Have you been diagnosed with coeliac disease but still feel bloated, gassy or have irregular bowel movements even after months on a strict gluten-free diet?

You’re not alone. Many people do everything “right” strictly avoiding all foods with gluten and still don’t feel better.

One reason may be linked to Small intestinal bacterial overgrowth (SIBO) a condition whereby bacteria overgrows in the small intestine.

Research shows SIBO is found in about 21% of people with coeliac disease when diagnosed by SIBO breath tests and approximately 13% by culture.

This guide explains the missing link between Coeliac disease and SIBO, how to test in the UK, and what a practical treatment and diet plan looks like.

Key stats: SIBO occurs in ~18–21% of coeliac patients overall; it’s a recognised cause of non-responsive coeliac disease when gluten exposure has been excluded.

What’s the link between coeliac disease and SIBO?

SIBO may be the reason you remain symptomatic despite doing everything right on a gluten-free diet—“non-responsive” coeliac disease.

Why the overlap? These are the main links between the two conditions:

1) Injured small-bowel lining
Active coeliac disease flattens the villi (villous atrophy) and inflames the mucosa. With fewer brush-border enzymes and weaker local defences (e.g., secretory IgA/antimicrobial peptides), bacteria can colonise the small intestine more easily and irritate the lining. This can cause bloating and gas and erratic bowel movements.

2) Slower gut movement
When the small intestine is healthy, it runs a between-meals “housekeeping” program called the migrating motor complex (MMC)—rhythmic waves that sweep residual food and bacteria downstream every 90–120 minutes.

Active coeliac inflammation and under-nutrition blunt these waves and slow overall transit, which gives microbes extra time to linger and multiply in the small bowel.

Constant grazing/snacking also suppresses the MMC (it switches off when you’re digesting), so even a few bites can reset the clock. On top of that, methane-producing microbes (IMO) directly slow intestinal movement, creating a loop: slower transit → more overgrowth → even slower transit.

3) Extra substrate for bacteria

Malabsorption leaves more carbohydrate in the small bowel. Bacteria ferment these sugars to hydrogen and methane, driving bloating, pain and altered bowel habit. Methane-producing archaea slow transit further, so constipation becomes more likely.

4) Secondary effects that sustain symptoms
Overgrowth organisms deconjugate bile acids (worsening fat absorption, pale/greasy stools) and compete for micronutrients such as vitamin B12 and iron, contributing to fatigue and deficiency. Ongoing mucosal irritation can keep symptoms “coeliac-like” even when gluten is excluded.

5) Common co-factors (often present in coeliac disease)

• Acid suppression: long-term PPIs (e.g., omeprazole, lansoprazole) reduce stomach acid and make cause bacteria to overgrow.
• Anatomy/stasis: prior gut surgery (blind loops, strictures, adhesions), small-bowel diverticula, weak ileocaecal valve.
• Motility disorders: diabetes (autonomic neuropathy), hypothyroidism, connective-tissue disease.
• Gut-slowing medicines: opioids and anticholinergics.
• Selective IgA deficiency (more common in coeliac) may weaken mucosal defence.
  
  

What this means in practice
If symptoms (bloating, pain, diarrhoea/constipation, nutrient deficiency) persist 6–12 months after following a sctrict gluten-free diet, consider hydrogen–methane breath testing for SIBO.

What exactly is SIBO?

SIBO means excessive bacteria (and sometimes methane-producing archaea) colonise the small intestine. They ferment carbohydrates, producing hydrogen and/or methane along with other by-products that irritate the gut. That can lead to bloating, pain, diarrhoea or constipation, malabsorption and fatigue. A methane-heavy pattern is often called intestinal methanogen overgrowth (IMO) and tends to slow motility and cause constipation.

Read Jason’s story

Jason was diagnosed with coeliac disease and started a strict gluten-free diet and remained on it for about six months. Despite doing it properly, he saw no improvement in his symptoms- he had constant bloating, excess gas, and erratic bowel movements. He eventually stopped the diet because nothing changed.

His GP referred him to a gastroenterologist. He underwent blood tests, a gastric emptying study, and a colonoscopy with biopsies. All results were negative.

Jason then contacted our IBS clinic as he was still searching for answers.

We recommended he complete a breath test for small intestinal bacterial overgrowth (SIBO) and the breath test was indeed positive for a Hydrogen overgrowth.

