Proton pump inhibitors (PPIs) are among the most commonly used medicines for reducing stomach acid. Millions of people rely on them to relieve acid reflux, indigestion, and to protect against stomach ulcers, including for people who take anti-inflammatory painkillers such as naproxen. While they can be very effective at managing symptoms, growing evidence suggests that long-term use of PPIs may affect gut health, especially the balance of your gut microbiome.
This guide explains how PPIs such as omeprazole and lansoprazole work, the side effects people most often ask about, what long-term use may mean for your gut bacteria, and where testing and diet may help. It is for information only and is not a reason to stop or change a medicine your doctor has prescribed. If a PPI is causing you problems, the right next step is to speak to your GP or pharmacist, not to stop on your own.
How PPIs work
Proton pump inhibitors work by stopping the proton pumps in your stomach lining from working properly. Proton pumps are the tiny structures that help the stomach to produce acid, which is then used to digest food.
Taking a proton pump inhibitor reduces how much acid the stomach makes, which eases the symptoms of problems like acid reflux and gastro-oesophageal reflux disease (GORD). It also helps stomach ulcers to heal, because there is less acid to irritate them.
When you start a proton pump inhibitor you may feel better within a day or so, but it can take up to 4 weeks to reach its full effect, so you may still notice some acid symptoms during the first month.
Stomach acid does more than break down food. It also:
- Breaks down food
- Helps you absorb key nutrients
- Kills many of the harmful bacteria that enter the body through food and drink
By lowering stomach acid, PPIs relieve symptoms such as:
- Heartburn
- Acid reflux
- Gastro-oesophageal reflux disease (GORD)
- Stomach ulcers
- Indigestion
That same drop in acid is also why PPIs can affect the gut. Because stomach acid acts as a barrier to harmful microbes, suppressing it over the long term can shift the environment further down the digestive system, leading to changes in the gut microbiome and, in some people, imbalances.
Do PPIs affect the gut microbiome?
Yes. The gut microbiome is the community of trillions of bacteria, fungi and other microbes that lives mainly in the large intestine and relies on a fairly stable environment to work well.
In one of the largest studies to look at this, researchers examined the gut bacteria of 1,815 people and found that PPI users had a measurably lower variety of bacteria in their gut, along with a rise in bacteria more typically found in the mouth and in some potentially harmful species. The authors noted that, at a population level, the effect of PPIs on the gut microbiome was more pronounced than that of antibiotics (Imhann F, et al. (2016). Proton pump inhibitors affect the gut microbiome. Gut. https://pubmed.ncbi.nlm.nih.gov/26657899/).
Across the research, PPI use has been linked to:
- A lower variety of bacteria, including a reduction in beneficial types such as Lactobacillus and Bifidobacterium
- A rise in potentially harmful bacteria
- A higher risk of SIBO (small intestinal bacterial overgrowth), where bacteria that usually live in the colon increase in the small intestine
- Greater vulnerability to gut infections, including Clostridioides difficile (previously called Clostridium difficile)
The SIBO link is one of the better studied. A review that pooled 19 studies covering just over 7,000 people found that PPI users were moderately more likely to have SIBO than non-users (Su T, et al. (2018). Meta-analysis: proton pump inhibitors moderately increase the risk of small intestinal bacterial overgrowth. Journal of Gastroenterology. https://pubmed.ncbi.nlm.nih.gov/28770351/). A more recent review of 29 studies reached a similar conclusion and found that the risk rose the longer someone stayed on a PPI (Khurmatullina AR, et al. (2025). The duration of proton pump inhibitor therapy and the risk of small intestinal bacterial overgrowth: a systematic review and meta-analysis. Journal of Clinical Medicine. https://pubmed.ncbi.nlm.nih.gov/40649078/).
These shifts may help explain why some people notice bloating, wind, or changes in bowel habit during or after a long course of a PPI. It is worth keeping this in proportion: most of this research shows an association rather than proof of cause, and for many people short courses cause no lasting change at all.
The most common PPIs
Several PPIs are in regular use in the UK. Their effect on acid is broadly similar, and each may affect the gut slightly differently depending on the dose, how long it is taken, and the individual. The two you are most likely to be prescribed are omeprazole and lansoprazole.
