Professor Anthony Hobson from The Functional Gut Clinic joined us to discuss the important role of gut bacteria and diet in managing reflux, particularly when medication doesn’t work.
This session was a must-watch for anyone living with acid reflux.
We hope you enjoy reading this very informative transcript of the hour-long session in this blog post. If you would like to watch the event please head over to our Expert Speaker events page to see the full video recording.
The Functional Gut Clinic
Anthony has worked in the field of reflux since 1991, when he began as a student under John Bansovich, an upper GI surgeon in Salford. In 2014, he established his own clinic in London and has since expanded with additional clinics in Manchester and Cambridge. His work focuses on GI physiology — understanding how the gut functions — with a particular interest in identifying the root causes of reflux, determining the most effective treatments, and providing evidence-based care to improve patient outcomes.
Each year, his clinics test around 4,000 NHS and private patients for reflux. They also offer a broad range of complementary gut health tests to build a fuller picture of each patient’s condition.
Their mission is to deliver the highest quality gut testing to accurately identify the causes of symptoms, so that patients receive the right treatment rather than relying on trial-and-error approaches. The need is significant: reflux affects an estimated 8.5 million people in the UK. Of those, around 5 million are on acid suppression medication – but only 3 million report good symptom control. That leaves another 5 million who either don’t respond adequately to medication or remain untreated, often relying solely on lifestyle changes. This has a major impact on quality of life.
One of the main challenges clinicians face is that patients rarely present with a clear diagnosis – instead, they present with symptoms. These can include heartburn, regurgitation, diarrhoea, bloating, abdominal pain, and dysphagia. Many people who come to the clinic have a mix of these symptoms and have found little relief through conventional medications. In these cases, clinicians must take a Sherlock Holmes-like approach – identifying which symptoms matter most, what’s causing them, and how best to treat them.
Anthony introduced the concept of the brain–throat–gut axis in reflux. While it may sound complex, the idea is simple: everything from the brain to the colon is connected. It’s a bidirectional flow of information – the brain affects the gut, the gut affects the brain, and everything in between communicates constantly. So when evaluating a reflux patient, it’s not just about the oesophagus and stomach – it’s about considering the entire system and what might be contributing to their symptoms.
A Quick Overview of Reflux
The liquid contents of the stomach can move upward when the lower oesophageal sphincter – located at the bottom of the oesophagus – relaxes. This process is normal in most people. However, when these relaxations become excessive, especially in individuals with a weakened sphincter or a hiatus hernia, problems can arise. These include conditions such as esophagitis (inflammation of the oesophagus) and Barrett’s oesophagus.
The most common causes of reflux include delayed stomach emptying, hiatus hernia, excessive sphincter relaxations, and poor oesophageal motility. Most patients are initially prescribed anti-reflux medications, typically antacids or proton pump inhibitors (PPIs) – such as omeprazole or lansoprazole – which will be a key focus of this talk. These medications can be very effective, especially in the early stages.
Research has shown that when patients first present with reflux, they often report classic symptoms like heartburn and regurgitation. After being on medication for around 8 weeks to six months, these initial symptoms often improve. However, new symptoms frequently emerge – such as bloating, flatulence, abdominal pain, and diarrhoea.
While the original reflux symptoms may decrease, these new digestive symptoms can become confused with ongoing reflux issues. This raises important questions about the interaction between the upper gut, the brain, and the medications we take – something we’ve been working hard to better understand.
Understanding Digestion, the Microbiome, and Their Link to Reflux
Digestion primarily occurs in the small bowel, and one of the best ways we can support the beneficial bacteria – or microbiome – in our gut is through a varied, balanced diet. The key is moderation: not too much of any one food, but a healthy mix of fruits, vegetables, meats, eggs, nuts, and grains. Variety truly is the spice of life, and it plays a vital role in maintaining a strong and diverse gut microbiome.
Certain foods, like carbohydrates and proteins, are digested early in the small intestine. If you refer to the blue graph in the image above, it shows the number of bacteria present throughout different parts of the digestive tract – from the upper small intestine all the way to the colon. In the upper small bowel, bacterial counts are relatively low (around 1,000 to 10,000). But as you move further down, particularly into the colon, the number increases significantly – reaching up to 100 billion (10¹¹).
