Can antibiotics cause gluten intolerance?


I first came across this idea in Darwin when a six year old boy in our network was diagnosed with "antibiotic-induced gluten intolerance" by his doctor and told to avoid gluten strictly for 12 months. He was then able to manage gluten without problems.

Twenty years on, there is considerable controversy about what has caused the dramatic increase in gluten intolerance presenting as either coeliac disease (1) or non-coeliac gluten sensitivity (NCGS) (2); whether NCGS really exists or is it really a sensitivity to FODMAPs (3), and whether antibiotics may be implicated by disturbing beneficial gut bugs (4).

In the meantime, I myself developed gluten intolerance after taking antibiotics for a gastro bug. I was so sensitive to gluten that I had to stick to a strictly gluten free version of failsafe eating. Two years later, while trekking through high altitude villages in Nepal, I had the opportunity to eat homemade yak milk yoghurt that contained very different probiotics than Western yoghurt - and it restored my gluten tolerance.

Since then I have developed gluten sensitivity again several times after taking antibiotics for travellers' diarrhoea. Fortunately I have found a way to overcome it without having to trek to a remote mountain pasture while yaks are having their babies. If I stick strictly to gluten free failsafe eating until my symptoms are gone, then do another month strictly gluten free while taking a certain kind of probiotic, I can recover from gluten intolerance.

In the US, Dr Martin Blaser has been researching this issue for over 30 years. He is now director of NYU's Human Microbiome Program and his view is presented in his 2014 book, Missing Microbes. The subtitle says it all: "How the Overuse of Antibiotics Is Fueling Our Modern Plagues" - including coeliac disease. In a 2013 Swedish study, his team found an association between antibiotic use and increasing risk of coeliac disease (5).

His idea is that the damaging effect of antibiotics on beneficial gut bugs - microbes - can start in childhood. The average American child takes nearly three courses of antibiotics in the first two years of life, and eight more during the next eight years. During my lecture tour in 2012, only 4 Australians out of 2029 attendees (0.2%) had never taken antibiotics and 77% had IBS symptoms in their family (6). Even a short course of antibiotics can cause long-term changes in the body’s microbial environment.

Effect of probiotics

Probiotics are the opposite. They can help foster beneficial microbes in the gut. There are many different probiotics, and according to Dr Blaser, probiotics are going to be to be an important part of medicine in the future. Currently, however, they are mostly untested and unregulated, although they seem to be generally safe.

One of the few probiotics that has been tested is a yeast called Saccharomyces boulardii. I take an S boulardii-containing product called Travel Bug to prevent travellers' diarrhoea during travel and discovered by accident that it also works to overcome my gluten sensitivity. In Europe, it is normal for people taking antibiotics to be given probiotics at the same time, but that has not been the case in Australia until recently. I was surprised last year to find our local pharmacy now recommends S boulardii when filling a script for Ciprofloxacin antibiotics (7,8).

What if gluten isn't the problem?

In a survey of 986 attendees at our 2013 roadshow, 1% said they were diagnosed coeliacs and 155 (16%) per cent said they were avoiding gluten.  The gluten free claim is increasing on food labels but there is no medically recognised laboratory test for non-coeliac gluten intolerance, so how do you know if you are sensitive to gluten?

If you stop eating gluten and notice an improvement, you can't assume you are sensitive to gluten. It is easy to misinterpret the effects of foods. A woman at one of our talks who thought she was gluten sensitive was surprised she reacted to gluten free bread whereas she could manage spelt bread. As it turned out, the gluten free bread contained bread preservative 282 whereas the spelt bread was preservative free. (Spelt is an ancient form of wheat, not gluten free though many wheat-sensitive responders can manage it.) See how to avoid preserved bread below.

How to avoid bread preservatives 

no 282 or other propionate preservatives 280, 281

no other preservatives such as sorbates 200, 202

no "cultured" anything - such as cultured dextrose

no synthetic antioxidants such as 319, 320

no vinegar


How to do a wheat challenge

To confirm that you really have a gluten sensitivity, you can do a challenge. Your dietitian can help with this – the recommended RPAH wheat challenge is (after 3 symptom free days in a row): eat 1 cup plain uncoloured cooked pasta plus 12 plain preservative-free water crackers per day for 3 days. If no reaction, add in 4 slices of plain preservative free bread e.g. Bakers Delight or Brumbys (9) per day and continue for another 4 days.  

Could you be an undiagnosed coeliac?

If you are likely to have coeliac disease, it is important to know for sure, because the only treatment is a lifelong strictly gluten free diet and undiagnosed coeliac disease can lead to premature death. One failsafer said she wasn’t prepared to put her son on gluten so he could have a blood test or to have a bowel biopsy for coeliac disease because ‘it’s too invasive’.  In this case, genetic testing may be useful. Over 99% of people affected by coeliac disease have the HLA DQ2 or DQ8 genes and a negative test for these genes effectively rules out coeliac disease. Some people with these genes say they are happy to remain gluten free without further testing. More information 

Wheat is a nutritious food

For people who don't have wheat or gluten intolerance, wheat is a nutritious food. An Australian study found gluten-free products in supermarkets were overall less nutritious than those containing wheat (10). At my talks I have come across people who have been mistakenly avoiding gluten for years because they didn't realise their problems were actually caused by other components in the bread.  This is a good reason to do your RPAH elimination diet and challenges under the supervision of an experienced and supportive dietitian. You can see our list of recommended dietitians and other health professionals.

Read more

1. The considerable controversy about what causes celiac / coeliac disease includes infant feeding, early or late introduction of gluten, and the possible protective role of breastfeeding:
Does Breast Feeding Protect Against Celiac Disease? by Butzner and Zarkadas (2004) 
Infant feeding and risk of developing celiac disease: a systematic review, Silano and others (2016) 

2. Gluten Sensitivity, Catassi C. Ann Nutr Metab 2015;67(suppl 2):16-26 

3. In 37 subjects with irritable bowel syndrome, gastrointestinal symptoms consistently and significantly improved during reduced FODMAP intake, but significantly worsened to a similar degree when their diets included gluten or whey protein. Gluten-specific effects were observed in only 8% of participants.  Biesiekierski JR and others, No effects of gluten in patients with self-reported non-celiac gluten sensitivity after dietary reduction of fermentable, poorly absorbed, short-chain carbohydrates., Gastroenterology. 2013 Aug;145(2):320-8.e1-3. 

4. Modern Medicine May Not Be Doing Your Microbiome Any Favors: Interview with Martin Blaser, April 14, 2014  

5. Antibiotic exposure and the development of coeliac disease: a nationwide case-control study, Mårild K, Ye W, Lebwohl B, Green PH, Blaser MJ and others, BMC Gastroenterol. 2013  8;13:109.  


7. Probiotics: eat your bugs, ABC Health & Wellbeing See also factsheet  

8. Our blog: SB & DE - are these failsafe supplements that can help with irritable bowel symptoms?  

9. RPAH Elimination Diet - how to do challenges. Preferably ask your dietitian (see our list of experienced and supportive dietitians). See factsheet

10. Wu JH and others, Are gluten-free foods healthier than non-gluten-free foods? An evaluation of supermarket products in Australia.Br J Nutr. 2015 Aug 14;114(3):448-54.