Jason was recommended a protocol that consisted of a 4 week course of antimicrobials and a low-FODMAP diet as well as strict avoidance of gluten. He had a noticeable improvement in his symptoms with bloating and gas much reduced.

Jason’s questions were: did SIBO explain why the gluten-free diet didn’t help? In his case this did seem likely.

Symptoms: why coeliac and SIBO look so similar

Both conditions can cause bloating, abdominal discomfort, wind, diarrhoea or constipation, weight change and fatigue. Both can lead to iron, B12 or folate deficiency.

If you’ve been strictly gluten-free for 6–12 months and still have digestive symptoms, it’s a good idea to screen for SIBO alongside other common causes of non-responsive coeliac disease.

Consider testing after 6–12 months of gluten avoidance if any of these apply:

• Persistent bloating, pain, diarrhoea or troublesome wind
• Constipation with “methane-type” features (hard stools, sluggish transit)
• Ongoing iron deficiency or other nutrient shortfalls
• Known risk factors (PPI use, prior abdominal surgery, diabetes, motility problems)

What is the best test to consider for SIBO?

Hydrogen–methane breath testing

You’ll follow a simple prep diet, fast overnight and then drink a glucose or lactulose solution. Breath samples will be taken over 3 hours to measure hydrogen and methane in your breath.

• Glucose is more specific for the upper small bowel.
• Lactulose samples further along but is more prone to false positives if you have a very rapid transit time.

Other Tests to consider

A targeted nutrient blood panel (iron studies, B12, folate, vitamin D).

Selected stool tests when indicated (faecal calprotectin, faecal elastase). If symptoms still don’t fit, consider bile acid diarrhoea or microscopic colitis.

What treatment exists for SIBO?

1) Antibiotics/Herbs

If you have been diagnosed with SIBO antibiotics may be required

• Hydrogen-dominant SIBO: a common regimen is rifaximin 550 mg three times daily for 10–14 days.
• Methane-dominant (IMO): often rifaximin 550 mg three times daily + neomycin 500 mg twice daily for 10 days (or an alternative combination per clinician). Methanogens are harder to shift, so combinations perform better than rifaximin alone.
• Hydrogen-sulfide: your clinician may tailor therapy (sometimes using bismuth-based or combination protocols).

Herbal route (non-prescription).

The other option is to buy over the counter herbs that are equivalent to antibiotics. Common botanicals include berberine blends, oregano oil, neem, allicin, and olive-leaf polyphenols; these can be rotated or combined and are often paired with a short, structured low-fermentable diet.

Herbal supplements are equally effective and useful as it is very costly to obtain rifaximin- £200-£400. We have had great success using herbal antibiotics at we use at our IBS and SIBO clinic.

Diet for coeliac disease and SIBO

It is essential that you follow a strict gluten-free diet long-term as well as a low-fermentable (low-FODMAP-style) plan for 4 weeks, then systematically reintroduce the high FODMAPS to avoid long-term restriction.

For confirmed or strongly suspected coeliac disease, a strict gluten-free (GF) diet is lifelong, not “mostly GF.” That means avoiding wheat, barley, rye (and their derivatives) and preventing cross-contamination (separate toaster/chopping boards, check sauces, “may contain” warnings, etc.).

Alongside this, a short, structured low-fermentable (low-FODMAP-style) phase can calm bloating, gas and urgency if SIBO/IBS-type mechanisms are present. The key is short-term use (about 4 weeks) to settle symptoms, followed by a systematic reintroduction so you don’t end up on an unnecessarily restrictive diet or harm gut-microbiome diversity.

• Stay 100% GF the whole time.
• Choose simple, low-fermentation meals:
  • Carbs: white or brown rice, quinoa, GF oats (moderate portions), potatoes.
  • Proteins: eggs, fish, chicken, tofu/firm tempeh, lean meats.
  • Fats: olive oil/infused garlic oil (not whole garlic), avocado in small portions.
  • Veg (lower-FODMAP): courgette, carrots, spinach, peppers, green beans, aubergine.
  • Fruit (lower-FODMAP portions): berries, kiwi, oranges, grapes.
• Drinks: water, peppermint/ginger tea; limit sugar alcohols and very fizzy drinks.

