Health Conditions O - Z

SIBO (Small Intestine Bacterial Overgrowth)

By Graeme Bradshaw

Around one person in eight has IBS, or Irritable Bowel Syndrome. Are you one of them? If not, perhaps one of your friends or family suffers from this problem?

The symptoms of IBS are common enough—bloating and abdominal pains along with abnormal bowel habits. Many times women say they look four months pregnant from the bloating, and its not usually caused by stress—although like most conditions it may aggravate with stress.  Sometimes the irregular bowels are predominantly too loose, with diarrhea at times (IBS-D), for others too constipated (IBS-C) while for some its mixture of both (IBS-M).

Using recent diagnostic criteria, IBS is the most common digestive disorder. It is also a condition that reduces the patient’s quality of life considerably. [1] Those with IBS also suffer from diminished work productivity, and high medical expenditures [2, 3].

What Is IBS? What Is SIBO?

IBS seemed to be an unrelenting condition... until now.

It had been conventionally thought to be a disorder without an organic basis, because the causes were unknown. Some people do have a “nervous tummy”, whose vagus nerve is overactive, especially related to anxiety.

However, recently data are emerging to show that it has a diagnosable organic basis at least in a major subset of patients, as many IBS sufferers actually have SIBO—which stands for Small Intestine Bacterial Overgrowth. (There is a wide variation in the estimates of IBS sufferers who have SIBO, some as high as eight out of ten cases [3], but on the average of several studies it’s believed that over half of IBS sufferers actually have SIBO. SIBO is more commonly found in older patients and women. [4]

SIBO can be identified and treated successfully by functional medicine practitioners and naturopathic doctors.

What You Need To Know about SIBO: 

  • SIBO is an infection in your small intestine [4]
  • The small intestine lies between your stomach and your colon, and is the place where our food is absorbed
  • Bacteria there interfere with digestion, causing mal-absorption, gas, bloating and changes in the bowel motility
  • The infections also cause fermentation of certain sugars such as lactose and fructose, and it turns out a lot of foods that cause bloating only do so because of the SIBO infections (some people go on the FODMAP diet to eliminate these foods which reduces the foods that support the SIBO bacteria, though its a tough diet to achieve)
  • SIBO is best diagnosed with a breath test, where the gasses hydrogen and methane indicate the infection
  • Herbal treatments are more effective than the approved medical antibiotics for SIBO
  • Over 80% cure rates are being achieved for IBS with the natural treatments  

So the good news is you no longer have to live with the illness and discomfort of IBS. Here are some successful stories of people who overcome IBS with naturopathic treatment:

Mike's Case

“Mike” is an athlete and coach these days after giving up corporate life. Used to being fit and achieving ironmans and record-breaking swims, it was a huge disappointment to find his performance dropping significantly for no apparent reasons.

Mike came to see me with complaints of painful abdominal bloating with constipation. “My gut's poisoning me!” he said, as he felt his gut was toxic, causing debilitation physically and mentally. His muscle pain after training had become terrible. His moods had become negative, and an odd symptom—his weight would fluctuate from 77kg up to 83 within 2 days, clearly not owing to dietary changes. He looked tired with darkness around his eyes.

Under my recommendation, Mike decided to take a SIBO Breath Test, which showed he was producing a lot of methane gas in his gut—a telltale sign of bacterial infection in the small intestines.

After 6 weeks of treatment he reported “a million times better.” His weight had returned to within 1-2 kilo of his optimal goal, muscle pains had gone, and the depressed, grumbling disposition had also completely gone. Mike's performance had gone straight back to his old form, and training was a pleasure again.

Michelle's Case

"Michelle" is an advertising executive from the UK who had a more simple and common case of irritable bowel with bloating and diarrhea, lasting for the previous 5 years. She complained of running to the toilet straight after most meals. People often asked her when is the baby due, because she was so bloated. She didn't know what to eat and expected that would be the focus of my consultation.

We did the SIBO breath test, but since she was only holidaying with family over Christmas for 3 weeks, we started a herbal antimicrobial treatments for SIBO before the results returned. After New Year, just before heading back to London, Michelle returned, beaming. The symptoms had all gone on the anti-microbial herbal and probiotic treatments given to her. The SIBO test indeed showed high hydrogen gas production, whihc indicated the easier form of bacterial infection in her gut.  She now knew why she had IBS, and how to effectively treat it.

Michelle's and Mike's breath test results as well as the treatmenrts can be found further on in this article.

