Can Antibiotics Cause IBS?

Antibiotics can be a lifesaver when fighting infections, but for some people, they may come with unwanted side effects, particularly digestive issues. If you’re struggling with bloating, stomach pain, or worsening IBS symptoms after a course of antibiotics, you’re not alone. Or perhaps you need to take antibiotics but are worried about how they might affect your gut health. If you are seeking personalised advice to help you work out the underlying cause of your gut symptoms, or you’d like to find out how working with a nutritionist could help you, why not book a free 15 minute online consultation with a qualified nutritionist?

In this article, we’ll explore how antibiotics can trigger or worsen IBS symptoms, how long these digestive issues might last, and what you can do to manage and prevent them. With the right strategies, you can protect your gut health and find relief from these uncomfortable symptoms. For more information, take a look at our article on IBS and SIBO Treatment Online.

Do Antibiotics Trigger IBS Symptoms?

Antibiotics work by eliminating harmful bacteria that cause infections, but unfortunately, they can also disrupt the delicate balance of beneficial bacteria in your gut. This disturbance can lead to digestive symptoms that mimic or worsen Irritable Bowel Syndrome (IBS).

How Antibiotics Disrupt Gut Bacteria Balance

Your gut is home to trillions of bacteria that help regulate digestion, immune function, and even mood. Antibiotics don’t distinguish between harmful and helpful bacteria, often wiping out both. This disruption can reduce bacterial diversity in your gut, making it more vulnerable to inflammation, poor digestion, and altered bowel habits – all common features of IBS.

Common Digestive Issues Linked to Antibiotic Use

After taking antibiotics, many people report symptoms like bloating, diarrhoea, constipation, stomach cramps, and gas. For those already with IBS, you may find these symptoms worsen or persist longer. In some cases, antibiotics can even trigger IBS in individuals who have never experienced it before, particularly if the gut microbiome struggles to recover [1].

IBS Symptoms to Look Out for After Taking Antibiotics

After a course of antibiotics, you may experience symptoms similar to IBS, as antibiotics can upset the balance of gut bacteria and trigger digestive issues. Common symptoms include:

Bloating: Persistent swelling or discomfort in the abdomen.
Diarrhoea: Loose, watery stools that may last for days or weeks.
Constipation: Difficulty passing stools, sometimes alternating with diarrhoea.
Stomach pain or cramping: Pain may occur in different parts of the abdomen, often after eating.
Gas: Excessive flatulence or a feeling of fullness in the stomach.
Changes in bowel habits: Irregular or unpredictable bowel movements.

If you notice these symptoms after taking antibiotics, it may indicate post-antibiotic IBS. Monitoring your symptoms and supporting your gut health through diet, probiotics, and hydration can help manage and reduce discomfort. If symptoms persist or worsen, consult a healthcare professional for personalised advice.

Is There a Connection Between IBS and Specific Antibiotics?

Not all antibiotics affect the gut in the same way. Some are more likely to cause or worsen IBS symptoms due to their impact on the gut microbiome. Knowing which antibiotics are more likely to trigger digestive issues can help you make informed choices when discussing treatment options with your doctor.

Choosing the Right Antibiotic

If you are prone to digestive issues or IBS, it’s important to discuss antibiotic options with your doctor. In some cases, targeted antibiotics may be more appropriate to reduce the risk of post-antibiotic IBS symptoms, while probiotics and a gut-supportive diet can help mitigate the effects of broad-spectrum treatments.

Broad-Spectrum vs Targeted Antibiotics: Impact on the Gut Microbiome

When treating bacterial infections, the type of antibiotic used can significantly affect the gut microbiome. Antibiotics are classified as either broad-spectrum or targeted (narrow-spectrum), with each having different effects on beneficial gut bacteria.

Broad-Spectrum Antibiotics

Broad-spectrum antibiotics, such as amoxicillin, ciprofloxacin, and tetracycline, target a wide range of bacteria. These antibiotics are useful for treating infections when the specific bacteria are not yet identified or when multiple bacterial strains are involved. However, they can have a profound impact on the gut microbiome by killing both harmful and beneficial bacteria. This disruption can:

Reduce bacterial diversity in the gut.
Cause imbalances, leading to symptoms like bloating, diarrhoea, and constipation.
Increase the risk of developing or worsening IBS symptoms due to the loss of protective gut bacteria.

Common broad-spectrum antibiotics linked to gut issues include clindamycin and cephalosporins, which are known for causing significant microbiome disturbances [2], [3].

