IBS, the gut microbiome and antibiotic use: What the evidence says

Does the gut microbiome cause IBS symptoms? A look at current research

Your digestive system is home to trillions of microorganisms. These include bacteria, viruses and fungi that live mainly in your large intestine. Together, they’re called the gut microbiome.

These microbes help with many important jobs in the body. They:

• break down parts of food that humans can’t digest.
  
  
• produce helpful chemicals that support your gut lining.
  
  
• influence your immune system.
  
  
• affect how quickly food moves through your bowel.
  
  
• communicate with your brain through your gut–brain axis.

Irritable bowel syndrome (IBS) is now understood to be a disorder of gut–brain interaction, meaning symptoms arise from interactions between the digestive, nervous and immune systems and environmental factors, such as diet and stress.

Research increasingly suggests that the gut microbiome may play a role in IBS, but microbiome changes seem to be one contributing factor, rather than the sole cause of the condition.

What research shows about the gut microbiome and IBS

Differences in gut bacteria

Studies comparing people with IBS and healthy individuals often find differences in the make-up of the gut microbiome and activity of gut bacteria.

Some studies have found that people with this condition may have:

• Less variety of bacteria in their gut (a less diverse gut microbiome).
  
  
• Lower levels of certain helpful bacteria that normally support digestion and gut health.
  
  
• Differences in how gut bacteria work, including the substances they produce and how they break down food.

However, research findings aren’t always the same. Results often differ between studies and between the different types of IBS. Reviews that analyse many studies together have found that there’s no single gut bacteria pattern that clearly identifies IBS.

Because of this, scientists currently describe these microbiome differences as being linked with IBS, rather than proving that they directly cause the condition.

What is the role of gut bacteria in IBS?

Researchers have suggested several ways that gut bacteria might play a role in IBS symptoms:

Microbial fermentation and gas production

Gut bacteria break down certain carbohydrates that reach your large bowel, by a process called fermentation. During this process, gases and other substances are produced. In some people, these can affect how their gut works and may contribute to bloating and abdominal discomfort.

Microbial metabolites

Gut bacteria produce a range of substances when they break down food. These include short-chain fatty acids (SFCAs – small molecules made when gut bacteria digest fibre), bile acids (chemicals that help digest fats), and other by-products of digestion.

These substances can affect how the gut works, including how quickly food moves through the bowel, how the immune system behaves in the gut, and how well the gut lining acts as a protective barrier.

Changes in these substances may play a role in IBS by affecting bowel habits (such as diarrhoea or constipation) and by increasing gut sensitivity, which can make normal digestive processes feel painful or uncomfortable.

Gut lining and immune activity

Some research suggests that changes in gut bacteria (sometimes called dysbiosis, meaning an imbalance in the gut microbiome) may affect how well the gut lining works as a protective barrier. This may allow small amounts of substances from the gut to interact more with the immune system.

This may be associated with low-grade immune activity in the gut lining. In some people, this may make the nerves in the gut more sensitive and contribute to abdominal pain.

Communication between the gut and brain

Your gut microbiome and nervous system are constantly communicating. Signals travel between them through nerve pathways, immune signals, and chemical substances produced during digestion (such as short-chain fatty acids and bile acids mentioned above).

Changes in these communication pathways may influence how sensitive the gut feels, how the body responds to stress, and how symptoms are experienced for those living with IBS.

Post-infectious IBS: one of the strongest clues

One of the clearest examples linking changes in gut bacteria with IBS is post-infectious IBS. Changes in gut bacteria can develop after a stomach or bowel infection, such as gastroenteritis.

Research reviews suggest that around 1 in 10 people develop IBS after a gastrointestinal infection.

Several explanations have been suggested for why this happens, including:

• Changes in the balance of gut bacteria.
  
  
• Ongoing low-level immune activity in the gut.
  
  
• Changes in how the bowel moves food through the digestive system.
  
  
• Increased sensitivity of the gut nerves, meaning normal digestion may feel painful.

These findings support the idea that disruption to the gut’s normal ecosystem may contribute to long-lasting digestive symptoms in some people.

