complications are suspected,
  • other conditions with similar symptoms need to be ruled out, prompting referral to a specialist (e.g. gastroenterologist)

Diagnostic tests for suspected reflux (GERD)

While functional medicine focuses more on identifying root causes and promoting lifestyle changes, it is helpful to understand traditional diagnostic methods—especially for persistent or severe cases.

  • Gastroscopy (endoscopy): Allows direct examination of the oesophagus, stomach, and duodenum, and can detect complications such as inflammation, ulcers, or Barrett’s oesophagus. Tissue samples can also be taken if needed. [9]
  • pH monitoring: A 24-hour test (via nasal catheter or capsule) to precisely measure acid reflux. The patient logs meals and symptoms.
  • Barium swallow test: An X-ray using contrast medium to reveal narrowing or hernias in the oesophagus. Mainly used to investigate swallowing difficulties.
  • Manometry: Measures oesophageal muscle function; useful when motility disorders or swallowing problems are suspected.
  • Transnasal oesophagoscopy: A thin camera is inserted through the nose without anaesthesia, offering a quick, low-stress alternative. [1]

Causes and pathophysiology of reflux

Reflux symptoms result from a complex imbalance in the body. Disruption of the LES, increased stomach pressure, acid imbalance, and altered digestive motility can all contribute to the backward flow of stomach contents into the oesophagus. These dysfunctions often coexist, and research increasingly highlights the importance of the condition of the gut microbiome, acid levels, stress, and nervous system involvement.

Below is an overview of the anatomical, physiological, and lifestyle-related factors contributing to reflux and its long-term symptoms.

Main pathophysiological mechanisms

  1. LES dysfunction and transient relaxation (TLESR)

Transient lower oesophageal sphincter relaxation (TLESR) is a common trigger. These spontaneous, non-swallowing-related relaxations typically occur after meals or when lying down, especially if the stomach is full. Contributing factors include stomach distension, certain foods (e.g. fatty meals, chocolate, alcohol), and vagal reflex activation. [10]

  1. Persistently low LES pressure

Under normal conditions, LES resting pressure is sufficient to resist gastric pressure. If it drops below 6 mmHg for an extended period, the sphincter fails to close adequately, leading to reflux, mucosal inflammation, and potentially ulcers, strictures or Barrett’s oesophagus.

  1. Diaphragmatic hernia (hiatal hernia)

A hernia caused by weakness of the diaphragm allows part of the stomach to slip into the chest cavity, mechanically impairing the closing function of the LES. A hiatal hernia not only weakens the function of the sphincter, but often creates a kind of ‘acid reservoir’ from which stomach contents can easily flow back into the oesophagus.

  1. Hypochlorhydria (low stomach acid)

Although it may seem paradoxical, too little stomach acid can also promote reflux. Reduced acidity does not adequately stimulate the closing function of the LES, impairs digestion and increases stomach tension – all of which together increase the risk of reflux. In addition, poorly digested food leads to more frequent bloating and gas formation, further increasing abdominal pressure.

  1. Delayed gastric emptying

If food remains in the stomach for too long – for example, due to nervous regulation disorders, diabetes or certain medications – this increases stomach pressure, which puts strain on the sphincter. Delayed emptying is often accompanied by postprandial (after-meal) reflux, bloating and a feeling of fullness.

  1. Acid reflux clearance disorder

Under physiological conditions, gastric acid that enters the oesophagus is quickly returned to the stomach by peristaltic waves, while the alkaline buffering effect of saliva helps to neutralise the acid. If these mechanisms are slowed down, for example during sleep or as a result of medication, the acid reflux can come into prolonged contact with the mucous membrane of the oesophagus, causing increased irritation and damage.

  1. Weakened mucosal protection

The mucous membrane of the oesophagus does not have such strong protective mechanisms as the stomach. If the connections between cells, buffer capacity or ion channel function are impaired, acid can more easily enter the tissues. This can lead to inflammation, sensitivity, pain and, in the long term, cell damage.

  1. Visceral hypersensitivity

Not all reflux symptoms stem from actual acid reflux. Some individuals have hypersensitive oesophageal nerves, overreacting even to mild stimuli—this phenomenon is linked to altered central nervous system pain regulation. [11]

Comorbidities and predisposing factors

The risk of developing GERD can be increased by various external and internal factors. While not direct causes, these factors significantly contribute to triggering the underlying mechanisms.

Hormonal and neuromuscular effects

  • Connective tissue diseases (e.g. scleroderma) affecting oesophageal muscles
  • Hormonal imbalances (e.g. increased progesterone during pregnancy, relaxing the LES)

Conditions affecting motility and emptying

  • Delayed gastric emptying (e.g. diabetes, vagus nerve dysfunction, viral infections) increases stomach pressure and reflux risk

Lifestyle factors

  • Western diets (high in fat, sugar, and processed foods)
  • Late-night, heavy meals consumed just before bedtime increase the likelihood of reflux when lying down.
  • Smoking, which lowers LES pressure and inhibits saliva production
  • Alcohol and caffeine, which relax the LES and increase acid production

Medication effects

  • Certain medications, such as antidepressants, blood pressure meds (e.g. nitrates, calcium channel blockers), non-steroidal anti-inflammatory drugs (NSAIDs)
  • Paradoxically, long-term use of proton pump inhibitors (PPIs) to treat reflux reduces stomach acid production, which can lead to hypochlorhydria, thereby impairing digestion, promoting bloating and increasing stomach pressure, and thus contributing to the mechanisms that maintain reflux in the long term.

What causes the acid-base balance to be upset, and how does this relate to reflux?

Reflux is often oversimplified as a problem of “too much stomach acid,” but its underlying causes are more complex. Symptom development is influenced not only by the amount of acid, but also by its location, the manner of its presence in the body, and the body’s ability to counteract it. Acid-base balance plays a key role in this process, especially in protecting the stomach lining and regulating the buffering mechanisms of the bicarbonate system, respiration, and kidney function.

The inner surface of the stomach is protected by a multi-layered defence system that ensures even highly corrosive stomach acid does not damage its own tissues. This system includes mucin (a slippery glycoprotein), aqueous layers, and bicarbonate ions. Mucin provides mechanical protection, while bicarbonate neutralises hydrochloric acid locally to prevent cellular damage—together forming the stomach’s “acid shield.”

The stomach’s pH is highly acidic (1.5–3), which is essential for digestion and pathogen destruction. This acidity also activates pepsin, a key digestive enzyme that only functions at low pH. If stomach acid is too low—due to stress, age, or medication—pepsin activity is impaired, leading to incomplete protein digestion, fermentation, gas formation, and nutrient deficiencies.