The Common Causes for IBS

The infectious cause of IBS in many cases is no surprise, since new IBS onset often develops after food poisoning, for instance when travelling or new to a city such as Hong Kong, and the odds of developing IBS are high following these bouts of gastroenteritis. If gastroenteritis preceded the onset of your IBS and you never got well since, most likely you have SIBO—the bacterial infection remaining. Or perhaps if you went to India, Pakistan or Bali, an amoeba (Blastocystis or Giardia parasites) or both bacteria and amoeba could still be travelling inside you. A parasite called Blastocystis, is found in 17% of Western patients with IBS, and far more often in South Asians [5].

In my own case, I once unknowingly carried amoeba (Blastocystis hominidus)—likely from my travel to Nepal—for 4 years, before stool testing finally identified my gut issues. The infections had caused food intolerances in me and I looked pretty bad at that time. I treated the amoeba, and then the food intolerances went away.

Lets look at a couple of other often under diagnosed factors:

While IBS is most often an undiagnosed gut infection, it is commonly associated with the easily diagnosable food intolerances. Wheat or gluten intolerance is found in about one in five IBS sufferers. Overall 4% of patients meeting criteria for IBS are confirmed to have Celiac Disease (a severe gluten intolerance) based on a meta-analysis of 14 studies [8]. Interestingly from the findings in this study if you do have IBS you are around 4 times more likely to have Celiac Disease than people without IBS. There are other wheat related issues apart from Gluten Intolerance, called wheat sensitivity, and this is more common.

Symptoms and signs that usually characterize wheat sensitivity occur soon after gluten or wheat flour product ingestion, improving or disappearing (within hours or a few days) on gluten withdrawal and relapsing following its reintroduction. Clinical presentation of wheat sensitivity is of IBS-like symptoms, such as abdominal pain, bloating, and bowel habit abnormalities, whereas systemic manifestations range from fatigue to foggy mind, headache and depression, joint and muscle pain, dermatitis (eczema or skin rash), or anemia. Most patients with wheat sensitivity usually report having experienced at least two of the non gut manifestations, primarily foggy mind and fatigue [8]. An IgG Food Intolerance test can identify this issue of wheat or gluten intolerance accurately.

Finally, about one person in six IBS suggers has a lactose (milk sugars) intolerance, often undiagnosed [10].

To sum it up, the causes for IBS is often a combination of a wheat sensitivity, a gluten or lactose intolerance, a parasite infection, or most commonly SIBO.

Can SIBO Cause Other Symptoms?

Being an infection in the gut, these problems can occur with SIBO:

  • Lactose intolerance [10]
  • Celiac disease, and wheat sensitivity [11]
  • Fibromyalgia or chronic muscle pain [12]
  • Acne rosacea [13]
  • Restless leg syndrome [14]
  • Interstitial Cystitis [15]
  • Hypothyroidism and elevated cholesterol [16]
  • Crohn’s disease [17]

SIBO can cause malabsorption of the following nutrients: Iron, Vitamin B1, B3, B12, D3, Fats, Magnesium, Zinc, and each is associated with its own deficiency systems [19]. For instance iron deficiency may cause restless leg syndrome at night, or magnesium aggravate muscle cramps or pains. [19].

The SIBO Breath Test

The diagnosis of SIBO is not usually based on direct stool testing. Though the most accurate method, it's inconvenient and costly since the sample has to be taken directly from the small intestine via an endoscopy. A more suitable clinic-based method has been developed. It is based on a positive breath test to a lactulose sugar drink. This entails drinking a sugary solution of lactulose, then breathing into a collection tube every 20 minutes for at least 2 hours. The lactulose is fermented into hydrogen or methane by the small intestine bacterial overgrowth, and these gases are captured in the breath test-tube, sent to be assessed in a lab. This was the test taken by "Mike" and "Michelle".

Here is what the breath test result look like:

ibs d

Hydrogen Dominant Bacteria is associated with IBS-D

An overgrowth of hydrogen dominant bacteria can cause diarrhea. If you have diarrhea related SIBO predominantly, you are very likely suffering from an overgrowth of hydrogen producing bacteria in your small intestine, as we see in Michelle’s report here. Here the blue line indicates high Hydrogen levels, but low methane in the green line. 

Methane Dominant Archaea and SIBO-C 

If we find methane the green line goes up, as in Mikes report here, then your intestinal flora is comprised of organisms known as Archaea. Archaea in our digestive system feed off of hydrogen that other bacteria produce during the fermentation of carbohydrates in our gut. Archaea then produce methane as a byproduct of their digestion. [4] The Archaea are the hardest infection to kill, few antibiotics are effective - because they are not bacteria.

