The Sensitive Gut

Understanding IBS

SIBO. Is it a major cause of IBS?

mark pimentel

Dr Mark Pimentel

When I was training to be a gastroenterologist way back then, Small Intestinal Bacterial Overgrowth (SIBO) was a rare diagnosis, most often found in patients with blind loop syndrome.  This was a time before treatments for Helicobacter pylori, when surgeons would remove part of the stomach for ulcer disease and cancer and connect it directly to the small intestine, leaving a blind loop of duodenum to carry the bile and pancreatic juices into the digestive stream.  It was known as the Roux-en-Y procedure – nothing to do with cooking, but a lot to do with digesting.  Deprived of the antibacterial effect of acid and subject to stagnation, this blind loop would get colonized by bacteria.  These would infect the digesta, fermenting carbohydrate and protein, degrading fats and bile acids and causing malabsorption, pain, bloating and diarrhoea.  The only treatment was high doses of powerful antibiotics.

Such blind loops are part of surgical history, but SIBO has experienced a resurgence which has split the gastroenterology community of experts.  For many American physicians, it is the most common single cause of IBS while others, mainly in Europe, tend to regard it as a misinterpretation of the tests that are used to diagnosis it.  Allow me to explain.

The Problem with Breath Tests

SIBO is diagnosed by breath tests.  The patient drinks a dose of lactulose, in effect a FODMAP, a unabsorbable disaccharide that is known by many as the laxative, Duphalac.  This travels down the small intestine and when it meets sufficient bacteria, usually in the colon, it is fermented, releasing hydrogen gas.  Hydrogen permeates into the blood stream and can be detected in breath samples.  It usually takes about two to four hours for a dose of 25g lactulose to reach the colon and cause a spike of hydrogen, but the time can be much shorter if the small intestine is colonized by fermentative bacteria. Dr Mark Pimentel’s group in Los Angeles have shown that as many 80% of people with IBS might have SIBO1.

It seems a ‘no brainer’, but hang on a bit.  All the lactulose breath test shows is that the sugar is reaching a pool of bacteria much quickly than usual.  In the nineteen eighties, Dr Immanuel Bergman, a scientist at The Safety in Mines Research Establishment in Sheffield, invented a portable hydrogen monitor, which he generously let us use to measure small bowel transit time in people with IBS.  We gave our patients a couple of spoons of baked beans (another FODMAP) as our source of unabsorbable sugars.  For us an early rise in breath hydrogen indicated an abnormally rapid small bowel transit.  We proved this by tagging our meal with radioactive Technetium 99, screening the patient with a gamma camera and showing that the rise in breath hydrogen coincides with both the arrival of the marker in the colon2 and the onset of symptoms of  pain and bloating3.

So what does the lactulose breath test show?  Is it small intestinal bacterial overgrowth or rapid small bowel transit?  Some diagnostic centres have refined the breath test by using a dose of glucose, which would normally be rapidly absorbed in the small intestine, but small bowel transit could be so rapid in some patients with IBS and diarrhoea that even some glucose might reach the colon and be fermented.

Other tests

Things are rarely absolute in medical science and there certainly is a strong case to be made for SIBO in some patients with IBS.  The gold standard for diagnosing SIBO is to put a tube into the small intestine and culture the fluid aspirated.  Dr Mark Pimentel has shown that about 30% of a sample of his patients with IBS have a positive small bowel aspirate, though one wonders whether  samples could be contaminated by bacteria picked up in the mouth and throat.  Moving on, in a neat series of experiments, his group has demonstrated that mice infected with Campylobacter jejuni develop a paralysis of the small intestine with bacterial overgrowth.  This is caused by a toxin that resembles vinculin, a naturally occurring transmitter.  An assay of vinculin antibodies has recently been released as a test for SIBO and heralded as a biomarker for IBS4.