Antibiotic use and the gut microbiome

Antibiotics are important medicines used to treat bacterial infections. However, they can also affect the balance of bacteria that normally live in the gut.

Studies show that antibiotics can:

• Reduce the variety of gut bacteria.
  
  
• Lower levels of helpful bacteria.
  
  
• Change how gut bacteria process food and produce chemicals.
  
  
• Allow other types of microbes to grow more easily.

Research also suggests that these changes to the gut microbiome may last for months, or sometimes longer, after antibiotic treatment has finished.

Some studies have found that people who have taken antibiotics may be more likely to develop IBS later on, particularly after repeated courses. However, these studies show an association only and can’t prove that antibiotics directly cause IBS.

Why can antibiotics sometimes help IBS?

While certain antibiotics may increase the odds of developing IBS, a type of antibiotic called rifaximin has actually been studied as a treatment for IBS without constipation, especially IBS with diarrhoea (IBS-D). Unlike many antibiotics, rifaximin is poorly absorbed into the bloodstream and mainly works within the gut.

Clinical trials comparing rifaximin with a placebo (a dummy treatment) have found that some people taking rifaximin experience an improvement in overall IBS symptoms.

Studies that combine results from many trials also show a small but meaningful improvement in symptoms for some patients. However, the overall benefit is considered modest, meaning it helps some people but not everyone.

Interestingly, research suggests rifaximin may only cause temporary or limited changes in gut bacteria. This has led researchers to think that its benefits may come from changing how gut bacteria behave or function, rather than permanently changing which bacteria are present.

Do probiotics help IBS?

Probiotics are the gut microbes that make up your gut microbiome. They can also be found in products that contain live microorganisms, usually types of bacteria that are thought to support gut health.

Reviews of many studies suggest that some probiotic products may help improve IBS symptoms, including abdominal pain, overall symptom severity, and sometimes bloating and flatulence (wind/gas).

However, the results are mixed. Research shows that:

• Different studies find different results.
  
  
• Benefits depend on the specific bacterial strain used.
  
  
• The best dose, length of treatment, individual species and strains are still unclear.

Because of this uncertainty, clinical guidance often suggests trying a probiotic for a limited period of time to see whether it helps a person’s symptoms.

Diet, IBS and the gut microbiome

What we eat has a strong influence on the bacteria living in our guts.

One dietary approach often used for IBS is the low-FODMAP diet. This diet reduces the intake of certain types of carbohydrates that are easily fermented by gut bacteria and can trigger symptoms such as gas, bloating and abdominal pain.

Clinical studies show that this diet can reduce IBS symptoms in many people.

However, some research suggests that restricting fermentable carbohydrates,particularly during strict restriction phases, may reduce some helpful bacteria in the gut, including Bifidobacterium species.

For this reason, the low-FODMAP diet is usually recommended as a short-term, structured approach, followed by gradual reintroduction of foods to identify personal triggers.

Fibre and gut bacteria

Some types of dietary fibre appear to support both digestion and gut bacteria.

Soluble fibres, such as psyllium and partially hydrolysed guar gum, have been linked with improvements in IBS symptoms. These fibres can also be fermented by gut bacteria, helping them produce SCFAs (see above), which support gut health.

How to restore gut health after antibiotics IBS

Antibiotics can temporarily change the balance of bacteria in the gut. As mentioned above, research indicates that these changes may last for months, or sometimes even longer, after antibiotic treatment has ended. While the microbiome often begins to recover naturally over time, research suggests that diet and lifestyle patterns can influence how this recovery happens.

There is currently limited scientific evidence to support extreme “gut reset”, detox, or cleansing approaches. Instead, most research supports steady, practical steps that help create an environment where healthy gut bacteria can grow again.

A gradual, food-based approach is usually recommended.

1. Reintroduce a wide range of plant-based foods

Large microbiome studies show that people who eat a greater variety of plant-based foods tend to have greater diversity of gut bacteria.

Plant-based foods provide different types of fibre and natural compounds that act as fuel for beneficial microbes.

Examples include:

• vegetables
• fruits
• whole grains
• beans and lentils
• nuts and seeds
• herbs and spices

Increasing variety, rather than simply increasing quantity of one food, appears to be particularly important for supporting microbial diversity.