Thus, the stomach lining actively participates in maintaining acid-base balance, not merely serving as a passive barrier. Bicarbonate is crucial to this process—not just in the stomach, but throughout the entire body.

The body’s acid–base balance is a tightly regulated system that keeps blood pH stable within a slightly alkaline range of 7.35 to 7.45. This balance is maintained through three primary mechanisms:

  • Bicarbonate buffer system: Quickly neutralises acid or base shifts, for example in the stomach or cellular environments.
  • Breathing helps regulate the acid-base balance by controlling carbon dioxide (CO₂) levels: when the body becomes more acidic, breathing rate increases to expel more CO₂, thereby reducing acidity.
  • The kidneys are slower but effective long-term compensatory organs: they can excrete hydrogen ions and reabsorb bicarbonate to counteract acidification or alkalisation.

If these systems become overloaded or fail to function properly—due to factors such as chronic stress, metabolic disorders, or inflammatory processes—the acid-base balance may be disrupted. This can lead not only to general fatigue and inflammation, but also to increased risk and severity of reflux, as the protective capacity of the mucous membranes is reduced.

The oesophagus is particularly vulnerable in this respect, as it lacks bicarbonate protection. While the columnar epithelial cells of the stomach produce both mucus and bicarbonate to buffer acidity, the multilayered squamous epithelium of the oesophagus provides only mechanical protection and is entirely unprotected against an acidic environment. When the lower oesophageal sphincter (LES) malfunctions, acid can reflux into the oesophagus, where even small amounts may trigger a strong inflammatory response. Over time, this can result in structural changes.

The connection between the vagus nerve and digestion

The vagus nerve plays a key role in the parasympathetic nervous system, which regulates functions such as digestion, heart rate, and breathing. It directly influences stomach function, including the production of stomach acid. Stress—particularly chronic stress—can affect vagal nerve activity, disrupting acid secretion and resulting in either excessive or insufficient stomach acid production.” [12]

Vagus nerve and stomach acid levels

Stress and excess acid:

Stress activates the sympathetic nervous system, triggering the ‘fight or flight’ response. In this state, the body prioritizes immediate survival over digestion, suppressing digestive functions. However, acute stress can not only inhibit but also, in some cases, indirectly increase stomach acid production—for example, by elevating gastrin or histamine levels. As vagal nerve activity declines, the parasympathetic nervous system becomes less capable of counterbalancing sympathetic overactivity. This imbalance may lead to increased acid production in the short term, and over time, contribute to the development of stomach ulcers, reflux, and other digestive issues.

Stress and low acid:

In cases of chronic stress, the situation can reverse: prolonged dysfunction of the vagus nerve leads to a significant reduction in parasympathetic activity—a condition known as vagal hypoactivity. As a result, the mechanisms that regulate stomach acid production become impaired, leading to reduced acid levels, a condition called hypochlorhydria. This makes it more difficult to break down food, potentially leaving undigested material in the stomach, which can cause bloating, gas, and even reflux.” [13]

Inadequate digestion and low stomach acid levels can also contribute to the development of leaky gut syndrome. In this condition, the tight junctions between the cells of the intestinal wall become compromised, allowing larger molecules—such as undigested food particles, toxins, or bacteria—to pass into the bloodstream, which would not normally occur. This can trigger an immune response, inflammation, and a range of other symptoms throughout the body.

In addition, low stomach acid levels are often linked to reduced activity of the enzyme diamine oxidase (DAO), which is responsible for breaking down histamine. When DAO function is impaired, histamine can accumulate in the body. During meals, this histamine release may trigger symptoms such as heartburn, bloating, and even reflux. If DAO activity is compromised, the resulting histamine buildup can further disrupt digestion and worsen acid-related symptoms—even when stomach acid levels are actually low. [14]

Figure 3. Main risk factors for the development of reflux

The link between reflux and gut microbiome

One of the lesser-known but increasingly studied links between reflux and gut health is dysbiosis—an imbalance in the gut microbiota. In this state, beneficial bacteria are diminished while harmful, pro-inflammatory microorganisms thrive. Dysbiosis may not only result from treatments used for reflux, but could also contribute to its onset and the worsening of symptoms. [15]

Reflux is often not caused by excessive, but rather by reduced stomach acid production (hypochlorhydria). When acid levels are low, food is not properly digested, leading to fermentation, bloating, and gas formation. This increased pressure in the stomach places strain on the lower esophageal sphincter (LES) from below, reducing its ability to close effectively. As a consequence of low acid levels, undigested food and increased bacterial load may also contribute to greater intestinal permeability, known as ‘leaky gut syndrome.’ Cytokines and inflammatory mediators released from the inflamed gut further disrupt digestive regulation—including the function of the LES.

In reflux, not only the microbial composition of the intestinal tract may change, but also that of the oesophageal mucosa. Studies have shown that bacteria such as Proteobacteria, Campylobacter, and E. coli are more prevalent in patients with GERD, while the presence of beneficial bacteria, such as Bacteroidetes strains, is reduced. This microbial shift creates an inflammatory environment in the lower oesophagus, increasing mucosal irritation and potentially contributing to the development of more serious conditions, such as Barrett’s oesophagus or adenocarcinoma, over time.

Paradoxically, drug therapy for reflux—especially proton pump inhibitors (PPIs)—can also contribute to the development of dysbiosis. While these medications reduce stomach acid production and relieve reflux symptoms, they also suppress the acidic environment that normally prevents the overgrowth of pathogens in the stomach and small intestine. A persistently alkaline environment encourages bacterial overgrowth (SIBO), which can further impair digestion, increase bloating, and indirectly exacerbate reflux. Moreover, PPIs may reduce the absorption of magnesium and vitamin B12, potentially leading to nutrient deficiencies and a weakened immune system over time.

Scientific studies have shown that approximately 25% of PPI users experience significant imbalances in their intestinal flora. The risk of Clostridium difficile infection increases, while the proportion of beneficial Lactobacillus and Bifidobacterium strains decreases—both of which are crucial for immune defence, mucosal integrity, and healthy digestion.

Reflux can therefore be both a cause and a consequence of dysbiosis, creating a vicious cycle in which digestive disorders, inflammation, microbiome imbalance, and impaired LES function reinforce one another. For this reason, effective reflux treatment should go beyond merely reducing stomach acidity—restoring the balance of the intestinal flora is also essential.