A Clinical Diagnosis

Trained at a time when we used good old fashioned clinical history and examination to diagnose most conditions, I wonder if there are features about SIBO that might be recognized clinically.  A few months ago in this blog, I reported a case (me) of nausea, bloating, abdominal pain and diarrhoea brought on by inadvertently swallowing river water.  I had had what I recognized as attacks of more ‘typical’ IBS before, but this was quite different.  The first thing that alerted me to the possibility of SIBO was the eggy burps.  Something (possibly the parasite giardia lamblia) has clearly stopped acid being secreted in my stomach, which was then being colonized by bacteria.  At the same time, I had bloating and what I can only describe as flickering pains high up in my gut accompanied by the high pitched squelches and gurgles I associate with an irritated small intestine.  And then the diarrhoea started, frequent, watery (7++ on Dr Ken Heaton’s Bristol Stool Scale) and large volume.  It lasted for three days and then my stomach started secreting acid again and everything returned to normal.  I never took any medication.  I just drank large amounts of lemon juice in warm water.  I have since had the same attacks on three separate occasions, each time caused by wild swimming and swallowing water.  So was I like Dr Pimentel’s mice?  I must admit I didn’t spot any in the river?  Can SIBO clear up spontaneously? And if doesn’t, what causes the symptoms to persist?


Dr Pimentel and others have shown that a poorly absorbed, broad spectrum antibiotic, Rifaximin, can effectively resolve symptoms of IBS in again about 80% of cases, presumably by blocking fermentation5. A low FODMAP diet would presumably work in a similar way, as might some probiotics or even colonic irrigation.  There’s more than one way to skin cats or treat IBS.

The question is whether Rifamixin is a specific treatment for SIBO. Would it not reduce fermentation by depleting the normal colonic bacteria flora?  Not necessarily, say the experts.  Rifaximin is soluble in bile and since bile acids are almost completely absorbed in the normal small intestine, it should not work in the colon.  Well, that may be so in people who do not have IBS, but, as I have argued in a recent post, bile acid malabsorption is common in IBS-diarrhoea, so Rifaximin would remain active and destroy the colonic bacteria.

Is that a good thing?  We already know that broad spectrum antibiotics can bring on IBS and there is a whole industry around taking probiotics to replenish these.  Even the advocates of a low FODMAP diet are concerned about the depletion of beneficial Bifidobacteria spp.


I am sorry if this sounds negative.  We have had ‘breakthroughs’ so many times with IBS that I do wonder if medical scientists are not in danger of creating another philosophical blind loop with SIBO. IBS does seem the Bermuda triangle of medical research.

But what is your experience?  Was the diagnosis of SIBO a turning point for you?  Did Rifaximin resolve your IBS?  Did the effect last? Do write and tell us.          



  1. Pimentel, Mark (2006).A new IBS solution : bacteria, the missing link in treating irritable bowel syndrome. Sherman Oaks, CA: Health Point Press. ISBN 0977435601.
  1. Read, N.W., Al-Janabi, M.N., Holgate, A.M. and Barber, D.C. (1986) Simultaneous measurement of gastric emptying, small bowel residence and colonic filling of a solid meal by the use of the gamma camera. Gut 27: 300-308.
  1. Cann PA, Read NW, Brown C, Hobson N, Holdsworth CD (1983). Irritable bowel syndrome: relationship of disorders in the transit of a single solid meal to symptom patterns.Gut 24: 405–411.
  1. Pimentel M, Morales W, Rezaie A, Marsh E, Lembo A, Mirocha J, et al. (2015) Development and Validation of a Biomarker for Diarrhea-Predominant Irritable Bowel Syndrome in Human Subjects. PLoS ONE 10(5): e0126438. doi:10.1371/journal.pone.0126438
  1. Schey R.  Rao SS (2011) The role of rifaximin therapy in patients with irritable bowel syndrome without constipation. Expert review of gastroenterology & hepatology.  5(4):461-4,



14 comments on “SIBO. Is it a major cause of IBS?

  1. Joan Ransley
    April 11, 2016

    Very interesting post. Can lactulose/glucose be given a radioactive tag to establish where the fermentation occurs? Do patients who have been ‘diagnosed’ with SIBO experience symptoms associated with paralysis of the small intestine? Has any one asked them/described their symptoms?


  2. nickwread
    April 11, 2016

    Yes it can, though scientists are more wary of radiation exposure these days. In the one study I have seen, the rise in breath hydrogen occurred when the tag reached the caecum. I do not think there has ever been a study to identify whether patients with a definite diagnosis of SIBO have symptoms similar to the ones I described. I was very struck by the association of bacterial overgrowth of the stomach and the unusual nature of the intestinal sensations that seemed to be coming from the small bowel, but I could not, of course, prove that – it was Christmas. Something for somebody to follow up!