2. Include fibre that feeds beneficial bacteria

any gut bacteria rely on dietary fibre as a food source. This enables them to produce substances, such as the SCFAs we discussed above, when they break down fibre, helping to support gut health and healthy digestion.

Gradually increasing fibre intake from whole foods can help support this process. Examples include:

• oats and whole grains
  
  
• beans, lentils and chickpeas
  
  
• vegetables, such as onions, leeks and asparagus
  
  
• fruits, such as apples and berries

Changes should usually be introduced gradually, as rapid increases in fibre can temporarily worsen bloating in some people.

3. Consider fermented foods

Fermented foods (also known as probiotic foods) naturally contain live microbes produced during the fermentation process.

Some intervention studies suggest that regularly eating fermented foods may increase gut microbial diversity and reduce markers of inflammation.

Examples of fermented foods include:

• yoghurt with live cultures
• kefir
• kimchi
• sauerkraut
• miso

While these foods may support microbial diversity, responses vary between individuals.

4. Support your overall digestive health

Other lifestyle factors may also influence the gut microbiome and digestive health, including:

• regular physical activity,
  
  
• adequate sleep,
  
  
• stress management,
  
  
• limiting unnecessary antibiotic use where possible.

These broader lifestyle patterns appear to play an important role in shaping the gut microbiome over time.

Overall, current evidence suggests that supporting microbiome recovery is best approached through long-term dietary diversity and balanced lifestyle habits, rather than short-term “reset” strategies.

Faecal microbiota transplantation (FMT) for IBS

Faecal microbiota transplantation (FMT) involves transferring gut bacteria from a healthy donor into another person’s digestive system.

Although it has been studied as a treatment for IBS, research results have been mixed, and evidence at the time of writing doesn’t support routine use of FMT for IBS.

Routine testing for microbiome “dysbiosis” isn’t currently (at the time of writing) recommended in standard clinical practice for IBS alone, because the evidence is still evolving.

What to expect from antibiotics and IBS symptoms

Microbiome recovery usually happens gradually over weeks to months.

It’s normal for IBS symptoms to fluctuate during this time. Introducing foods slowly and monitoring symptoms can help identify what works best for you.

IBS, antibiotic use and the gut microbiome: Key message

Research increasingly suggests that the gut microbiome may play a role in IBS symptoms. However:

• Changes in gut bacteria vary between individuals
  
  
• No single gut microbiome pattern has been identified for IBS
  
  
• Treatments aimed at the microbiome show mixed and often modest benefits

Current evidence supports a balanced approach, combining dietary strategies, symptom-guided treatment, careful use of antibiotics and attention to overall lifestyle factors, rather than trying to achieve a “perfect” microbiome.