Targeted (Narrow-Spectrum) Antibiotics

Targeted antibiotics are designed to act on specific types of bacteria. Examples include rifaximin (used for IBS with diarrhoea) and penicillin. These antibiotics aim to minimise collateral damage to beneficial bacteria in the gut. They are often chosen to treat infections where the causative bacteria are known.

The impact of targeted antibiotics on the gut microbiome is generally less severe, with:

Lower risk of long-term gut imbalance.
Reduced likelihood of triggering IBS symptoms.
Shorter recovery time for the gut microbiome post-treatment.

Amoxicillin and IBS: What You Need to Know

Amoxicillin is a commonly prescribed broad-spectrum antibiotic used for a range of bacterial infections. While generally well-tolerated, it can still cause gastrointestinal side effects like diarrhoea, bloating, and cramping. For people with IBS, these symptoms may become more pronounced. Unlike some antibiotics that target a broader range of bacteria, amoxicillin has a moderate impact on gut flora, but individual responses can vary [4]. If you’ve experienced gut issues with amoxicillin in the past, it’s worth mentioning this to your doctor.

The Best Antibiotic Options for IBS Management

In cases where antibiotics are necessary, some may be more suitable for IBS patients. Rifaximin, for example, is often used to treat IBS with diarrhoea (IBS-D) as it primarily targets bacteria in the small intestine without significantly disrupting the gut microbiome [5]. Other antibiotics that minimise broad-spectrum effects might also be considered. Always consult your doctor to balance infection treatment with gut health protection.

Can Antibiotics Make Existing IBS Worse?

For those with IBS, antibiotics can sometimes worsen symptoms, leading to increased discomfort and prolonged digestive issues. Understanding why this happens and which antibiotics are higher risk can help you manage your condition more effectively.

Why Antibiotics May Exacerbate IBS Symptoms

Antibiotics can disrupt the natural balance of bacteria in the gut, which plays a crucial role in digestion and overall gut health. When beneficial bacteria are reduced, harmful bacteria may thrive, leading to symptoms like bloating, diarrhoea, constipation, and cramping. This disruption can exacerbate IBS symptoms by causing inflammation, increased gut sensitivity, and changes in bowel habits.

Additionally, antibiotics can slow down the recovery of your gut microbiome, meaning IBS symptoms may persist longer than usual after finishing a course of treatment.

High-Risk Antibiotics for IBS Patients

Broad-spectrum antibiotics, which target a wide range of bacteria, are more likely to trigger or worsen IBS symptoms. These include:

Clindamycin – known for causing severe diarrhoea and gut issues [2]
Cephalosporins – often associated with significant microbiome disruption [3]
Fluoroquinolones (e.g., ciprofloxacin) – linked to long-term gut imbalance in some cases [6].

If you have IBS, your doctor may recommend antibiotics that have a more targeted effect on infection while sparing much of the beneficial gut bacteria. Communicating your concerns about IBS before starting antibiotics can help tailor your treatment to minimise symptoms.

Can Antibiotics Cause Long-Term Stomach Problems?

While antibiotics are crucial for treating infections, their impact on gut health can sometimes extend beyond the short term. For some individuals, especially those with IBS, antibiotics may contribute to prolonged or chronic digestive issues.

Potential Long-Term Effects on Digestion and Malabsorption

Repeated or prolonged use of antibiotics can lead to long-term changes in the gut microbiome, sometimes referred to as dysbiosis [7]. This imbalance may cause ongoing symptoms such as bloating, irregular bowel movements, and increased gut sensitivity. In more severe cases, it can impair the absorption of nutrients, leading to malabsorption conditions.

Malabsorption occurs when the body struggles to break down or absorb essential nutrients, which can result in symptoms like chronic diarrhoea, fatigue, and nutrient deficiencies. Over time, these issues may further aggravate IBS symptoms, creating a cycle of digestive discomfort.

To minimise long-term effects, it’s important to support gut health during and after antibiotic use. This can include dietary changes, probiotics, and regular medical check-ups to monitor digestive function and nutrient levels.

Preventing IBS Caused by Antibiotics

If you’ve been prescribed antibiotics, it’s natural to worry about how they might affect your gut health, especially if you’re prone to IBS. Fortunately, there are steps you can take to minimise the risk of IBS symptoms during and after antibiotic treatment.