Omeprazole
Omeprazole is one of the most commonly prescribed PPIs in the UK and is also available in lower doses over the counter for heartburn and indigestion.
It works by reducing how much acid your stomach produces, which makes it effective for stomach ulcers and acid reflux. Aside from lowering acid, it can help the stomach and oesophagus heal from acid damage. Always take it as instructed, and do not take more than the recommended amount if you do not feel better straight away.
Does omeprazole cause bloating, gas and stomach pain?
Bloating, wind and mild stomach discomfort are among the side effects people most often ask about with omeprazole, and they are listed among its recognised side effects. There are two separate reasons this can happen. In the short term, changes in how food is broken down when there is less stomach acid can leave some people feeling more bloated or windy. Over a longer course, the shift in gut bacteria described above, including a greater chance of SIBO, can produce similar symptoms (Su T, et al. (2018), as above).
Persistent stomach pain is not something to put up with or self-diagnose. If it is new, severe, or lasting, speak to your GP or pharmacist so the cause can be checked properly rather than assumed.
Does omeprazole cause constipation or diarrhoea?
Both constipation and diarrhoea are listed side effects of omeprazole, and people can experience either. Diarrhoea in particular is worth mentioning to a pharmacist or GP if it is severe or persistent, because reducing stomach acid can make the gut a little more vulnerable to infections such as C. difficile. A recent review found that the risk of C. difficile infection rose with both the dose and the duration of PPI treatment, though the overall risk for any one person remains low (Finke M, et al. (2025). Proton pump inhibitors and the risk of Clostridioides difficile infection: a systematic review and dose-response meta-analysis. Journal of Infection. https://pubmed.ncbi.nlm.nih.gov/40239816/).
Lansoprazole
Lansoprazole is another frequently used PPI, often prescribed for GORD, ulcers, and more severe reflux. It is a prescription-only medicine that can be taken by both adults and children, but only when a doctor has prescribed it. It is used for heartburn and acid reflux, GORD, and to treat and prevent stomach ulcers, and occasionally for a rare condition called Zollinger-Ellison syndrome.
Like other PPIs, lansoprazole works by stopping the proton pumps in your stomach lining from working, so your stomach makes less acid.
Does lansoprazole cause bloating or constipation?
Bloating, wind, stomach pain and changes in bowel movements, including constipation, are all recognised side effects of lansoprazole. As with omeprazole, part of this can come from the drop in stomach acid changing how food is digested, and part may come from longer-term changes in gut bacteria. A 2023 review of how PPIs affect the gut set out these mechanisms and looked at whether live-culture supplements might help offset them (Kiecka A, Szczepanik M (2023). Proton pump inhibitor-induced gut dysbiosis and immunomodulation: current knowledge and potential restoration by probiotics. Pharmacological Reports. https://pubmed.ncbi.nlm.nih.gov/37142877/).
How long does lansoprazole take to work?
Many people notice some improvement within a day or two, but as with other PPIs it can take up to 4 weeks to feel the full benefit. If you have taken it as prescribed for several weeks and your symptoms have not improved, that is a reason to go back to your GP or pharmacist rather than to increase the dose yourself.
What are the long-term effects of PPIs?
Short courses of PPIs are generally safe and well tolerated. It is long-term or high-dose use, often over many months or years, that is linked with a greater chance of effects on the gut.
Potential concerns with extended PPI use include:
- Persistent imbalance in the gut bacteria
- Reduced absorption of some nutrients, particularly magnesium and vitamin B12. The way PPIs affect magnesium in particular has been studied in detail (Gommers LMM, et al. (2022). Mechanisms of proton pump inhibitor-induced hypomagnesemia. Acta Physiologica. https://pubmed.ncbi.nlm.nih.gov/35652564/)
- A higher chance of gut infections, including C. difficile
- A weaker gut barrier, which can lead to increased intestinal permeability, sometimes called "leaky gut"
None of this means a PPI is the wrong medicine for you. For many people the benefit of controlling reflux or protecting the stomach clearly outweighs these risks. It is a reason to make sure you are on the lowest dose that works for the shortest time you need it, which is a conversation to have with your GP or pharmacist, and never a decision to make alone.
