SIBO and Crohn's Disease: Treatment Options

SIBO and Crohn’s share symptoms like bloating, pain, and nutrient deficiencies, but they need different treatments. While Crohn’s requires careful medical management, SIBO may be addressed with breath testing, dietary strategies, and antibiotics. IBS Clinics offers testing, consultations, and an online course to support patients managing both conditions.

Living with Crohn’s disease often means dealing with unpredictable flare-ups, food worries, and the constant effort to keep your digestion as stable as possible. For some people, though, even when Crohn’s seems under control, symptoms like bloating, diarrhoea, pain, or fatigue persist. This can be confusing and frustrating, and it’s one reason why doctors and nutrition practitioners are paying closer attention to the overlap between Crohn’s and Small Intestinal Bacterial Overgrowth (SIBO).

SIBO occurs when too many bacteria build up in the small intestine, interfering with digestion and nutrient absorption. Because Crohn’s can affect gut motility, surgery history, and even immune responses, people with Crohn’s may be at higher risk of developing SIBO alongside their existing condition.

The good news is that with the right testing, treatment strategies, and support, it’s possible to identify when SIBO is playing a role and take steps to manage both conditions more effectively.

In this article, we’ll explore the connection between SIBO and Crohn’s, look at the treatment options available, and share practical ways to support your gut health. We’ll also highlight how the team at IBS Clinics can provide personalised testing (take a look at our article SIBO Test UK Cost for more details on how to access this test affordably from home), practitioner-led guidance, and structured strategies for how to treat SIBO at home, to help you take control of your symptoms and feel more confident in daily life.

Understanding the Link Between SIBO and Crohn’s Disease

Small Intestinal Bacterial Overgrowth (SIBO) happens when too many bacteria build up in the small intestine – a part of the gut that normally contains relatively low levels of bacteria compared with the large intestine. Think of the small intestine as a motorway that usually flows smoothly with light traffic. When too many vehicles pile in, congestion builds, movement slows down, and problems start to appear.

Many of the symptoms of SIBO, such as bloating, abdominal pain, diarrhoea, constipation, and nutrient deficiencies, overlap with those of Crohn’s disease [1]. This overlap can make it hard to tell whether ongoing symptoms are caused by Crohn’s itself or by bacterial overgrowth in the small intestine. For some people, treating SIBO can help relieve digestive distress that persists even when Crohn’s seems otherwise well-managed.

People with Crohn’s may be more prone to developing SIBO for several reasons:

Gut motility changes – Inflammation or scarring from Crohn’s can slow down the natural movement of the gut, creating an environment where bacteria can stagnate and multiply [2].
Surgery – Operations such as bowel resections can change the structure of the small intestine. These changes may lead to “blind loops” or narrowed sections where bacteria can collect [3].
Medications – Some treatments for Crohn’s, including immunosuppressants and steroids, can alter the balance of bacteria or weaken the gut’s natural defences [4].

These factors mean that Crohn’s patients often have “perfect storm” conditions for bacterial overgrowth – slower movement, altered anatomy, and reduced protective barriers. Identifying SIBO in Crohn’s patients is therefore an important step, because treating it may ease symptoms and improve nutrient absorption without changing Crohn’s medication plans.

Shared Symptoms and Why Diagnosis Matters

If you live with Crohn’s disease, you’ll already know how exhausting it can be when symptoms flare up: the bloating after meals, the rushing to the toilet, or the heavy fatigue that makes even simple tasks harder. What can feel particularly discouraging is when these problems continue even though your Crohn’s seems “under control.” This is where Small Intestinal Bacterial Overgrowth (SIBO) may be playing a role.

The difficulty is that SIBO and Crohn’s share many of the same symptoms: bloating, diarrhoea, abdominal pain, constipation, and even nutrient deficiencies like low iron or vitamin B12 [5]. It’s no wonder many people end up feeling confused, wondering why their body still isn’t responding the way they’d hoped.

Why accurate testing matters for you

This is where testing becomes so valuable. Without it, you may be left second-guessing – is it Crohn’s, or is something else going on? By identifying whether SIBO is present alongside Crohn’s, you can finally understand what’s driving your symptoms. For many people, that knowledge alone is empowering. It gives you and your practitioners a clearer path forward and helps avoid unnecessary changes to Crohn’s medication when the issue might actually be bacterial overgrowth [6].

How the SIBO breath test helps you move forward

The SIBO breath test is a simple, non-invasive way of getting those answers. After drinking a sugar solution, your breath is measured for hydrogen and methane gases. High levels show that bacteria are fermenting food in the small intestine, where they shouldn’t be [7].

For people with Crohn’s, this test can be a turning point. Instead of living with uncertainty, it gives you clarity. And with clarity comes choice and the chance to explore targeted strategies, from diet to supplements and beyond, that may ease your daily discomfort and move you closer to a better quality of life.