Dysbiosis may be suspected if reflux is accompanied by:

  • frequent bloating,
  • constipation or diarrhoea,
  • food intolerances,
  • skin issues,
  • persistent fatigue.

In such cases, a stool microbiome test, SIBO breath test, or gastroenterological examination is recommended to help identify the underlying causes.

Do you suffer from reflux?

Examining the composition of the gut microbiome can help uncover the underlying root causes behind your symptoms.

SIBO (Small Intestinal Bacterial Overgrowth)

SIBO is a condition in which an excessive number of bacteria accumulate in the small intestine—an area that normally contains relatively few microbes compared to the large intestine. GERD and SIBO are often linked. Common symptoms of SIBO include belching, abdominal bloating, and various digestive disturbances.

Why does SIBO cause reflux?

Several factors may explain the link between SIBO and reflux:

  • Imbalance in the intestinal flora: Bacterial overgrowth in the small intestine can lead to increased gas production, raising pressure within the abdomen. Elevated intra-abdominal pressure may weaken the lower oesophageal sphincter (LES), promoting the reflux of stomach acid into the oesophagus.
  • Delayed gastric emptying is one mechanism that links SIBO and reflux. When bacteria proliferate in the small intestine, they can slow the movement of food through the digestive tract, resulting in delayed gastric emptying. This, in turn, increases the likelihood of stomach acid flowing back into the oesophagus.
  • Inflammation and irritation: SIBO can cause inflammation in the intestinal tract, which may indirectly weaken the oesophageal sphincter, increasing its sensitivity and the likelihood of reflux. [17]

What is the link between reflux and Helicobacter pylori?

Helicobacter pylori (H. pylori for short) is a bacterium that resides in the stomach lining and is known to play a role in the development of stomach ulcers, chronic gastritis, and certain types of stomach cancer. Less widely known—but increasingly studied—is its potential impact on reflux symptoms. [18]

The relationship between H. pylori and reflux is complex and not entirely understood, as the bacterium can influence stomach acid production in different ways. When inflammation is concentrated in the lower part of the stomach (the antrum), H. pylori may stimulate acid production, potentially worsening reflux. However, if the upper part of the stomach (the corpus) is also affected, acid production may decrease, which could relieve symptoms.

After successful eradication of the infection, inflammation typically subsides, and acid production often increases. In some individuals—especially those with a weakened lower oesophageal sphincter (LES)—this may lead to new or worsened reflux symptoms. Several studies, including those by Labenz and Koike, have shown that the incidence of reflux can rise after H. pylori eradication in predisposed individuals. [19]

Nonetheless, treating the infection is essential in cases of ulcers, gastritis, or long-term use of acid-suppressing medications. According to the Maastricht IV Consensus, eradication is recommended, although the potential risk of reflux should be evaluated on a case-by-case basis.

Treatment of reflux: From symptom relief to root-cause resolution

The treatment of gastroesophageal reflux disease (GERD) involves more than just relieving unpleasant symptoms—it also aims to reduce inflammation, protect the mucous membranes, identify underlying causes, and prevent long-term complications. While conventional medicine focuses primarily on suppressing acid production, functional medicine takes a more holistic approach: it seeks to identify individual triggers, restore gastrointestinal balance, and implement strategies that support the body’s natural healing processes.

1. Lifestyle and dietary changes

The cornerstone of reflux treatment is lifestyle modification. Numerous studies have confirmed that weight loss—particularly in cases of abdominal obesity—avoiding large late-night meals, and elevating the head of the bed reduce pressure on the oesophagus, thereby relieving the LES and decreasing the frequency of acid reflux. Additionally, quitting smoking, limiting caffeine and alcohol intake, and practising stress-reduction techniques such as meditation, yoga, or forest bathing (Shinrin-yoku) can help promote gastrointestinal balance.

2. Medication and medical treatment

The most common approach to managing symptoms is to reduce stomach acid production, which can be achieved through several methods:

  • Antacids: Provide quick relief but may cause rebound acid production with long-term use.
  • H2 blockers (e.g., famotidine) moderately reduce stomach acid and, unlike PPIs, cause less disruption to the stomach’s microbiome because they do not raise gastric pH to the same extent.
  • Proton pump inhibitors (PPIs) are effective, but with long-term use, it is recommended to use the lowest effective dose and, if possible, transition to H2 blockers or adopt intermittent use over time.
  • Prokinetics: help promote stomach emptying, thereby reducing gastric pressure and the likelihood of reflux.
  • Endoscopic treatments (e.g., TIF – transoral incisionless fundoplication): minimally invasive procedures aimed at improving LES function.
  • Surgical solution (e.g., Nissen fundoplication): this is an option if other therapies prove ineffective or if the patient prefers not to take medication long-term. During the procedure, the upper part of the stomach is wrapped around the oesophagus to strengthen the sphincter’s closure. [20]

3. Restoring gastrointestinal balance

Functional medicine recognises that reflux is often driven by low stomach acid (hypochlorhydria) and dysbiosis. Addressing these underlying conditions not only relieves symptoms but also targets the root cause of the disorder.

A) Rebuilding gut microbiome:

  • Targeted antimicrobial herbs (e.g., berberine, oregano oil) help suppress harmful bacteria.
  • Probiotics (such as Lactobacillus and Bifidobacterium strains) support the intestinal immune system and help reduce inflammation.
  • Herbs that promote mucosal healing and stimulate gastric emptying (e.g., ginger, artichoke) may also play an important role. [17]

B) Supporting digestion:

  • Replenishing digestive enzymes and stomach acid (e.g., betaine HCl with pepsin) supports the restoration of optimal gastric acid levels—provided there is no significant mucosal irritation or active ulceration.
  • A betaine HCl challenge test (with dosage adjusted to meals) can help determine the appropriate level of acid supplementation.

C) Protecting the mucosa and reducing inflammation:

  • Nutrients and bioactive compounds: zinc carnosine, DGL (deglycyrrhizinated liquorice root), melatonin, omega-7, and vitamin U.
  • Herbs that protect the mucous membrane and reduce inflammation: marshmallow root, meadowsweet, chamomile, aloe vera, turmeric, and mallow.
  • Slippery elm powder creates a mucilaginous coating on the oesophagus, providing mechanical protection against acid irritation. [17]

D) Targeted diagnostics with functional tests: Proper treatment requires identifying the underlying factors:

  • H. pylori infection (breath test, biopsy)
  • SIBO breath test (hydrogen/methane)
  • Stool microbiome analysis: bacterial ratios, inflammatory markers, digestive functions
  • Food intolerance and malabsorption testing (e.g., histamine, fructose, lactose)
  • Basic laboratory tests: inflammation, liver function, B12, iron, zinc, magnesium, etc. [17]

Complications of untreated GERD

  • Oesophagitis, ulcers, strictures
  • Barrett’s oesophagus, a potential precursor to oesophageal cancer
  • Tooth enamel erosion, chronic cough, asthma, hoarseness
  • Sleep disturbances, fatigue, anxiety, depression [17]

When should you see a doctor immediately?