Biofilm and Archaea 

ibs c

Biofilm is produced as a covering my many microbes in the sinus, tonsils, and gut, leading to recurrent antibiotics being needed owing to the protective coverings from the biofilm the organisms produce. Treatment with enzymes or essential oils appears necessary and thyme oil and oregano as well as garlic oil have been studied as effective in animal research for the Archaea . A new herbal treatment called Atrantil is effective as well. It is more difficult to lower Archaea overgrowth because they tend to be more antimicrobial-resistant and form thick biofilms. [8]

Decreased bowel motions – less MMC i.e. migrating motor complex

Compared with hydrogen producers, human methane producers have significantly (P<0.05) lower serotonin levels. Serotonin is a nerve to nerve transmitter or communicator, and 80% of our bodies serotonin is not in the brain, its in the guts. Data indicate that methane-producing IBS patients have reduced serotonin.[18] Low serotonin may cause anxiety and or depressive symptoms too.

Good levels of Serotonin allows in the gut to work better by regulating proper nerve functions in the intestines, allowing proper bowel movements – and also causing calmer happier moods.

SIBO Treatments (Medical Therapy and Natural Program)

Antibiotic Therapy

An early report on SIBO being related to IBS appeared in 2002. Of 202 Irritable Bowel Syndrome patients (diarrhea type), nearly 4 out of 5 IBS patients selected had SIBO. Of these 202 patients, 47 had follow-up testing after a medical antibiotic therapy on Rifaximin. They showed that antibiotic eradication of the small intestine bacterial overgrowth in about half of the subjects [6]. (Note the high failure rate of the best indicated medical drug.)

However, in the successfully treated cases eradication of this overgrowth lead to a 75% reduction in IBS symptoms [4]. So the practical problem here is that the medical treatment for SIBO only works to remove the infection in around half the patients treated at best given on its own.[23]

Not only SIBO, but other qualitative change in the gut bacteria (dysbiosis) has been reported among patients with IBS [20], including high prevalence of Blastocystus (a parasite). These studies have led to a paradigm shift in understanding pathological rather than the psychological genesis of IBS, including fecal transplants [21, 22]

Treatment with Herbal Antimicrobials 

Treatment of the overgrowth might require multiple natural antimicrobial agents, antibiotics, and anti-biofilm agents such as thyme oil, oregano oil and garlic oil.

I will choose between 6 options of herbal-based antimicrobials based on clinical symptoms, the SIBO breath test. Treatments will take several antimicrobial therapies at one time and likely for six to eight weeks.

An equally important post-treatment stage of Replace, Repair and Reinoculate follows. The follow up treatment is vital owing to the otherwise high recurrence rate, whether taking a natural or medical program.


SIBO is a challenge to treat effectively whether taking medical antibiotics or our natural therapies. For this reason I strongly recommend you consult with an experienced practitioner.

A Call to Action

It is possible to treat IBS or SIBO. Here are the steps:

  1. Find an experienced practitioner who knows about SIBO and Food Intolerance Tests, and make the booking.
  2. Discuss your IBS symptoms with a qualified Functional Medicine Practitioner or Naturopathic physician.
  3. Under the practitioner's recommendation, complete one or a combination of these tests: SIBO Breath Test (only means to find Archaea methane issues), Food Intolerance Test, Cn accurate stool culture with Doctors Data, or the GI MAP (for more accurate DNA micro-biome testing that finds any intestinal inflammation, leaky gut, gluten intolerance and digestive enzyme deficiencies). With the appropriate testing, you can gather all necessary data on your gut infections including Virus, Bacteria, Candida/Fungi, Parasites and Amoeba.
  4. Your practitioner can treat you with natural antimicrobials, biofilm treatments and initial probiotics, as well as correcting the digestion and food intolerances if presented.
  5. Follow up treatment to boost the beneficial probiotic levels, and to diversify the diet to encourage a healthy gut flora.
  6. For some people with a more chronic infection, the gut lining may need to be repaired, which involves suitable nutrients and herbal anti-inflammatories, taken after the initial bacterial and amoebal killing is done.




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[3] Pimentel M, Chow EJ, Lin HC. Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. Am J Gastroenterol. 2000;95:3503–3506. [PubMed]

[4] Pimentel M. The prevalence of overgrowth by aerobic bacteria in the small intestine by small bowel culture: relationship with irritable bowel syndrome. Dig Dis Sci. 2012;57(5):1321-1329. also see Bures J. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol. 2010;16(24):2978-2990.