How to Prevent Antibiotics Causing IBS if You’ve Been Prescribed a Course of Antibiotics

To protect your gut health, you can take the following precautions to help minimise the effects on your gut health. However, its important to note that no prevention strategy can guarantee prevention of gut health being affected by antibiotic use:

Ask about antibiotic options: Discuss with your doctor whether a more targeted antibiotic might reduce the risk of gut disruption.
Take probiotic supplements: Probiotics help replenish beneficial gut bacteria. Look for strains like Lactobacillus and Bifidobacterium, which support digestive balance. Follow instructions carefully as you may need to allow a certain window of time between taking your antibiotics and taking probiotics in order to receive maximum benefit.
Eat a fibre-rich diet: Foods like fruits, vegetables, and whole grains can nourish good bacteria and promote gut healing.
Stay hydrated: Adequate water intake helps support digestion and reduce constipation or diarrhoea.
Monitor your symptoms: Early intervention can help manage any worsening of symptoms quickly.

How to Prevent Antibiotics Causing IBS in Long-Term or Ongoing Antibiotic Treatment

For those on long-term antibiotics, maintaining gut health is especially important to prevent chronic issues. However, its important to note that no prevention strategy can guarantee prevention of gut health being affected by antibiotic use:

Consider regular probiotic use: Continuous probiotic support may help counteract the depletion of good bacteria over time.
Focus on gut-healing foods: Include prebiotic foods (such as bananas, onions, and asparagus) to feed healthy bacteria.
Space out antibiotics and probiotics: Take probiotics at least two hours after your antibiotics to maximise their effectiveness.
Work with a specialist: A gastroenterologist or functional medicine trained nutritionist can help you develop a tailored gut health plan to minimise long-term side effects.

By being proactive, and seeking help from a qualified nutritionist, you can reduce the likelihood of IBS symptoms while benefiting from the necessary antibiotic treatment.

Healing Gut Health After Antibiotics

If you’ve recently completed a course of antibiotics and are experiencing IBS symptoms such as bloating, stomach pain, or irregular bowel movements, it’s important to take steps to help your gut recover and restore balance.

How to Heal IBS Symptoms Caused by Antibiotics After Finishing Antibiotic Treatment

The gut microbiome can take time to recover after antibiotic treatment. Here are steps you can take to support healing:

Increase fibre intake: Soluble fibre (found in oats, bananas, and sweet potatoes) can help regulate bowel movements and ease bloating.

Stay hydrated: Adequate hydration helps reduce cramping and supports smoother digestion. Adequate water intake varies based on factors like age, body size, activity level, and climate, but general guidelines recommend the following:

Daily Water Intake Recommendations

Men: Around 3.7 litres (about 13 cups) per day, including water from food and beverages.
Women: Around 2.7 litres (about 9 cups) per day, including water from all sources.

For most people, aiming for 6-8 glasses (1.5 to 2 litres) of water per day is a good starting point. To stay hydrated, sip water regularly throughout the day rather than drinking large amounts all at once. Foods like fruits and vegetables (e.g., cucumbers, watermelon) also contribute to hydration. If you’re dealing with IBS or gut issues, hydration is particularly important to support digestion and bowel regularity.

Avoid trigger foods: For those with IBS, foods high in fat, sugar, or FODMAPs may worsen symptoms and should be limited until symptoms stabilise. FODMAPs are fermentable short-chain carbohydrates that can trigger IBS symptoms by causing bloating, gas, and diarrhoea in sensitive individuals. Foods high in FODMAPs include onions, garlic, wheat, apples, and beans.

Monitor symptoms: Keeping a symptom diary can help you or your nutritionist identify what works best for your recovery.

Strategies to Relieve Bloating and Other Symptoms

Antibiotic-related bloating and discomfort can persist, but these strategies may help alleviate symptoms:

Gentle physical activity: Light exercises like walking or yoga can help reduce bloating by stimulating digestion.
Peppermint oil supplements: Peppermint has natural anti-spasmodic properties that can ease bloating and cramping.
Warm compress: Applying a warm compress to your abdomen may help relax tight muscles and reduce discomfort.

Restoring Gut Health with Diet and Probiotics

Rebuilding a healthy gut microbiome is key to long-term recovery. Focus on:

Probiotics: Supplement with probiotics that include beneficial strains like Lactobacillus and Bifidobacterium. Fermented foods like yoghurt, kefir, and sauerkraut can also help.

Prebiotic foods: Support probiotic growth with prebiotic-rich foods, including oats, bananas (ripe), carrots, chia seeds, and potatoes. These foods can help support gut health without exacerbating IBS symptoms.

Balanced diet: A diet rich in diverse, plant-based foods can promote microbiome diversity, speeding up recovery and reducing IBS symptoms.

With these strategies, you can improve gut function, ease symptoms, and support long-term digestive health after antibiotics.

How Quickly Can You See Improvements?

The speed of recovery after antibiotics depends on whether you are dealing with antibiotic-triggered IBS or chronic IBS.

