The Relationship Between PPIs and Gut Microbiome
Proton pump inhibitors (PPIs) are widely prescribed to reduce acid production in the stomach, treating conditions like acid reflux, gastro-oesophageal reflux disease (GERD), and stomach ulcers.
While they’re highly effective, doctors are increasingly noticing a connection between PPI usage and the gut microbiome. Your gut is home to trillions of microorganisms that support core functions, including digestion, vitamin synthesis, and even heart and brain health.
Specialists at our gut microbiome clinic and researchers alike are exploring how changes in stomach acidity can alter this delicate balance of bacteria throughout the digestive tract. But what are the effects of PPIs on the gut microbiome? And can they negatively impact your health?
What are Proton Pump Inhibitors?
Proton pump inhibitors (PPIs) reduce stomach acid by blocking the proton pumps in gastric cells. Protons (or H+ ions) are what determine if something is acidic. Blocking these pumps will continue lowering the acidity in the stomach for as long as you take the medication.
Common examples of PPIs include omeprazole, lansoprazole, and pantoprazole.
PPIs are a first-line treatment for people with persistent or severe acid reflux. Continual acid reflux can damage the oesophagus and stomach lining, potentially causing permanent damage. But by reducing acid production, it also alters the digestive environment — setting the stage for microbiome changes.
The Effects of PPIs on Gut Health
Your gut microbiome is highly sensitive to what you consume. Dietary changes, such as eating ultra-processed foods, can have a major impact on the composition of your gut microbiota. But this is also true of PPIs.
In one study, PPI use was associated with a sharp decrease in microbial diversity and caused changes in 20% of bacterial species. There was a big increase in oral bacteria, especially Enterococcus, Streptococcus, Staphylococcus, and the potentially pathogenic species Escherichia coli.
The risk of a Clostridioides difficile (C. difficile) infection is a concern. C. difficile infections cause severe diarrhoea and inflammation, often after taking antibiotics. Another issue is small intestinal bacterial overgrowth (SIBO), which often leads to bloating, abdominal pain, nausea, and or diarrhoea.
Many of the “good” microbes in our gut serve crucial functions — for example, synthesising certain vitamins, aiding in the absorption of nutrients, regulating the immune system, and digesting fibre. Altering the microbiome via PPIs can cause:
Reduced synthesis of essential vitamins such as B12, K, and folate, as the bacteria responsible for producing them decline.
Impaired breakdown of dietary fibre, lowering levels of short-chain fatty acids that nourish the gut lining and reduce inflammation.
Weakened regulation of the immune system, increasing susceptibility to infection and inflammation.
Reduced protection against harmful pathogens that healthy bacteria normally keep in check.
Disrupted signalling between the gut and brain, which can influence mood, stress response, and cognitive function.
Can You Restore Your Gut Microbiome After PPIs?
In short, yes.
Your gut microbiome is wholly unique to you. Even between identical twins, the gut microbiome is only 30-40% similar. So, it may not be possible to restore your original gut microbiome. But you can return it to a balanced, diverse, and healthy gut flora that supports your health.
Here’s how:
Eat a diet rich in prebiotics and probiotics. Prebiotics are a type of fibre that feeds your beneficial bacteria. They’re found in bananas, onions, garlic, leeks, oats, asparagus, and more. Probiotics are the live beneficial bacteria themselves. Introduce them with fermented foods like yoghurt, kefir, sauerkraut, and kimchi.
Gradually decrease your use of PPIs. If possible, address the underlying cause of your acid reflux. You can then slowly decrease your use of PPIs and return your digestive tract to normal.
Get your microbiome tested. You can’t know if your gut microbiome is disrupted without getting tested. The Functional Gut Clinic offers stool microbiome analysis, using the latest techniques to determine the species composition, diversity, and effects of your current microbiome.
Limit your intake of ultra-processed foods. Some ultra-processed foods are as bad for your gut as they are for you. These foods feed the negative bacteria and microbes, disrupting normal gut function.
When Are PPIs Still Necessary?
In some cases, PPIs will still be necessary.
PPIs remain vital for certain conditions — like Barrett’s oesophagus, peptic ulcers, and severe GERD — where the downsides to gut bacteria are outweighed by the negative effects of excessive stomach acid.
That being said, you can alter your lifestyle to reduce your dosage or try alternative medications like H2 blockers. Never stop PPIs abruptly or without medical advice.
Get Your Microbiome Tested
If you’re worried about the link between proton pump inhibitors (PPIs) and your gut microbiome, the best option is to get tested. The Functional Gut Clinic offers a suite of tests that analyse your gut microbiome, diagnose SIBO, and tackle other microbe-related gut problems.
Book your test today to take control of your health and resolve any PPI and gut microbiome issues.