This bacterial population in the colon is extremely helpful. It assists in the secondary digestion of fibrous foods that our bodies can’t break down on their own, helping release nutrients, calories, and important chemicals that support gut health. In a healthy digestive system, easily digestible foods are broken down in the upper gut, and the more complex, harder-to-digest foods pass to the lower gut, where the bacteria help finish the job. This balance supports a healthy microbial environment.
What Happens When Things Go Wrong – Dysbiosis and SIBO
Sometimes, this system gets disrupted – a condition known as dysbiosis, which is essentially an imbalance or disorganisation of the gut microbiome. A simple way to understand this is with two examples:
- If you eat an easily digestible carbohydrate, like white rice, it should be fully broken down in the small intestine before reaching the colon.
- If you eat something like beans, which are more complex, they may pass into the colon and be digested there by bacteria – which is perfectly healthy.
In both cases, the bacteria are doing their job where they’re supposed to.
However, in Small Intestinal Bacterial Overgrowth (SIBO), this system becomes disrupted. You either have too many bacteria in the small intestine or the wrong types of bacteria in that area. This leads to premature fermentation – meaning, even easily digestible foods like rice start fermenting too early in the digestive process. Because the small intestine is highly sensitive, this can trigger a wide range of symptoms: abdominal pain, bloating, flatulence, diarrhoea or constipation, nausea, and even skin issues. These changes can also worsen reflux symptoms.
The By-products of Fermentation – What They Mean for Your Symptoms
When fermentation occurs, instead of producing stomach acid (which we often hear about in reflux), the gut produces short-chain fatty acids (SCFAs) and gases. SCFAs are naturally occurring and have benefits for gut health – they even help with muscle growth and energy. But they come with strong smells: some resemble cheese, fish, or sweaty socks. All of these are completely normal compounds, but if they’re produced in the wrong place or in excessive amounts, they can cause discomfort and symptoms.
Fermentation also leads to the production of gases like hydrogen, carbon dioxide, methane, and hydrogen sulfide (the culprit behind that infamous rotten egg smell). Again, these gases are normal – but in the wrong balance, they can irritate the gut and contribute to symptoms like bloating and reflux.
In addition to gases, the body also produces volatile organic compounds (VOCs) during digestion. These are another group of chemicals that, in excess or in the wrong environment, can irritate the gut lining and contribute to digestive symptoms.
How We Measure What’s Happening
Understanding these processes helps us make better diagnoses and tailor treatments. One of the first tests we use for reflux patients involves a thin, flexible tube that’s gently passed through the nose into the stomach. It’s well tolerated and only takes about 20 minutes. The tube is equipped with sensors that measure pressure, liquid, and gas levels throughout the digestive tract.
The readings are displayed as colour images:
- Warm colours indicate high pressure
- Cool colours show low pressure
- Purple represents liquid
- Blue indicates gas
These detailed readings give us insight into how the oesophagus and stomach are functioning – allowing us to see not just acid levels, but also gas and pressure changes that could be contributing to symptoms.
Belching – When It’s More Than Just a Nuisance
Let’s start with a symptom that doesn’t usually respond well to PPIs: belching. While belching isn’t dangerous or linked to increased mortality, it can significantly affect quality of life. This example shows how belching can be controlled either by the brain or the gut.
To begin, we place a tube down the oesophagus. The first concept here is “brain-related” or supragastric belching – a behavioural issue. It’s often a coping mechanism for discomfort in the upper stomach area. People suck air into the oesophagus and then expel it. This can happen hundreds of times a day. Patients are often able to reproduce the behaviour on command in clinic. Sometimes there’s an underlying issue that triggers this, but it becomes an ingrained habit over time.
Measuring Belching with Manometry
We use a technique called manometry to measure this. Imagine a dotted line representing the tube that goes down the oesophagus. At the top, there’s the upper oesophageal sphincter, and at the bottom, the lower oesophageal sphincter – a band of pressure in each place. When you swallow, the upper sphincter opens, the tongue and throat muscles push the food down, and a coordinated wave of contraction moves through the oesophagus while the lower sphincter relaxes. That’s normal swallowing.
When someone belches supragastrically, we see a different pattern: they increase pressure in their throat, open the upper sphincter, and suck air into the oesophagus. Then they contract the abdomen and push the air back out. This can happen repeatedly and frequently.