Antibiotic-triggered IBS (also known as post-antibiotic IBS) may resolve over time as the gut microbiome recovers. With proper care, including probiotics, prebiotic-rich foods, and a healthy diet, improvements can typically be seen within 4-8 weeks [8]. Some individuals may experience a full recovery, especially if their gut health stabilises.
Chronic IBS, on the other hand, tends to be a long-term condition. While symptoms can be significantly reduced or managed through diet and lifestyle changes, IBS often involves ongoing sensitivity to certain triggers, meaning flare-ups may still occur.

Can IBS Be Treated Permanently?

For those with antibiotic-triggered IBS, there is a higher likelihood that symptoms can be resolved with consistent gut-healing strategies, particularly if the gut microbiome is restored successfully. In contrast, general IBS is a chronic disorder. While it cannot typically be cured, many people achieve lasting symptom relief by managing triggers such as stress, diet, and gut irritants. This allows for extended periods of minimal or no symptoms, improving their overall quality of life.

In both cases, it is important to work closely with specialist health practitioners, such as functional medicine practitioners and nutritionists, to determine whether your symptoms are likely to be temporary, chronic or aggravated. They can offer IBS Tests and analyse the results, developing a personalised plan to help restore balance and improve long-term digestive health.

Conclusion

Whether you suspect you have IBS or are dealing with other gut and fatigue-related problems, IBS Clinics can support you in addressing your health concerns. Digestive health plays a critical role in overall well-being. If your body isn’t able to eat, drink, digest, absorb, detoxify, and excrete properly, achieving optimal health becomes almost impossible. That’s why we prioritise improving gut function as a foundation for your long-term health.

Once your gut is functioning optimally, the body is better equipped to absorb nutrients and detoxify itself, often resolving other underlying health issues. We also recognise that many people operate with chronically low energy, which can make life feel exhausting. Unfortunately, pharmaceuticals often target symptoms rather than the root causes and can bring unwanted side effects.

At IBS Clinics, we offer personalised health therapies designed to provide long-term solutions to your health problems. If you’re feeling fatigued or are experiencing chronic digestive issues, we will work with you to restore balance in both your body and mind. Our goal is not just symptom management but to help you optimise how you feel and think about your health holistically.

Let us guide you on the path to better gut health and greater overall vitality. Together, we’ll develop a plan tailored to your unique needs, helping you overcome chronic symptoms and regain control of your health.

References

Krogsgaard et al. (2018) Antibiotics: a risk factor for irritable bowel syndrome in a population-based cohort. Scandinavian journal of gastroenterology. https://pubmed.ncbi.nlm.nih.gov/30189148/
Rashid et al. (2015) Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. https://pubmed.ncbi.nlm.nih.gov/25922405/
Wang et al. (2022) Cephalosporins-induced intestinal dysbiosis exacerbated pulmonary endothelial barrier disruption in streptococcus pneumoniae-infected mice. Frontiers in cellular and infection microbiology. https://pubmed.ncbi.nlm.nih.gov/36093187/
Olivares et al. (2025) A modelling framework to characterize the impact of antibiotics on the gut microbiota diversity. Gut microbes. https://pubmed.ncbi.nlm.nih.gov/39711113/
Chey et al. (2020) Mechanism of action and therapeutic benefit of rifaximin in patients with irritable bowel syndrome: a narrative review. Therapeutic advances in gastroenterology. https://pubmed.ncbi.nlm.nih.gov/32047534/
Dethlefsen and Relman (2011) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences of the United States of America. https://pubmed.ncbi.nlm.nih.gov/20847294/
Zyl et al. (2022) Effect of antibiotics on the human microbiome: a systematic review. International journal of antimicrobial agents. https://pubmed.ncbi.nlm.nih.gov/34929293/
Yoon et al. (2014) Effect of multispecies probiotics on irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial. Journal of gastroenterology and hepatology. https://pubmed.ncbi.nlm.nih.gov/23829297/

Author – Tracey Randell

At IBS Clinics, Tracey Randell, a renowned Nutritional Therapist and one of the few IFM Certified Practitioners in the UK, extends her specialised knowledge and unique approach to managing and treating IBS and other gut-related conditions effectively.

Tracey’s profound understanding of Functional Medicine allows her to connect the dots for complex health conditions, identifying and addressing the root causes to curate personalised and comprehensive health plans for her patients. Her holistic approach focuses on resolving underlying imbalances and optimising gut health, enabling the body to correct other issues and attain overall well-being.

At IBS Clinics, we are dedicated to being your partner in navigating your gut-related health concerns, offering expert care and individualised treatment plans to alleviate your IBS symptoms and enhance your quality of life.

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