Although reflux can often be improved with lifestyle changes, such as diet and posture, there are warning signs that require prompt medical evaluation.

  • Severe, tight chest pain – This symptom can easily be mistaken for a heart problem. If the pain radiates to the arm or jaw, or is accompanied by shortness of breath, seek immediate medical attention.
  • Bloody or black stools, bloody vomiting – These may signal bleeding in the oesophagus or stomach and require urgent medical evaluation.
  • Unexplained weight loss – A decrease in appetite or unintentional weight loss could indicate that reflux is becoming more serious.
  • Persistent difficulty swallowing – If eating becomes increasingly difficult due to narrowing or inflammation of the oesophagus, medical assessment is necessary.
  • Frequent choking or shortness of breath – Regular episodes of choking or feeling unable to breathe properly may reflect severe irritation in the oesophagus or airways. [21]

Summary

Reflux is a global issue that significantly affects quality of life. Traditional treatments like PPIs offer symptom relief but don’t address the root causes and may lead to long-term side effects such as dysbiosis.

Functional medicine offers a comprehensive, root-cause approach—exploring dysbiosis, chronic stress, and digestive dysfunction. Rebuilding gut microbiome with probiotics, managing stress, and supporting digestion are essential steps toward lasting relief.

Functional medicine aims not only to relieve symptoms but to provide lasting solutions by addressing the underlying systemic causes of reflux.

At Healways, we use functional medicine tools like microbiome testing to identify the root causes of reflux. Based on this, we provide tailored therapeutic recommendations, including dietary advice, active ingredients (e.g. probiotics, enzymes, trace elements), and lifestyle support. Our goal is to relieve symptoms and restore the digestive system’s natural balance.

Do you suffer from reflux?

Examining the composition of the gut microbiome can help uncover the underlying root causes behind your symptoms.

References

[1] ‘Gastroesophageal reflux disease (GERD) – Symptoms and causes’, Mayo Clinic

https://www.mayoclinic.org/diseases-conditions/gerd/symptoms-causes/syc-20361940

[2] ‘Acid Reflux & GERD: What To Know’, Cleveland Clinic https://my.clevelandclinic.org/health/diseases/17019-acid-reflux-gerd

[3] ‘Addressing The Root Of Acid Reflux With Functional Medicine’, Dec. 31, 2023 https://torontofunctionalmedicine.com/integrative-functional-medicine/acid-reflux/

[4] Jarrod, ‘Indigestion and Reflux(GERD) – Assistance & Advanced Treatments’, Advanced Functional Medicine, Jul. 30, 2019 https://advancedfunctionalmedicine.com.au/gerd-symptoms-causes-natural-treatment/

[5] ‘GERD Symptoms & Treatment | Aurora Health Care’ https://www.aurorahealthcare.org/services/gastroenterology-colorectal-surgery/gastroesohageal-reflux-gerd

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Table of contents

What is reflux?

Reflux is a common digestive issue in which stomach acid flows back into the oesophagus, irritating its lining. While nearly everyone experiences this sensation occasionally, if it occurs at least twice a week, it is classified as gastroesophageal reflux disease (GERD).

GERD is caused by a malfunction of the lower oesophageal sphincter (LES). This muscle normally prevents stomach acid from flowing backward into the oesophagus. When it fails to close properly, acidic stomach contents can easily backflow and, over time, damage the oesophageal wall. [1]

This issue is becoming increasingly prevalent worldwide. It is estimated to affect 20% of adults [2], and its incidence continues to rise due to modern lifestyles, dietary habits, and other environmental factors. Although most people manage their symptoms with lifestyle changes and medication, these measures do not address the underlying causes and may not result in long-term improvement.

Therefore, reflux is not merely an unpleasant condition—it can have serious long-term health consequences, making timely recognition and treatment essential. [3]

Symptoms of GERD – When reflux is more than just discomfort

Many people have experienced the unpleasant sensation of heartburn, especially after a heavy meal or when lying down immediately afterward. However, if these symptoms recur and worsen over time, they may signal a more serious digestive disorder, one that not only affects quality of life but may also lead to complications. [4]

The most common symptoms

  • Burning sensation in the chest or stomach

The burning pain caused by acid reflux typically starts in the middle of the chest or the pit of the stomach and may spread to the neck, jaw, shoulders, or back. This pain often worsens after meals, particularly when bending over, lifting heavy objects, or lying down.

  • Sour or bitter taste in the mouth

A hallmark of reflux is the backflow of stomach acid into the throat or mouth, producing a burning, unpleasant taste. This occurs most frequently in the morning or after meals and may damage teeth over time.

  • Regurgitation or backflow of stomach contents

People with GERD often feel not only acid but also partially digested food coming back into the mouth. This is not only unpleasant but may lead to nausea and aversion to eating.

  • Difficulty swallowing and a lump-in-the-throat sensation

Chronic acid irritation may cause inflammation and mild narrowing of the oesophagus, resulting in the sensation that food is moving slowly or that something is constantly stuck in the throat.

  • Chronic cough and hoarseness

Acid can irritate the airways as well as the oesophagus. This often leads to a persistent dry cough, frequent throat clearing, and hoarseness. These symptoms are often mistaken for respiratory issues, though they may be reflux-related. [5]

  • Shortness of breath and asthma-like symptoms

Reflux can impact the respiratory tract, especially if acid vapours reach the windpipe and lungs. This can cause shortness of breath, wheezing, or even asthma attacks, particularly at night when lying down facilitates acid backflow.

  • Bloating and frequent belching

Reflux sufferers often feel bloated, as though their digestion isn’t functioning properly. Accumulated stomach acids and gases create a feeling of fullness and lead to increased belching.