References

1. Canakis A, Haroon M and Weber HC. Irritable bowel syndrome and gut microbiota. Curr Opin Endocrinol Diabetes Obes. 2020 Feb; 27(1): 28-35. doi: 10.1097/MED.0000000000000523.
2. Cryan JF, O’Riordan KJ, Cowan CSM, et al. The Microbiota-Gut-Brain Axis. Physiol Rev. 2019 Oct; 99(4): 1877-2013. doi: 10.1152/physrev.00018.2018.
3. Ford AC, Harris LA, Lacy BE, et al. Systematic review with meta-analysis: the efficacy of prebiotics, probiotics, synbiotics and antibiotics in irritable bowel syndrome. Aliment Pharmacol Ther. 2018 Nov; 48(10): 1044-1060. doi: 10.1111/apt.15001.
4. Ford AC, Sperber AD, Corsetti M, et al. Irritable bowel syndrome. The Lancet. 2020 Nov; 396 (10263): 1675-1688.
5. Ford AC, Quigley EM, Lacy BE, et al. Efficacy of prebiotics, probiotics, and synbiotics in irritable bowel syndrome and chronic idiopathic constipation: systematic review and meta-analysis. Am J Gastroenterol. 2014 Oct; 109(10): 1547-61; quiz 1546, 1562. doi: 10.1038/ajg.2014.202.
6. Goodoory VC and Ford AC. Antibiotics and Probiotics for Irritable Bowel Syndrome. Drugs. 2023 May; 83: 687-699. doi: 10.1007/s40265-023-01871-y.
7. Halmos EP, Power VA, Shepherd SJ, et al. A diet low in FODMAPs reduces symptoms of irritable bowel syndrome. Gastroenterology. 2014 Jan; 146(1): 67-75.e5. doi: 10.1053/j.gastro.2013.09.046.
8. Jernberg C, Löfmark S, Edlund C, et al. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology (Reading). 2010 Nov; 156(Pt 11): 3216-3223. doi: 10.1099/mic.0.040618-0.
9. Khan Z, Khan SK, Reyaz I, et al. Effectiveness of Rifaximin on the Outcomes of Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. Cureus. 2023 Sep; 15(9): e44807. doi: 10.7759/cureus.44807.
10. Li X, Yuan Q, Huang H, et al. Gut microbiota in irritable bowel syndrome: a narrative review of mechanisms and microbiome-based therapies. Front Immunol. 2025 Nov;16 :1695321. doi: 10.3389/fimmu.2025.1695321.
11. McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May 15; 3(3): e00031-18. doi: 10.1128/mSystems.00031-18.
12. Moloney RD, Johnson AC, O’Mahony SM, et al. Stress and the Microbiota-Gut-Brain Axis in Visceral Pain: Relevance to Irritable Bowel Syndrome. CNS Neurosci Ther. 2016 Feb; 22(2): 102-17. doi: 10.1111/cns.12490.
13. Pimentel M, Lembo A, Chey WD, et al. Rifaximin therapy for patients with irritable bowel syndrome without constipation. N Engl J Med. 2011 Jan 364(1): 22-32. doi: 10.1056/NEJMoa1004409.
14. Pittayanon R, Lau JT, Yuan Y, et al. Gut Microbiota in Patients With Irritable Bowel Syndrome-A Systematic Review. Gastroenterology. 2019 Jul; 157(1): 97-108.
15. Shaikh SD, Sun N, Canakis A, et al. Irritable Bowel Syndrome and the Gut Microbiome: A Comprehensive Review. J. Clin. Med. 2023 Mar; 12(7): 2558. doi: 10.3390/jcm12072558.
16. Staller K, Olén O, Söderling J, et al. Antibiotic use as a risk factor for irritable bowel syndrome: Results from a nationwide, case–control study. Alimentary Pharmacology and Therapeutics. 2023 Dec; 58 (11-12): 1175-1184. doi: 10.1111/apt.17736.
17. Staudacher HM, Lomer MCE, Farquharson FM, et al. A Diet Low in FODMAPs Reduces Symptoms in Patients With Irritable Bowel Syndrome and A Probiotic Restores Bifidobacterium Species: A Randomized Controlled Trial. Gastroenterology. 2017 Oct; 153(4): 936-947. doi: 10.1053/j.gastro.2017.06.010.
18. Tap J, Derrien M, Tӧrnblom H, et al. Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome. Gastroenterology. 2017 Jan; 152(1): 111-123.
19. Thabane M, Kottachchi DT and Marshall JK. Systematic review and meta-analysis: The incidence and prognosis of post-infectious irritable bowel syndrome. Aliment Pharmacol Ther. 2007 Aug 26(4): 535-44. doi: 10.1111/j.1365-2036.2007.03399.x.
20. Vandeputte D and Joossens M. Effects of Low and High FODMAP Diets on Human Gastrointestinal Microbiota Composition in Adults with Intestinal Diseases: A Systematic Review. Microorganisms. Oct 2020; 8(11): 1638: doi: 10.3390/microorganisms8111638.
21. Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. Aug 2021; 184(16): 4137-4153.e14. doi: 10.1016/j.cell.2021.06.019.
22. Wielgosz-Grochowska JP, Domanski N and Drywień ME.Efficacy of an Irritable Bowel Syndrome Diet in the Treatment of Small Intestinal Bacterial Overgrowth: A Narrative Review. Nutrients. 2022 Aug; 14(16): 3382. doi: 10.3390/nu14163382.