2) Find the underlying cause (prevents quick relapse)

• PPI review: If you’re on acid blockers like omeprazole or lansoprazole, it’s worth a quick chat with your GP about whether they’re essential. Too little stomach acid can allow more bacteria to thrive, so a review or a gentle step-down may help.
  
• Support motility: leave 4–5 hours between meals to activate the migrating motor complex; aim for a 12-hour overnight fast; daily walking; address constipation (hydration, magnesium citrate if appropriate). Clinician-guided prokinetics (e.g., ginger, or prescription options like low-dose erythromycin/prucalopride) can help in select cases.
  
• Metabolic & endocrine checks: optimise thyroid and diabetes control; correct iron, B12, folate, vitamin D deficiencies.
  
• Anatomy & medications: prior GI surgery/adhesions, opioids, and anticholinergics slow transit—tackle what’s modifiable.
  
  
  If you need help undestanding what caused SIBO and how to eradicate it please book a consultation with our IBS and SIBO specialists.
  

Coeliac versus SIBO

What you feel	Likely drivers in coeliac	Likely drivers in SIBO/IMO	Useful next step
Bloating & pain	Active mucosal injury, hidden gluten	Carb fermentation	Confirm gluten-free; arrange SIBO breath test
Diarrhoea	Inflammation, bile acid diarrhoea, pancreatic insufficiency	Rapid fermentation; osmotic effects; IBS-D overlap	Breath test; consider calprotectin ± bile acid work-up
Constipation	Slow transit, low fibre after diagnosis	Methane (IMO) slows transit	SIBO testing; consider prokinetic/soluble fibre
Iron/B12/folate deficiency	Villous atrophy → malabsorption	Nutrient competition; mucosal irritation	Replace deficits; treat overgrowth; re-check levels
Fatigue/brain fog	Inflammation, deficiencies, sleep issues	Gas/by-products; deficiencies	Treat root cause; restore micronutrients

Summary

1. Audit your diet for hidden gluten (labels, cross-contamination, eating out).
2. If you are still experiencing symptoms arrange a hydrogen–methane breath testing SIBO test
3. Treat confirmed SIBO (consider combination therapy if methane-positive).
4. Pair treatment with a short, structured low-fermentable plan; avoid long-term over-restriction.
5. Address drivers: motility support, medication review, endocrine/metabolic optimisation.
   
   
   

FAQs

Does coeliac disease cause SIBO?
Not in everyone, but coeliac-related mucosal damage and motility changes make SIBO more likely—hence the higher rates seen in coeliac cohorts.

Are breath tests accurate?
No test is perfect, but with correct preparation and modern cut-offs, hydrogen–methane breath testing is a practical, evidence-based way to diagnose SIBO/IMO.

Should I change my diet before testing?
Yes, follow the lab’s short prep (simple low-fermentable diet the day before and arrive fasted). It improves accuracy.

Can diet alone fix SIBO?
Diet reduces symptoms by lowering fermentation, but most people need a short antimicrobial course plus driver management for durable relief.

Book a SIBO breath test & consultation

Ready to move forward?

• Book a SIBO breath test – your results take 2 days
• Book a consultation with an IBS specialist today so you can receive immediate advice
  Prefer to talk? Call 0345 129 7996 and we’ll guide you.

References

1. NICE Guideline NG20. Coeliac disease: recognition, assessment and management.
2. British Society of Gastroenterology. Guidelines on the diagnosis and management of adult coeliac disease.
3. ACG Clinical Guideline. Small Intestinal Bacterial Overgrowth. Am J Gastroenterol.
4. AGA Clinical Practice Update. Use of breath tests for gastrointestinal disorders. Gastroenterology.
5. Shah A, et al. Links between coeliac disease and small intestinal bacterial overgrowth: a systematic review and meta-analysis. JGH Open (2022).
6. Penny HA, et al. Non-Responsive Coeliac Disease. Nutrients (2020).

About the Author

Victoria Tyler a UK registered Nutritional Therapist and member of the British Association of Nutritional therapy. She was awarded UK BSc Honours Degree in Nutritional Therapy and has trained in GI Functional Medicine. Victoria has been working with Gut disorders since 2004 after first experiencing digestive problems herself. She felt that the NHS was unable to provide the support individuals needed and went on to specialise in this area before offering a bespoke IBS service.

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