  • Tooth enamel damage

Constant exposure to acid can erode tooth enamel, increasing sensitivity and the risk of decay. A sour taste in the mouth in the morning is a sign that warrants regular dental check-ups. [2]

Symptoms of reflux

Figure 1. Symptoms of reflux

Types of reflux

Classic acid reflux (GERD)

Reflux varies depending on where the digestive fluids cause irritation. GERD primarily affects the lower oesophagus due to backflow of stomach contents. It typically results in heartburn, particularly after meals or while lying down. GERD is often caused by a weak lower oesophageal sphincter. Symptoms include chest pain, throat burning, sour or bitter taste, nausea, vomiting, regurgitation (backflow of acid or food), and difficulty swallowing, particularly in the chest where food seems to get stuck. [6]

Silent reflux – Laryngopharyngeal reflux (LPR)

Laryngopharyngeal reflux (LPR) is a lesser-known yet common form of reflux. Here, stomach acid travels past the oesophagus to the throat and vocal cords, causing different symptoms from classic GERD, which is why LPR is often referred to as ‘silent reflux’.

This condition affects areas beyond the oesophagus—especially the pharynx and larynx—thus falling under extraoesophageal reflux. Typical symptoms include hoarseness, throat clearing, laryngitis, chronic cough, and difficulty initiating swallowing.

Diagnosing LPR is difficult, because classic heartburn is often absent so its symptoms are frequently misattributed to colds or allergies. Yet medical findings show that more than half of patients with chronic hoarseness may have LPR.

Both GERD and LPR can cause difficulty swallowing, but in different ways: GERD causes pharyngoesophageal dysphagia (a sensation of food being stuck in the lower throat or chest), while LPR results in oropharyngeal dysphagia (discomfort at the start of swallowing). LPR often presents with red, irritated vocal cords, while GERD can cause mucosal damage, which over time may lead to ulcers, oesophageal stricture, and, rarely, oesophageal cancer. [7]

Bile reflux – When acid is not the culprit

The third type, bile reflux, is not caused by acid but by the backflow of bile produced during digestion. Bile is normally produced in the liver, stored in the gallbladder, and released into the small intestine to aid in fat digestion. However, if the sphincter between the stomach and the small intestine—the pylorus—is overly relaxed or obstructed, bile can flow back into the stomach and even into the oesophagus. This backflow irritates the mucosal lining of the stomach and oesophagus, leading to inflammation, pain, and tissue damage. The symptoms of bile reflux are similar to those of GERD and often include bloating or a sensation of fullness, but more commonly involve a burning feeling in the stomach, nausea, bile vomiting, and a bitter taste in the mouth. [8]

Types of reflux

Figure 2. Types of reflux

Recognition and diagnosis of reflux disease

In many cases, reflux causes only temporary symptoms that may resolve on their own. When this happens, it is not necessarily considered a disease—this condition is known as uncomplicated, intermittent GER (gastroesophageal reflux). However, when symptoms become persistent, recurring, or worsening, it indicates a more complex digestive disorder that affects not only the oesophagus but also the entire gastrointestinal system. In such cases, we speak of reflux disease (GERD), which, without proper treatment, can cause inflammation, complications, and permanent mucosal damage over time.

Accurate and timely diagnosis is therefore essential—not only to relieve symptoms but also to prevent complications and to enable personalised, cause-based treatment.

The diagnostic process

In most cases, doctors diagnose reflux or GERD based on a patient’s symptoms and medical history. If the symptoms are typical (e.g. frequent heartburn, acid regurgitation), treatment can often begin based on this alone, involving lifestyle changes and medication. Diagnostic tests may be necessary if:

  • symptoms do not improve with treatment,
  • complications are suspected,
  • other conditions with similar symptoms need to be ruled out, prompting referral to a specialist (e.g. gastroenterologist)

Diagnostic tests for suspected reflux (GERD)

While functional medicine focuses more on identifying root causes and promoting lifestyle changes, it is helpful to understand traditional diagnostic methods—especially for persistent or severe cases.

  • Gastroscopy (endoscopy): Allows direct examination of the oesophagus, stomach, and duodenum, and can detect complications such as inflammation, ulcers, or Barrett’s oesophagus. Tissue samples can also be taken if needed. [9]
  • pH monitoring: A 24-hour test (via nasal catheter or capsule) to precisely measure acid reflux. The patient logs meals and symptoms.
  • Barium swallow test: An X-ray using contrast medium to reveal narrowing or hernias in the oesophagus. Mainly used to investigate swallowing difficulties.
  • Manometry: Measures oesophageal muscle function; useful when motility disorders or swallowing problems are suspected.
  • Transnasal oesophagoscopy: A thin camera is inserted through the nose without anaesthesia, offering a quick, low-stress alternative. [1]

Causes and pathophysiology of reflux

Reflux symptoms result from a complex imbalance in the body. Disruption of the LES, increased stomach pressure, acid imbalance, and altered digestive motility can all contribute to the backward flow of stomach contents into the oesophagus. These dysfunctions often coexist, and research increasingly highlights the importance of the condition of the gut microbiome, acid levels, stress, and nervous system involvement.

Below is an overview of the anatomical, physiological, and lifestyle-related factors contributing to reflux and its long-term symptoms.

Main pathophysiological mechanisms

  1. LES dysfunction and transient relaxation (TLESR)

Transient lower oesophageal sphincter relaxation (TLESR) is a common trigger. These spontaneous, non-swallowing-related relaxations typically occur after meals or when lying down, especially if the stomach is full. Contributing factors include stomach distension, certain foods (e.g. fatty meals, chocolate, alcohol), and vagal reflex activation. [10]

  1. Persistently low LES pressure

Under normal conditions, LES resting pressure is sufficient to resist gastric pressure. If it drops below 6 mmHg for an extended period, the sphincter fails to close adequately, leading to reflux, mucosal inflammation, and potentially ulcers, strictures or Barrett’s oesophagus.

  1. Diaphragmatic hernia (hiatal hernia)

A hernia caused by weakness of the diaphragm allows part of the stomach to slip into the chest cavity, mechanically impairing the closing function of the LES. A hiatal hernia not only weakens the function of the sphincter, but often creates a kind of ‘acid reservoir’ from which stomach contents can easily flow back into the oesophagus.

  1. Hypochlorhydria (low stomach acid)

Although it may seem paradoxical, too little stomach acid can also promote reflux. Reduced acidity does not adequately stimulate the closing function of the LES, impairs digestion and increases stomach tension – all of which together increase the risk of reflux. In addition, poorly digested food leads to more frequent bloating and gas formation, further increasing abdominal pressure.

  1. Delayed gastric emptying

If food remains in the stomach for too long – for example, due to nervous regulation disorders, diabetes or certain medications – this increases stomach pressure, which puts strain on the sphincter. Delayed emptying is often accompanied by postprandial (after-meal) reflux, bloating and a feeling of fullness.

