Digestive Health

Dr. Kim’s Guide to SIBO Treatment

By Kim Crawford, M.D. Last updated: November 3, 2018
sibo treatment

What is SIBO?

Small intestinal bacterial overgrowth (SIBO) is an increased number and/or abnormal type of bacteria in the small intestinal section called the jejunum. For many years, a culture of the small bowel was the gold standard for diagnosing SIBO based on the presence of ≥1 × 105 bacteria (colony-forming units (CFU)) per cubic centimeter of jejunal aspiration. However, this definition is now under scrutiny, and current thinking is that “normal” rarely exceeds 1 × 103cfu/ml. In this article, I’ll cover SIBO basics and treatment including:

  • Who is prone to getting SIBO?
  • What are the symptoms?
  • How to diagnosis SIBO?
  • SIBO treatment: diet and antibiotics vs. herbals and probiotics

Who develops SIBO?

The underlying conditions for SIBO range from diabetes to hypothyroidism to inflammatory bowel disorders and even rosacea. For a full list, scroll to the last paragraph where I discuss underlying condition treatment.

SIBO Symptoms

The symptoms of SIBO are often confused with those of other GI disorders. However, if you are receiving treatment and have the following symptoms along with an underlying condition you need to have a medical examination. The most common symptoms are bloating and flatulence; especially after eating. Other symptoms include abdominal discomfort, diarrhea, and even constipation following the episode of bloating. Multiple food intolerances—often causing the symptoms just noted—are common. Due to malabsorption, you may develop vitamin deficiencies; most notably vitamin D and B12 with their attendant complications (anemia, neuropathy, autoimmune disease and so on).

Diagnosing SIBO

As noted above, the endoscopic procedure of bacterial sampling and quantification has fallen out of favor due to the variability of data regarding diagnostic parameters, patient comfort, and procedure risk. Breath tests are now a common practice as an alternative to direct aspiration because they are noninvasive and less expensive. The most commonly used breath test is the hydrogen breath test.

Hydrogen breath tests are based on the principle that carbohydrate fermentation by the gut flora, primarily anaerobic bacteria in the colon, is the only source of hydrogen in the body. The lactulose hydrogen breath test (LHBT) is the most widely used hydrogen breath test. The increase in hydrogen level after 10 grams of lactulose is ingested is measured. Intestinal bacteria ferment the lactulose, resulting in the production of hydrogen and/or methane. After the administration of the lactulose, we take breath samples at 15-minute intervals for 3 hours.

It is common to measure methane levels as well as hydrogen levels to differentiate between methane and non-methane bacterial dominance. This is necessary (mostly) because there are a huge number of false negatives with hydrogen testing only; diagnosing only about 40%. Because breath tests are not very sensitive or specific, many Functional doctors will treat a patient if they exhibit symptoms and have underlying reasons for them.


SIBO Treatment

Diet for SIBO   

sibo treatmentThere have been a variety of diets studied for SIBO treatment. A low-FODMAP diet shows good results, and most definitely someone with SIBO needs to avoid fructose and fructans.

The GAPS diet is successful in some cases, and reports also document the Specific Carbohydrate diet to be effective.

Studies have been done using what is called the Vivonex Plus formula diet. This diet is a product of a major food company which is full of additives and awful ingredients—I’d steer clear.

Lastly, the Elemental diet shows positive results as well.

I tend to err on the side of extreme caution when it comes to bothersome and life-altering GI issues such as SIBO or Crohn’s disease; follow the link above for the diet I use for patients which is a combo-platter of everything that works.

Antibiotics for SIBO 

There is currently no overwhelming consensus regarding the choice, dosing, and duration of antibiotic therapy. Broad-spectrum antibiotics which affect enteric aerobes and anaerobes include amoxicillin/clavulanate, metronidazole, ciprofloxacin, norfloxacin, cephalexin and, most recently, rifaximin. Rifaximin has gained popularity since it is not absorbed systemically, and has few side effects. A course of rifaximin is currently the antibiotic of choice due to these factors as well as having less frequent reported cases of antibiotic resistance. The average course of treatment is two weeks. The average reported cure rate is 40%.