Conventional Treatment Options for Crohn’s and SIBO

If you have Crohn’s disease, you’ll know how carefully it needs to be managed. Standard treatments such as anti-inflammatories, immunosuppressants, biologic therapies, and sometimes surgery are essential in controlling inflammation, protecting the gut, and preventing long-term complications [8]. These treatments are the foundation of Crohn’s care and remain vital in helping many people maintain stability.

But what if, even with these in place, you’re still living with bloating, diarrhoea, pain, or fatigue? This is where SIBO may be contributing to your symptoms. Unlike Crohn’s, which is an inflammatory bowel disease, SIBO is about bacterial overgrowth in the small intestine. The treatment options are different, and they can be combined with Crohn’s care when appropriate.

For SIBO, conventional treatment often starts with antibiotics such as rifaximin, which are designed to reduce bacterial overgrowth. Some people also find benefit from dietary changes (such as low-FODMAP or adapted elimination diets) and targeted supplements that support digestion, motility, or bacterial balance [9].

Where these approaches overlap is in the shared goal of helping you feel better day to day. Where they differ is in what they target: Crohn’s treatments control inflammation, while SIBO treatments focus on restoring balance in the small intestine.

If you’ve been doing all the right things for Crohn’s but still feel unwell, it may be worth exploring whether SIBO is part of the picture. The encouraging news is that this dual issue can be tackled with more than one approach. For many people, identifying and treating SIBO alongside their Crohn’s management plan has provided relief they hadn’t experienced before. It’s not about replacing your Crohn’s care but about adding another piece of the puzzle so you can move closer to the life you’ve been hoping for.

Dietary Strategies to Support Gut Health

Food plays a huge role in how both Crohn’s and SIBO show up day to day. The right dietary strategies can make a noticeable difference, not as a cure, but as a way to reduce symptoms, support healing, and give you back more control over how you feel.

Low FODMAP or adapted diets for SIBO

For people with SIBO, certain carbohydrates called FODMAPs can ferment in the small intestine and make symptoms worse. This is why a low-FODMAP diet, or an adapted version of it, is often recommended for a short time [10]. By reducing these fermentable foods, you can often ease bloating and discomfort while giving the gut a calmer environment in which to recover. Importantly, this approach is usually temporary and should be guided by a practitioner to avoid unnecessary restriction.

Anti-inflammatory approaches for Crohn’s

For Crohn’s, the focus is often on anti-inflammatory eating. Diets rich in whole, unprocessed foods, lean proteins, omega-3 fats, and easily digestible fruits and vegetables can help support overall gut health. Some people also benefit from avoiding ultra-processed foods and limiting high-fat or spicy meals that may worsen flare-ups [11]. Unlike SIBO-focused diets, the goal here is less about fermentation and more about reducing irritation and inflammation in the digestive tract.

How tailored nutrition helps manage both conditions

When Crohn’s and SIBO overlap, nutrition needs to be tailored to both conditions at the same time. For example, someone might follow a modified low-FODMAP plan to reduce fermentation while also making anti-inflammatory choices that are gentle on the bowel. This is where professional support can make a big difference: the right food plan can help you avoid unnecessary restriction while still targeting the key drivers of your symptoms.

In practice, that means you can eat in a way that feels safe, reduces discomfort, and still nourishes your body, giving you more energy and confidence in daily life.

Living Well With Crohn’s and SIBO

When Crohn’s and SIBO overlap, day-to-day life can feel unpredictable. The good news is that there are practical steps you can take to feel more comfortable and supported, but it’s important to always do this in consultation with your medical team. Crohn’s disease can cause complications that require specialist care, and any new strategy should be agreed with your doctor or gastroenterologist.

Practical tips for daily life

Prioritise rest and stress management – Stress can worsen digestive symptoms, so finding calming routines (gentle exercise, mindfulness, or breathing techniques) can help support overall wellbeing.
Eat balanced, gentle meals – Work with your care team to identify foods that are easier on your digestion, while making sure you’re still getting the nutrients you need.
Stay consistent with appointments – Regular check-ins with your doctor help ensure Crohn’s remains properly managed and monitored.
Probiotics and supplements – These may be discussed as part of your care, but they should always be introduced under professional guidance to avoid worsening symptoms.

How IBS Clinics can help

At IBS Clinics, we work alongside your medical care to provide supportive tools and guidance for managing SIBO in a safe and structured way:

SIBO breath test – A non-invasive test to identify whether bacterial overgrowth is present and what type (hydrogen, methane, mixed, or sulphide).
Online SIBO course – A 6-module, practitioner-led programme you can complete at home and at your own pace. It includes tailored food plans by SIBO type, step-by-step supplement and testing guidance, hormone-aware symptom tracking, and downloadable tools such as trackers and meal plans.
Private consultations – One-to-one sessions with nutritionists and functional medicine practitioners, offering tailored advice and support designed around your symptoms and needs.