  1. Acid reflux clearance disorder

Under physiological conditions, gastric acid that enters the oesophagus is quickly returned to the stomach by peristaltic waves, while the alkaline buffering effect of saliva helps to neutralise the acid. If these mechanisms are slowed down, for example during sleep or as a result of medication, the acid reflux can come into prolonged contact with the mucous membrane of the oesophagus, causing increased irritation and damage.

  1. Weakened mucosal protection

The mucous membrane of the oesophagus does not have such strong protective mechanisms as the stomach. If the connections between cells, buffer capacity or ion channel function are impaired, acid can more easily enter the tissues. This can lead to inflammation, sensitivity, pain and, in the long term, cell damage.

  1. Visceral hypersensitivity

Not all reflux symptoms stem from actual acid reflux. Some individuals have hypersensitive oesophageal nerves, overreacting even to mild stimuli—this phenomenon is linked to altered central nervous system pain regulation. [11]

Comorbidities and predisposing factors

The risk of developing GERD can be increased by various external and internal factors. While not direct causes, these factors significantly contribute to triggering the underlying mechanisms.

Hormonal and neuromuscular effects

  • Connective tissue diseases (e.g. scleroderma) affecting oesophageal muscles
  • Hormonal imbalances (e.g. increased progesterone during pregnancy, relaxing the LES)

Conditions affecting motility and emptying

  • Delayed gastric emptying (e.g. diabetes, vagus nerve dysfunction, viral infections) increases stomach pressure and reflux risk

Lifestyle factors

  • Western diets (high in fat, sugar, and processed foods)
  • Late-night, heavy meals consumed just before bedtime increase the likelihood of reflux when lying down.
  • Smoking, which lowers LES pressure and inhibits saliva production
  • Alcohol and caffeine, which relax the LES and increase acid production

Medication effects

  • Certain medications, such as antidepressants, blood pressure meds (e.g. nitrates, calcium channel blockers), non-steroidal anti-inflammatory drugs (NSAIDs)
  • Paradoxically, long-term use of proton pump inhibitors (PPIs) to treat reflux reduces stomach acid production, which can lead to hypochlorhydria, thereby impairing digestion, promoting bloating and increasing stomach pressure, and thus contributing to the mechanisms that maintain reflux in the long term.

What causes the acid-base balance to be upset, and how does this relate to reflux?

Reflux is often oversimplified as a problem of “too much stomach acid,” but its underlying causes are more complex. Symptom development is influenced not only by the amount of acid, but also by its location, the manner of its presence in the body, and the body’s ability to counteract it. Acid-base balance plays a key role in this process, especially in protecting the stomach lining and regulating the buffering mechanisms of the bicarbonate system, respiration, and kidney function.

The inner surface of the stomach is protected by a multi-layered defence system that ensures even highly corrosive stomach acid does not damage its own tissues. This system includes mucin (a slippery glycoprotein), aqueous layers, and bicarbonate ions. Mucin provides mechanical protection, while bicarbonate neutralises hydrochloric acid locally to prevent cellular damage—together forming the stomach’s “acid shield.”

The stomach’s pH is highly acidic (1.5–3), which is essential for digestion and pathogen destruction. This acidity also activates pepsin, a key digestive enzyme that only functions at low pH. If stomach acid is too low—due to stress, age, or medication—pepsin activity is impaired, leading to incomplete protein digestion, fermentation, gas formation, and nutrient deficiencies.

Thus, the stomach lining actively participates in maintaining acid-base balance, not merely serving as a passive barrier. Bicarbonate is crucial to this process—not just in the stomach, but throughout the entire body.

The body’s acid–base balance is a tightly regulated system that keeps blood pH stable within a slightly alkaline range of 7.35 to 7.45. This balance is maintained through three primary mechanisms:

  • Bicarbonate buffer system: Quickly neutralises acid or base shifts, for example in the stomach or cellular environments.
  • Breathing helps regulate the acid-base balance by controlling carbon dioxide (CO₂) levels: when the body becomes more acidic, breathing rate increases to expel more CO₂, thereby reducing acidity.
  • The kidneys are slower but effective long-term compensatory organs: they can excrete hydrogen ions and reabsorb bicarbonate to counteract acidification or alkalisation.

If these systems become overloaded or fail to function properly—due to factors such as chronic stress, metabolic disorders, or inflammatory processes—the acid-base balance may be disrupted. This can lead not only to general fatigue and inflammation, but also to increased risk and severity of reflux, as the protective capacity of the mucous membranes is reduced.

The oesophagus is particularly vulnerable in this respect, as it lacks bicarbonate protection. While the columnar epithelial cells of the stomach produce both mucus and bicarbonate to buffer acidity, the multilayered squamous epithelium of the oesophagus provides only mechanical protection and is entirely unprotected against an acidic environment. When the lower oesophageal sphincter (LES) malfunctions, acid can reflux into the oesophagus, where even small amounts may trigger a strong inflammatory response. Over time, this can result in structural changes.

The connection between the vagus nerve and digestion

The vagus nerve plays a key role in the parasympathetic nervous system, which regulates functions such as digestion, heart rate, and breathing. It directly influences stomach function, including the production of stomach acid. Stress—particularly chronic stress—can affect vagal nerve activity, disrupting acid secretion and resulting in either excessive or insufficient stomach acid production.” [12]

Vagus nerve and stomach acid levels

Stress and excess acid:

Stress activates the sympathetic nervous system, triggering the ‘fight or flight’ response. In this state, the body prioritizes immediate survival over digestion, suppressing digestive functions. However, acute stress can not only inhibit but also, in some cases, indirectly increase stomach acid production—for example, by elevating gastrin or histamine levels. As vagal nerve activity declines, the parasympathetic nervous system becomes less capable of counterbalancing sympathetic overactivity. This imbalance may lead to increased acid production in the short term, and over time, contribute to the development of stomach ulcers, reflux, and other digestive issues.

Stress and low acid:

In cases of chronic stress, the situation can reverse: prolonged dysfunction of the vagus nerve leads to a significant reduction in parasympathetic activity—a condition known as vagal hypoactivity. As a result, the mechanisms that regulate stomach acid production become impaired, leading to reduced acid levels, a condition called hypochlorhydria. This makes it more difficult to break down food, potentially leaving undigested material in the stomach, which can cause bloating, gas, and even reflux.” [13]

Inadequate digestion and low stomach acid levels can also contribute to the development of leaky gut syndrome. In this condition, the tight junctions between the cells of the intestinal wall become compromised, allowing larger molecules—such as undigested food particles, toxins, or bacteria—to pass into the bloodstream, which would not normally occur. This can trigger an immune response, inflammation, and a range of other symptoms throughout the body.