When to speak to your GP or pharmacist
See a pharmacist or GP if you have been on a PPI for a long time and want to review whether you still need it, or if you have ongoing bloating, wind or changes in bowel habit that are bothering you.
Some symptoms need prompt medical attention rather than a diet or testing plan. Speak to your GP, or seek urgent advice, if you have any of the following:
- Blood in your stool, or black, tarry stools
- Unexplained weight loss
- A persistent change in bowel habit lasting more than three weeks
- Difficulty or pain when swallowing
- Persistent vomiting, or vomiting blood
- New digestive symptoms that start over the age of 50, or a family history of bowel or ovarian cancer
These can have many causes, but they should always be assessed by a clinician rather than investigated at home.
Supporting your gut alongside a PPI
If you take a PPI regularly, there are things that may support your gut health at the same time. None of these is a reason to stop your medicine, and they work best alongside it rather than instead of it.
Diet
- Eat more prebiotic fibre: leeks, onions, oats, garlic, and bananas
- Limit ultra-processed foods and refined sugars
- Reduce personal trigger foods such as alcohol, spicy food, caffeine, and large fatty meals
- Include fermented foods if you tolerate them, such as kefir, live yoghurt, sauerkraut, or kimchi
Diet changes suited to acid reflux and gut health are usually the first thing tried before, or alongside, a PPI.
Live cultures
Foods and supplements containing live cultures, such as certain Lactobacillus and Bifidobacterium species, are being studied for whether they help restore microbial balance during or after PPI use. The evidence is still developing and results vary between people, so treat this as something that may help rather than a proven fix (Kiecka A, Szczepanik M (2023), as above). If you are considering a supplement while on other medicines, check with your pharmacist first.
Understanding your own gut
Because PPIs affect people differently, a broad view of your own gut bacteria can be more useful than general advice. A gut microbiome test that measures a wide range of gut bacteria can show whether your own balance looks disrupted, which can then guide diet changes. A test like this may help identify imbalances, low diversity, or markers linked with inflammation. It does not diagnose any condition, and it is not a substitute for seeing your GP about symptoms.
In summary
Proton pump inhibitors are widely used and effective medicines for acid-related problems. They are not without an effect on the gut microbiome, especially when taken long term, and side effects such as bloating, wind and changes in bowel habit are common reasons people have questions about them.
If you take omeprazole or lansoprazole and something does not feel right, the useful next step is a conversation with your GP or pharmacist about whether the dose and length of treatment are still right for you. Supporting your gut through diet, live cultures where they help, and understanding your own microbiome can sit alongside that, never instead of it.
Sources
- Imhann F, et al. (2016). Proton pump inhibitors affect the gut microbiome. Gut. https://pubmed.ncbi.nlm.nih.gov/26657899/
- Su T, et al. (2018). Meta-analysis: proton pump inhibitors moderately increase the risk of small intestinal bacterial overgrowth. Journal of Gastroenterology. https://pubmed.ncbi.nlm.nih.gov/28770351/
- Khurmatullina AR, et al. (2025). The duration of proton pump inhibitor therapy and the risk of small intestinal bacterial overgrowth: a systematic review and meta-analysis. Journal of Clinical Medicine. https://pubmed.ncbi.nlm.nih.gov/40649078/
- Finke M, et al. (2025). Proton pump inhibitors and the risk of Clostridioides difficile infection: a systematic review and dose-response meta-analysis. Journal of Infection. https://pubmed.ncbi.nlm.nih.gov/40239816/
- Kiecka A, Szczepanik M (2023). Proton pump inhibitor-induced gut dysbiosis and immunomodulation: current knowledge and potential restoration by probiotics. Pharmacological Reports. https://pubmed.ncbi.nlm.nih.gov/37142877/
- Gommers LMM, et al. (2022). Mechanisms of proton pump inhibitor-induced hypomagnesemia. Acta Physiologica. https://pubmed.ncbi.nlm.nih.gov/35652564/