With Crohn’s, medical supervision is always the priority. But by combining your Crohn’s management plan with safe, structured support for SIBO, many people find they can reduce daily discomfort, feel more in control, and take steady steps towards a better quality of life.

Conclusion: Next Steps for Patients With Crohn’s and SIBO

Living with Crohn’s disease is already complex, and when SIBO is added into the mix, it can feel like one more obstacle standing in the way of feeling well. The good news is that both conditions can be managed, often more effectively when they are recognised and treated together.

Standard Crohn’s treatments such as anti-inflammatories, biologics, or surgery remain essential, but alongside them, SIBO-focused options like antibiotics, dietary adjustments, and targeted supplements may provide additional relief when symptoms persist.

The most important step is to work closely with your doctor or gastroenterologist, ensuring your Crohn’s is properly managed while exploring whether SIBO could be part of the picture. If it is, addressing it may help reduce bloating, fatigue, and digestive discomfort, giving you a clearer path forward.

At IBS Clinics, we offer supportive tools that can complement your medical care, including the SIBO breath test, our structured online course (6 practitioner-led modules with tailored food plans, supplement and testing guidance, and practical resources), and private consultations for one-to-one advice. Together, these services are designed to give you the clarity, structure, and guidance you need to move toward better daily comfort and long-term gut health.

If you’re ready to explore whether SIBO may be contributing to your ongoing symptoms, consider contacting us for a free 15-minute consultation at IBS Clinics to help determine the best next step for you – whether that’s a breath test, an appointment for a private consultation, or learning more about our online SIBO course.

With the right support, it is possible to move past the uncertainty and take meaningful steps toward living more comfortably with Crohn’s and SIBO.

References

Quigley, E.M.M., & Quera, R. (2006). Small intestinal bacterial overgrowth: Roles of antibiotics, prebiotics, and probiotics. Gastroenterology, 130(2), S78–S90. https://pubmed.ncbi.nlm.nih.gov/16473078
Ghoshal, U.C., Shukla, R., & Ghoshal, U. (2017). Small intestinal bacterial overgrowth and irritable bowel syndrome: A bridge between functional organic dichotomy. Gut and Liver, 11(2), 196–208. https://pubmed.ncbi.nlm.nih.gov/28074702
Pimentel, M., Saad, R.J., Long, M.D., Rao, S.S.C. (2020). ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. American Journal of Gastroenterology, 115(2), 165–178. https://pubmed.ncbi.nlm.nih.gov/31977733
Battat, R., Duijvestein, M., Vande Casteele, N., et al. (2019). Small intestinal bacterial overgrowth in patients with Crohn’s disease: A systematic review and meta-analysis. Journal of Crohn’s and Colitis, 13(5), 660–671. https://pubmed.ncbi.nlm.nih.gov/30698792
Quigley, E.M.M., & Quera, R. (2006). Small intestinal bacterial overgrowth: Roles of antibiotics, prebiotics, and probiotics. Gastroenterology, 130(2), S78–S90. https://pubmed.ncbi.nlm.nih.gov/16473078
Battat, R., Duijvestein, M., Vande Casteele, N., et al. (2019). Small intestinal bacterial overgrowth in patients with Crohn’s disease: A systematic review and meta-analysis. Journal of Crohn’s and Colitis, 13(5), 660–671. https://pubmed.ncbi.nlm.nih.gov/30698792
Pimentel, M., Saad, R.J., Long, M.D., Rao, S.S.C. (2020). ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. American Journal of Gastroenterology, 115(2), 165–178. https://pubmed.ncbi.nlm.nih.gov/31977733
Feuerstein, J.D., Cheifetz, A.S. (2017). Crohn’s disease: Epidemiology, diagnosis, and management. Mayo Clinic Proceedings, 92(7), 1088–1103. https://pubmed.ncbi.nlm.nih.gov/28668222
Ghoshal, U.C., Shukla, R., & Ghoshal, U. (2017). Small intestinal bacterial overgrowth and irritable bowel syndrome: A bridge between functional organic dichotomy. Gut and Liver, 11(2), 196–208. https://pubmed.ncbi.nlm.nih.gov/28074702
Staudacher, H.M., Whelan, K. (2017). The low FODMAP diet: Recent advances in understanding its mechanisms and efficacy in IBS. Gut, 66(8), 1517–1527. https://pubmed.ncbi.nlm.nih.gov/28694265
Levine, A., Sigall Boneh, R., Wine, E. (2018). Evolving role of diet in the pathogenesis and treatment of inflammatory bowel diseases. Gut, 67(9), 1726–1738. https://pubmed.ncbi.nlm.nih.gov/29954892

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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