Once we identify this pattern in a clinic setting, it’s useful to show patients what’s happening so they can learn to prevent it. One simple technique is diaphragmatic breathing. When done properly, it strengthens the barrier at the lower oesophageal sphincter. Patients can clearly see on the monitor that when they breathe deeply and correctly, they don’t perform the air-sucking behaviour. This method is part of biofeedback, targeting the brain-driven components of symptoms that don’t improve with PPIs.
A practical trick: put a pen between your teeth while practicing diaphragmatic breathing. This makes it harder to suck in air, helping break the habit. It even works in everyday settings—if your partner is a frequent belcher, getting them to use the pen trick while watching TV can help reduce the behaviour.
Gastric Belching – The Normal but Bothersome Kind
Gastric belching is different. This involves air that has entered the stomach – either through eating, drinking fizzy drinks, or due to bacterial fermentation. Everything relaxes to let the air escape: the upper sphincter opens, air comes up, and then a swallow clears the remaining contents. This is normal, but it can become excessive and bothersome.
We can see these patterns clearly with manometry. In a gastric belch, pressure equalizes from the stomach to the oesophagus, allowing gas to travel upward. A swallow usually follows to clear any remaining liquid. Again, this is a normal process, but too much of it can cause discomfort.
Testing Reflux and Acid Levels
We can also objectively measure reflux over 24 hours using a small probe with pressure sensors. The patient wears a monitor that logs symptoms like chest pain, belching, and eating habits. It’s often easier to interpret this data visually, using colour rather than waveforms.
In supragastric belching, we see air being pulled into the oesophagus, then pushed back out—often along with stomach contents. If those contents are acidic, they can trigger chest pain or regurgitation. Because this is driven by behaviour rather than physiology, reducing the behaviour can lead to less acid exposure and fewer symptoms.
Understanding Non-Acidic Reflux and Its Symptoms
Another example: normally, the pH in the oesophagus is around 6. If acidic fluid from the stomach rises up and drops the pH below 4, even briefly, it can cause heartburn. This pattern is distinct and shows strong acidity, confirmed by a drop in electrical resistance – indicating stomach acid.
But not all reflux is acidic. Non-acidic reflux doesn’t show up in traditional pH tests like Bravo,but can still cause symptoms. For instance, liquid might rise into the oesophagus without changing pH much, but still cause heartburn. Impedance testing helps us detect this, and we now know that up to a third of reflux events fall into this category.
Throat symptoms are especially tricky. The throat is more sensitive than the oesophagus, and even one episode of acid entering the throat per week is considered abnormal. When this happens, PPIs usually help. But in many cases, acid doesn’t reach the throat – it stays lower and is cleared quickly. That’s why throat symptoms often don’t improve with PPIs.
The Topit trial showed that patients with persistent throat symptoms saw no difference between taking PPIs and taking a placebo after 16 weeks – at a one-year follow-up, there was still no benefit. That’s a big deal, considering that 18 million Americans are treated with antacids for throat issues. Many of them might be on unnecessary medication.
Breath Tests and the Role of Gut Bacteria
We can also measure gases produced by gut bacteria using hydrogen and methane breath tests. These are simple, using either test tubes or breath bags, and can be done at home or in a clinic. After introducing a carbohydrate (like glucose or lactulose), we monitor breath samples over two hours.
In bacterial overgrowth, gas levels rise quickly as the substrate reaches bacteria in the small intestine. A rise of 20 parts per million within 90 minutes suggests overgrowth. Methane, linked more to bloating and constipation, is usually consistently high throughout.
Gas production in the colon is also measurable. High fermentation levels – over 60 parts per million at the end of the test – can indicate excess gas production in the colon.
Diet, Fermentation, and the Gut–Reflux Link
Interestingly, even healthy people develop reflux symptoms if they consume highly fermentable carbs like onions, garlic, and some fruits or fibres. These foods put stress on the colon, which sends signals to the brain, stomach, and oesophageal sphincter. So for people with a weakened sphincter, the impact can be much worse.
In a study of 100 patients being assessed for reflux surgery, we found that 60% had abnormal breath tests. Those with stronger symptom associations, like regurgitation, produced more gas. This suggests that gut microbiome issues are common in surgical candidates and might be managed without surgery.
Why does this matter? Because gas bloat is one of the most common complaints after reflux surgery. If that bloating is due to bacterial imbalance, dietary or other treatments could reduce symptoms and improve surgical outcomes.