In addition, low stomach acid levels are often linked to reduced activity of the enzyme diamine oxidase (DAO), which is responsible for breaking down histamine. When DAO function is impaired, histamine can accumulate in the body. During meals, this histamine release may trigger symptoms such as heartburn, bloating, and even reflux. If DAO activity is compromised, the resulting histamine buildup can further disrupt digestion and worsen acid-related symptoms—even when stomach acid levels are actually low. [14]

Figure 3. Main risk factors for the development of reflux

The link between reflux and gut microbiome

One of the lesser-known but increasingly studied links between reflux and gut health is dysbiosis—an imbalance in the gut microbiota. In this state, beneficial bacteria are diminished while harmful, pro-inflammatory microorganisms thrive. Dysbiosis may not only result from treatments used for reflux, but could also contribute to its onset and the worsening of symptoms. [15]

Reflux is often not caused by excessive, but rather by reduced stomach acid production (hypochlorhydria). When acid levels are low, food is not properly digested, leading to fermentation, bloating, and gas formation. This increased pressure in the stomach places strain on the lower esophageal sphincter (LES) from below, reducing its ability to close effectively. As a consequence of low acid levels, undigested food and increased bacterial load may also contribute to greater intestinal permeability, known as ‘leaky gut syndrome.’ Cytokines and inflammatory mediators released from the inflamed gut further disrupt digestive regulation—including the function of the LES.

In reflux, not only the microbial composition of the intestinal tract may change, but also that of the oesophageal mucosa. Studies have shown that bacteria such as Proteobacteria, Campylobacter, and E. coli are more prevalent in patients with GERD, while the presence of beneficial bacteria, such as Bacteroidetes strains, is reduced. This microbial shift creates an inflammatory environment in the lower oesophagus, increasing mucosal irritation and potentially contributing to the development of more serious conditions, such as Barrett’s oesophagus or adenocarcinoma, over time.

Paradoxically, drug therapy for reflux—especially proton pump inhibitors (PPIs)—can also contribute to the development of dysbiosis. While these medications reduce stomach acid production and relieve reflux symptoms, they also suppress the acidic environment that normally prevents the overgrowth of pathogens in the stomach and small intestine. A persistently alkaline environment encourages bacterial overgrowth (SIBO), which can further impair digestion, increase bloating, and indirectly exacerbate reflux. Moreover, PPIs may reduce the absorption of magnesium and vitamin B12, potentially leading to nutrient deficiencies and a weakened immune system over time.

Scientific studies have shown that approximately 25% of PPI users experience significant imbalances in their intestinal flora. The risk of Clostridium difficile infection increases, while the proportion of beneficial Lactobacillus and Bifidobacterium strains decreases—both of which are crucial for immune defence, mucosal integrity, and healthy digestion.

Reflux can therefore be both a cause and a consequence of dysbiosis, creating a vicious cycle in which digestive disorders, inflammation, microbiome imbalance, and impaired LES function reinforce one another. For this reason, effective reflux treatment should go beyond merely reducing stomach acidity—restoring the balance of the intestinal flora is also essential.

Dysbiosis may be suspected if reflux is accompanied by:

  • frequent bloating,
  • constipation or diarrhoea,
  • food intolerances,
  • skin issues,
  • persistent fatigue.

In such cases, a stool microbiome test, SIBO breath test, or gastroenterological examination is recommended to help identify the underlying causes.

Do you suffer from reflux?

Examining the composition of the gut microbiome can help uncover the underlying root causes behind your symptoms.

SIBO (Small Intestinal Bacterial Overgrowth)

SIBO is a condition in which an excessive number of bacteria accumulate in the small intestine—an area that normally contains relatively few microbes compared to the large intestine. GERD and SIBO are often linked. Common symptoms of SIBO include belching, abdominal bloating, and various digestive disturbances.

Why does SIBO cause reflux?

Several factors may explain the link between SIBO and reflux:

  • Imbalance in the intestinal flora: Bacterial overgrowth in the small intestine can lead to increased gas production, raising pressure within the abdomen. Elevated intra-abdominal pressure may weaken the lower oesophageal sphincter (LES), promoting the reflux of stomach acid into the oesophagus.
  • Delayed gastric emptying is one mechanism that links SIBO and reflux. When bacteria proliferate in the small intestine, they can slow the movement of food through the digestive tract, resulting in delayed gastric emptying. This, in turn, increases the likelihood of stomach acid flowing back into the oesophagus.
  • Inflammation and irritation: SIBO can cause inflammation in the intestinal tract, which may indirectly weaken the oesophageal sphincter, increasing its sensitivity and the likelihood of reflux. [17]

What is the link between reflux and Helicobacter pylori?

Helicobacter pylori (H. pylori for short) is a bacterium that resides in the stomach lining and is known to play a role in the development of stomach ulcers, chronic gastritis, and certain types of stomach cancer. Less widely known—but increasingly studied—is its potential impact on reflux symptoms. [18]

The relationship between H. pylori and reflux is complex and not entirely understood, as the bacterium can influence stomach acid production in different ways. When inflammation is concentrated in the lower part of the stomach (the antrum), H. pylori may stimulate acid production, potentially worsening reflux. However, if the upper part of the stomach (the corpus) is also affected, acid production may decrease, which could relieve symptoms.

After successful eradication of the infection, inflammation typically subsides, and acid production often increases. In some individuals—especially those with a weakened lower oesophageal sphincter (LES)—this may lead to new or worsened reflux symptoms. Several studies, including those by Labenz and Koike, have shown that the incidence of reflux can rise after H. pylori eradication in predisposed individuals. [19]

Nonetheless, treating the infection is essential in cases of ulcers, gastritis, or long-term use of acid-suppressing medications. According to the Maastricht IV Consensus, eradication is recommended, although the potential risk of reflux should be evaluated on a case-by-case basis.

Treatment of reflux: From symptom relief to root-cause resolution

The treatment of gastroesophageal reflux disease (GERD) involves more than just relieving unpleasant symptoms—it also aims to reduce inflammation, protect the mucous membranes, identify underlying causes, and prevent long-term complications. While conventional medicine focuses primarily on suppressing acid production, functional medicine takes a more holistic approach: it seeks to identify individual triggers, restore gastrointestinal balance, and implement strategies that support the body’s natural healing processes.