    Liked by 1 person

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  10. Patricia
    June 12, 2017

    Yes, Rifaximin resolved by symptoms (diagnosed as SIBO) — for a few months. Now, several years later am muddling through the re-challenge stage of FODMAP


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  12. JK
    September 3, 2019

    Very interesting post from Dr Pimentel. In answer to some of his questions at the end, I can say that after suffering about 3 years of increasingly severe attacks of diarrhoea, to the point where I was losing all confidence to go anywhere for work or socially, and having wasted a lot of time and money with a nutritional therapist, taking herbs and trying to avoid antibiotics, I finally went to a gastroenterologist. I had a whole range of tests and the only one that was clearly positive was the SIBO breath test. I had high levels of “bad” gut bacteria, apparently. I took Rifaxamin for 3 weeks followied by 3 months of Symprove, an excellent probiotic, as well as having a course of gut-focussed hypnotherapy (for which there is good evidence for effective alleviation of symptoms and accompanying anxiety). I also followed the FODMAP diet gradually identifying trigger foods. My lifestyle also changed dramatically (for the better) – having semi-retired my stress levels reduced hugely and I was no longer eating meals on the run, on trains, on station platforms, etc. Over the next year my symptoms significantly reduced. It took a further year or so to stabilise further and, five years on, with careful management of my food intake (i.e. careful not to overload my sensitive gut with too much food through the day, especially at night), I am back to normal. Stress leaves me vulnerable to flare-ups but nothing like as bad as previously. I put it all down to a bug I think I picked up in Dubai in 2014, when my symptoms all started, and years of travel and stress that messed up my gut flora. So there is hope out there but it takes the right doctor, the right combination of treatment, a huge amount of patience, and highly supportive friends and family. Good luck….


  13. JR
    October 28, 2019

    Due to experiencing digestive issues for years I sought the advice of a nutritional therapist trained in the functional medicine approach. I went through a number of tests and was diagnosed with SIBO, Citrobacter freundii and yeast infections. I was recommended the SIBO Bi-Phasic diet (a version of the Specific Carbohydrate or SCD diet) & Elemental diets. Both diets reduce the food available to bacteria, which reduced but did not eliminate my symptoms. Also, pharmaceutical (Rifaxamin/Neomycin) and natural antibiotic treatments to reduce bacteria in my small intestine and later Ciprofloxacin to treat the Citrobacter freundii infection. I lost 1 stone in weight, so I became underweight in a matter of months and felt quite unwell, was unable to work and lost confidence in myself. Under the NHS I had a MRI of my small intestine to try to identify any physiological cause of SIBO. This test revealed that it was unlikely that I’d ever had SIBO. Overall I’d had a negative experience of this approach and had spent an enormous amount on it in terms of fees and supplements and was no further forward. As you allude to it, the breath test is not an accurate test. I also had a colonoscopy & CT virtual colonoscopy after NHS blood tests came back with inflammation. I was diagnosed with a redundant (long, loopy) colon, which typically causes IBS like symptoms and visceral hypersensitivity where the brain interprets normal bowel function as pain. One of the nutritional therapists suggested that she could have diagnosed SIBO just from my symptoms (bloating and pain). Two other therapists suggested I had SIBO from my symptoms. It seems to be the latest thing to earn money from. However, being pointed down that road when someone doesn’t actually have it can worsen someone’s health. I do wonder whether lots of people visiting such therapists are getting the same diagnosis when simply they have IBS with visceral hypersensitivity ( I appreciate there are some for whom Rifaxamin has been a life saver and I have seen some very promising studies (which is why I went ahead with it), but it appears it can be a bit of a shot in the dark and an expensive one at that since in the UK it is only available via a very pricey private prescription.


    • nickwread
      October 28, 2019

      Dear Jenny, Thank you for writing and telling all of us about your experience with the diagnosis of SIBO and its treatment. Unfortunately, I fear that what you have gone through is not uncommon. I am reluctant to believe that some therapists who diagnose SIBO are deliberately exploitative. Instead, I tend to think that the science is somewhat flawed and that in many cases, Rifamixin may appear to work because it suppresses colonic bacteria and fermentation, which in the longer term this may well lead to an increase in visceral sensitivity and more symptoms.

      Liked by 1 person

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This entry was posted on April 9, 2016 by in Small intestinal bacterial overgrowth and tagged , , .

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