Patients with gut dysbiosis often have more belching, bloating, acid exposure, and stronger symptom associations. So clearly, something in the lower gut is affecting reflux – and making it harder to treat.
Rethinking Reflux – It’s Not Always About Acid
We’re now using more sensitive tools to detect non-acidic, irritant reflux, which could explain persistent throat symptoms in patients on PPIs. These aren’t acid-related—they’re more like the byproducts of fermentation. The best comparison? It’s like gargling kombucha. Kombucha is mildly acidic and full of short-chain fatty acids. Not painful like vinegar but still irritating. If that lingers in the throat, it can cause soreness, hoarseness, coughing, and more.
It’s time to consider this a different kind of reflux – one that might respond better to lifestyle or dietary changes than medication.
The Role of Diet in Managing Reflux
You’ve probably been told to avoid things like alcohol, coffee, and spicy food – these can relax the sphincter or irritate the lining. But we’re also looking at the role of carbs and high-fat meals.
Fat slows down digestion, which increases pressure on the sphincter and contributes to reflux. Low-carb meals are easier to digest and might reduce acid exposure and symptoms – but we don’t yet know their impact on non-acidic reflux. There’s also limited research on low-fermentable diets, though it’s a promising area.
Back to basic stomach physiology: when you eat, the top part of the stomach relaxes to make space. At the same time, the sphincter tightens to prevent reflux. Then, the stomach grinds the food and slowly empties it into the small bowel. It’s a finely-tuned process.
High-fat meals need more time to digest and more bile to break down the fat. This delays digestion and puts added strain on the sphincter, increasing the risk of reflux. So after a fatty meal, taking steps to relieve that pressure can help.
High-Tech Testing for Stomach Function
We now use a new high-tech system – electrodes placed on the stomach wall – to monitor this process. In healthy people, you’ll see a rise in stomach activity after a meal, followed by a return to baseline as food moves along. But in reflux patients, especially those with a hiatus hernia, the stomach struggles to increase its activity. Each time it tries to contract, the sphincter relaxes – and reflux occurs. It’s like trying to pump water through a leaky valve.
If the hernia is surgically repaired, this activity often normalises.
The test itself takes about five hours and involves monitoring electrical signals from the stomach muscles. These usually fire at about three cycles per minute – like a slow-motion heartbeat. This is a new technique, currently only available privately or in research, but we hope it will eventually be adopted more widely, including in the NHS.
We’re presenting our recent findings in San Diego soon, and we’re optimistic that this research will help more doctors and surgeons understand why focusing on how the stomach functions is key to understanding, and treating, reflux more effectively.
Providing Clear, Evidence-Based Advice
So, what are we doing about it at The Functional Gut Clinic?
We’re aiming to provide free and objective digestive health advice. We’re working with companies to research different approaches, build evidence, and drive new scientific advances to explore alternative causes and types of reflux. And we’re using state-of-the-art technology to understand this better.
One of our major initiatives is Tummy MOT, our dedicated website launched about 18 months ago. It’s designed to guide people through the truths and myths of digestion – especially around popular products like probiotics, prebiotics, and supplements.
We offer:
- No-nonsense digestive health education
- Unbiased product reviews
- Recipes for patients
- Blogs covering topics like low stomach acid, reflux, and bacterial overgrowth
- Opportunities to join clinical trials
It’s been really popular – nearly 4 million views on social media, over 3,000 participants in our research database, and more than 5,000 email subscribers with a very high engagement rate.
Diet – Balance Over Restriction
When it comes to diet, we don’t support exclusion diets unless necessary. What you need is a varied diet – not too much of any one thing.
For example, when we say “low fat,” we mean low fat, not no fat – a bit of fat is good.
If you’re eating out, taking an alginate like Gaviscon after the meal can help control symptoms.
Carbohydrates are similar. Meals lower in carbs – especially ones low in highly fermentable carbs like onions and garlic—can help, but you don’t need to avoid them completely. Small amounts, if tolerated, are fine. It’s all about common sense.
There is evidence that a low fermentable diet, like the low FODMAP diet, can help – especially in people sensitive to fructose, lactose, or fructans (found in onions and garlic). But this should be done with a dietitian’s guidance.