1. Lifestyle and dietary changes

The cornerstone of reflux treatment is lifestyle modification. Numerous studies have confirmed that weight loss—particularly in cases of abdominal obesity—avoiding large late-night meals, and elevating the head of the bed reduce pressure on the oesophagus, thereby relieving the LES and decreasing the frequency of acid reflux. Additionally, quitting smoking, limiting caffeine and alcohol intake, and practising stress-reduction techniques such as meditation, yoga, or forest bathing (Shinrin-yoku) can help promote gastrointestinal balance.

2. Medication and medical treatment

The most common approach to managing symptoms is to reduce stomach acid production, which can be achieved through several methods:

  • Antacids: Provide quick relief but may cause rebound acid production with long-term use.
  • H2 blockers (e.g., famotidine) moderately reduce stomach acid and, unlike PPIs, cause less disruption to the stomach’s microbiome because they do not raise gastric pH to the same extent.
  • Proton pump inhibitors (PPIs) are effective, but with long-term use, it is recommended to use the lowest effective dose and, if possible, transition to H2 blockers or adopt intermittent use over time.
  • Prokinetics: help promote stomach emptying, thereby reducing gastric pressure and the likelihood of reflux.
  • Endoscopic treatments (e.g., TIF – transoral incisionless fundoplication): minimally invasive procedures aimed at improving LES function.
  • Surgical solution (e.g., Nissen fundoplication): this is an option if other therapies prove ineffective or if the patient prefers not to take medication long-term. During the procedure, the upper part of the stomach is wrapped around the oesophagus to strengthen the sphincter’s closure. [20]

3. Restoring gastrointestinal balance

Functional medicine recognises that reflux is often driven by low stomach acid (hypochlorhydria) and dysbiosis. Addressing these underlying conditions not only relieves symptoms but also targets the root cause of the disorder.

A) Rebuilding gut microbiome:

  • Targeted antimicrobial herbs (e.g., berberine, oregano oil) help suppress harmful bacteria.
  • Probiotics (such as Lactobacillus and Bifidobacterium strains) support the intestinal immune system and help reduce inflammation.
  • Herbs that promote mucosal healing and stimulate gastric emptying (e.g., ginger, artichoke) may also play an important role. [17]

B) Supporting digestion:

  • Replenishing digestive enzymes and stomach acid (e.g., betaine HCl with pepsin) supports the restoration of optimal gastric acid levels—provided there is no significant mucosal irritation or active ulceration.
  • A betaine HCl challenge test (with dosage adjusted to meals) can help determine the appropriate level of acid supplementation.

C) Protecting the mucosa and reducing inflammation:

  • Nutrients and bioactive compounds: zinc carnosine, DGL (deglycyrrhizinated liquorice root), melatonin, omega-7, and vitamin U.
  • Herbs that protect the mucous membrane and reduce inflammation: marshmallow root, meadowsweet, chamomile, aloe vera, turmeric, and mallow.
  • Slippery elm powder creates a mucilaginous coating on the oesophagus, providing mechanical protection against acid irritation. [17]

D) Targeted diagnostics with functional tests: Proper treatment requires identifying the underlying factors:

  • H. pylori infection (breath test, biopsy)
  • SIBO breath test (hydrogen/methane)
  • Stool microbiome analysis: bacterial ratios, inflammatory markers, digestive functions
  • Food intolerance and malabsorption testing (e.g., histamine, fructose, lactose)
  • Basic laboratory tests: inflammation, liver function, B12, iron, zinc, magnesium, etc. [17]

Complications of untreated GERD

  • Oesophagitis, ulcers, strictures
  • Barrett’s oesophagus, a potential precursor to oesophageal cancer
  • Tooth enamel erosion, chronic cough, asthma, hoarseness
  • Sleep disturbances, fatigue, anxiety, depression [17]

When should you see a doctor immediately?

Although reflux can often be improved with lifestyle changes, such as diet and posture, there are warning signs that require prompt medical evaluation.

  • Severe, tight chest pain – This symptom can easily be mistaken for a heart problem. If the pain radiates to the arm or jaw, or is accompanied by shortness of breath, seek immediate medical attention.
  • Bloody or black stools, bloody vomiting – These may signal bleeding in the oesophagus or stomach and require urgent medical evaluation.
  • Unexplained weight loss – A decrease in appetite or unintentional weight loss could indicate that reflux is becoming more serious.
  • Persistent difficulty swallowing – If eating becomes increasingly difficult due to narrowing or inflammation of the oesophagus, medical assessment is necessary.
  • Frequent choking or shortness of breath – Regular episodes of choking or feeling unable to breathe properly may reflect severe irritation in the oesophagus or airways. [21]

Summary

Reflux is a global issue that significantly affects quality of life. Traditional treatments like PPIs offer symptom relief but don’t address the root causes and may lead to long-term side effects such as dysbiosis.

Functional medicine offers a comprehensive, root-cause approach—exploring dysbiosis, chronic stress, and digestive dysfunction. Rebuilding gut microbiome with probiotics, managing stress, and supporting digestion are essential steps toward lasting relief.

Functional medicine aims not only to relieve symptoms but to provide lasting solutions by addressing the underlying systemic causes of reflux.

At Healways, we use functional medicine tools like microbiome testing to identify the root causes of reflux. Based on this, we provide tailored therapeutic recommendations, including dietary advice, active ingredients (e.g. probiotics, enzymes, trace elements), and lifestyle support. Our goal is to relieve symptoms and restore the digestive system’s natural balance.

Do you suffer from reflux?

Examining the composition of the gut microbiome can help uncover the underlying root causes behind your symptoms.

References

[1] ‘Gastroesophageal reflux disease (GERD) – Symptoms and causes’, Mayo Clinic

https://www.mayoclinic.org/diseases-conditions/gerd/symptoms-causes/syc-20361940

[2] ‘Acid Reflux & GERD: What To Know’, Cleveland Clinic https://my.clevelandclinic.org/health/diseases/17019-acid-reflux-gerd

[3] ‘Addressing The Root Of Acid Reflux With Functional Medicine’, Dec. 31, 2023 https://torontofunctionalmedicine.com/integrative-functional-medicine/acid-reflux/

[4] Jarrod, ‘Indigestion and Reflux(GERD) – Assistance & Advanced Treatments’, Advanced Functional Medicine, Jul. 30, 2019 https://advancedfunctionalmedicine.com.au/gerd-symptoms-causes-natural-treatment/

[5] ‘GERD Symptoms & Treatment | Aurora Health Care’ https://www.aurorahealthcare.org/services/gastroenterology-colorectal-surgery/gastroesohageal-reflux-gerd

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Published On: July 17th, 2025 / Categories: Uncategorized / Tags: /