[5] Ragavan ND et al. PLoS One. 2015 Sep 16;10(9): Blastocystis sp. in Irritable Bowel Syndrome (IBS)- - Detection in Stool Aspirates during Colonoscopy. PMID: 26375823]

[6] J Spiller RC Role of infection in irritable bowel syndrome. Gastroenterol. 2007 Jan;42 Suppl 17:41-7.

[7]. Pimentel M, Chow EJ, Lin HC. Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. Am J Gastroenterol. 2000;95:3503–3506. [PubMed]

[8] Ford AC  et al. Yield of diagnostic tests for celiac disease in individuals with symptoms suggestive of irritable bowel syndrome: systematic review and meta-analysis.Arch Intern Med. 2009 Apr 13;169(7):651-8. doi: 10.1001/archinternmed.2009.22

[8] Mansueto P, D’Alcamo A, Seidita A, Carroccio A. Food allergy in irritable bowel syndrome: The case of non-celiac wheat sensitivity. World Journal of Gastroenterology : WJG. 2015;21(23):7089-7109. doi:10.3748/wjg.v21.i23.7089.

[10] Almeida JA, Kim R, Stoita A, McIver CJ, Kurtovic J, Riordan SM. Lactose malabsorption in the elderly: role of small intestinal bacterial overgrowth. Scand J Gastroenterol. 2008;43(2):146-154.

[12] Goebel A, Buhner S, Schedel R, Lochs H, Sprotte G. Altered intestinal permeability in patients with primary fibromyalgia and in patients with complex regional pain syndrome. Rheumatology (Oxford). 2008;47(8):1223-1227.

[13] Parodi A, Paolino S, Greco A, et al. Small intestinal bacterial overgrowth in rosacea: clinical effectiveness of its eradication. Clin Gastroenterol Hepatol. 2008;6(7):759-764.

[14] Weinstock LB, Walters AS. Restless legs syndrome is associated with irritable bowel syndrome and small intestinal bacterial overgrowth. Sleep Med. 2011;12(6):610-613.

[15] Weinstock LB, Klutke CG, Lin HC. Small intestinal bacterial overgrowth in patients with interstitial cystitis and gastrointestinal symptoms. Dig Dis Sci. 2008;53(5):1246-1251.

[16] Lauritano EC, Bilotta AL, Gabrielli M, et al. Association between hypothyroidism and small intestinal bacterial overgrowth. J Clin Endocrinol Metab. 2007;92(11):4180-4184.

{17] Klaus J, Spaniol U, Adler G, Mason RA, Reinshagen M, von Tirpitz CC. Small intestinal bacterial overgrowth mimicking acute flare as a pitfall in patients with Crohn’s disease. BMC Gastroenterol. 2009;9:e61. Accessed November 7, 2012.

[18] John K. DiBaise, M.D., Professor of Medicine, Mayo Clinic, Scottsdale

[19] AZ Nutritional Consequences of Small Intestinal Bacterial Overgrowth PRACTICAL GASTROENTEROLOGY • DECEMBER 2008

[20] Ghoshal UC, Srivastava D. Irritable bowel syndrome and small intestinal bacterial overgrowth: Meaningful association or unnecessary hype. World Journal of Gastroenterology : WJG. 2014;20(10):2482-2491. doi:10.3748/wjg.v20.i10.2482.] and have led to increasing focus on therapeutic manipulation of gut microbiota to treat this disorder using antibiotics, probiotics and fecal transplantation[21-22]. 

[21] Ghoshal UC, Shukla R, Ghoshal U, Gwee KA, Ng SC, Quigley EM. The gut microbiota and irritable bowel syndrome: friend or foe? Int J Inflam. 2012;2012:151085.[PMC free article] [PubMed]

[22] Brown AC. Ulcerative colitis, Crohn’s disease and irritable bowel syndrome patients need fecal transplant research and treatment. J Crohns Colitis. 2014;8:179. [PubMed]

[23] Triantafyllou KSioulas ADGiamarellos-Bourboulis EJ1.Rifaximin: The Revolutionary Antibiotic Approach for Irritable Bowel Syndrome. Mini Rev Med Chem. 2015;16(3):186-92. and Maria Lia Scribano. Role of Rifaximin in Inflammatory Bowel Disease Treatment. Mini-Reviews in Medicinal Chemistry. 2016 16 (3): 225 - 229