Alginates – Simple and Effective
- Alginates are great because:
- They don’t suppress stomach acid
- They may have a prebiotic effect (due to fibre content)
- They’re ideal to take after meals and before bed
But timing matters! For best effect:
- Gaviscon should be taken 3–4 times a day, regularly
- PPIs work best when taken an hour before meals
- Alginates should be taken at the right time to work properly
Digestive Enzymes and Intestinal Absorbents
Digestive enzymes can be helpful, especially if you’re having a meal rich in garlic or onions and you know you’ll suffer afterwards.
Juvia, for example, is a natural malt extract that contains enzymes and peptides. It helps break down complex carbs earlier in digestion and can support gut health.
Another tool is Enterosgel, a silicon-based gel that acts like a sponge in the gut. Mixed with water, it soaks up:
- Bacterial toxins
- Inflammatory molecules
- Bile acids
We recommend it:
- When travelling (for traveler’s diarrhoea)
- After a heavy meal (alcohol, onions, fatty food)
- As a rescue remedy to reduce gut irritants
It’s been used successfully for IBS-D and acute diarrhoea, and we hope to study its role in reflux more formally.
Pepto-Bismol: An Old Favourite Revisited
Pepto-Bismol has been around for decades and is making a bit of a comeback. It’s licensed for:
- Reflux
- Nausea
- Stomach irritation
Its mechanism? It inhibits sulfur-producing bacteria, which are linked to:
- Smelly flatulence (due to hydrogen sulfide)
- Diarrhoea and inflammation
- We now have tests to measure hydrogen sulfide in the gut. If you have symptoms like diarrhoea and sulfurous gas, you might benefit from:
- A low-sulfur diet (reduce brassicas, protein-heavy meals)
- Short courses of Pepto-Bismol (5–7 days)
It’s not for long-term use, but it’s a handy option during flares.
Vagus Nerve Stimulation – Calming the Gut-Brain Axis
We’re also looking at how vagal nerve stimulation can help – especially for those whose symptoms are linked to stress, sensitivity, or inflammation.
In previous research, we showed that even putting acid into a healthy oesophagus can sensitise the nerves long-term. But if you stimulate the ear (which is connected to the vagus nerve), you can block that sensitization.
Now, we’re trialling vagal stimulation devices – non-invasive tools used 2–3 times a day for 20 minutes. They may:
- Reduce stress and anxiety
- Improve vagal tone
- Potentially ease reflux, nausea, and stomach symptoms
We’re gathering more data, but it’s a safe, adjunctive therapy worth exploring — especially if symptoms persist despite diet and medication.
Antibiotics for Dysbiosis – When Conservative Measures Fail
If nothing else is working, and you’ve had a positive breath test, then antibiotic treatment for dysbiosis may help.
Rifaximin is a non-absorbable antibiotic that targets gut bacteria.
It’s not widely available, and it’s not effective when used empirically (i.e. without a confirmed diagnosis).
But if used after a positive breath test, it can increase symptom relief by 30–40%.
That’s why it’s worth getting tested first, especially if you have symptoms like bloating, distension, nausea, and PPIs haven’t helped. Talk to your gastroenterologist to decide if this is the right path.
Clinical Trials – Exploring Alternatives to PPIs
We’re also launching the Archimedes Trial, in collaboration with the makers of Gaviscon.
The goal? To intercept reflux early and see if:
- Gaviscon + lifestyle advice, taken four times daily
- Can be as effective as—or even better than—going straight to PPIs
We’ll be randomizing 30 patients in each group and following them for 6 months, tracking:
- Medical outcomes
- Need for further investigations
- Development of bacterial overgrowth
The idea is to build evidence for alternatives to long-term PPI use.
Final Thoughts – Building a More Resilient Gut
To summarise:
- PPIs work for many, but not all. When they don’t, it’s time to explore other causes of reflux.
- Long-term PPIs can affect the microbiome and increase risks like intestinal infections and bacterial overgrowth.
- You can support your gut starting today: eat a varied diet, understand fermentable foods, and consider prebiotics or probiotics.
- Bacterial fermentation by-products may explain symptoms that PPIs don’t resolve – especially throat-based reflux.
- Testing and conservative management can guide a more tailored, effective, and holistic approach.
Ultimately, we’re trying to help people manage their symptoms, build gut resilience, and avoid unnecessary long-term medication. And through clinical trials and collaborations, we’re working hard to build the evidence to support these alternatives.