Herbals for SIBO 

Herbal therapies are at least as effective as rifaximin for resolution of SIBO. Herbals also appear to be as effective as triple antibiotic therapy for SIBO rescue therapy for rifaximin non-responders. Some effective herbals include the potent oregano oil (take with medical supervision), berberine, barberry, garlic, olive leaf extract, goldenseal, wormwood, Oregon grape and pau d’arco. There is even evidence for anti-microbial activity using cloves, thyme, cinnamon, rosemary, ginger, basil, fennel, coriander and black pepper.

The “cure rate” with various herbal mixtures, administered over four to six weeks tends to mirror the effects of the most effective antibiotic (rifaximin) given over two weeks’ time; 46% for the herbals compared to 40% for the rifaximin. For this reason, I usually treat patients for three months with a mixture of herbals that often includes oregano oil, olive leaf, berberine, and barberry. Note my findings confirm this “mixture” and length of time are effective in my medical practice; this is not an “official GI protocol.” I also use leaky gut supplements and add a multi-fiber power, and modified citrus pectin powder, too.

Probiotics for SIBO

Based on research listed in the references section, the majority of patients placed on probiotics showed a significantly higher SIBO decontamination rate than the non-probiotic groups. The probiotics used and quantities are generally the same as those as I have discussed in previous articles regarding bloating, Crohn’s disease and so on. Some cases require avoidance of d-lactate forming probiotics such as the Lactobacillus acidophilus species. All cases do better with the addition of Saccharomyces boulardii. And some cases require the addition of the biofilm disruptor nattokinase.

Treat the Underlying Disorder and Nutritional Deficiencies 

It should go without saying that treatment of the underlying disorder is of critical importance if we want to clear and maintain a SIBO cure. Underlying problems include CIRS (mold and Lyme), heavy metal toxicity, hypothyroidism (common!), celiac disease, inflammatory bowel disease, irritable bowel syndrome, and decreased stomach acid (often from proton pump inhibiting medications). Other underlying conditions include prolonged bouts of low progesterone, diabetes, diverticulosis, aging, high cortisol, and even rosacea! One of the side effects of antibiotics is not just leaky gut, but SIBO. B vitamins are often deficient as is magnesium and other trace minerals.

Summary thoughts 

You may have visited your primary care doctor for things such as gas and bloating, and left their office with a prescription for drugs to patch up your symptoms; not treat them. If you suffer from the symptoms described above, notably bloating after eating, and have a predisposing condition, then find yourself a functional specialist to get a proper diagnosis and treatment regimen.

Selected References
  2014 May;3(3):16-24. doi: 10.7453/gahmj.2014.019.

Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth.

Chedid V, Dhalla S, Clarke JO, Roland BC, Dunbar KB, Koh J, Justino E, Tomakin E, Mullin GE.
. 2013 Sep; 4(5): 223–231.
doi:  10.1177/2040622313496126
PMCID: PMC3752184
PMID: 23997926

Gastrointestinal bacterial overgrowth: pathogenesis and clinical significance

Amit H. Sachdev and Mark Pimentel
 2010 Dec;24(4):943-59, viii-ix. doi: 10.1016/j.idc.2010.07.007.

Small intestinal bacterial overgrowth.

Quigley EM, Abu-Shanab A.
 2018 Mar;47(1):193-208. doi: 10.1016/j.gtc.2017.09.008. Epub 2017 Dec 7.

Small Intestinal Bacterial Overgrowth: Nutritional Implications, Diagnosis, and Management.

Adike A, DiBaise JK.
 2017 Apr;51(4):300-311. doi: 10.1097/MCG.0000000000000814.

Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth: A Meta-Analysis and Systematic Review of Current Evidence.

Zhong C, Qu C, Wang B, Liang S, Zeng B.
. 2016 May; 7(5): e173.
Published online 2016 May 26. doi:  10.1038/ctg.2016.32
PMCID: PMC4893683
PMID: 27228404

Effects of Rifaximin on Transit, Permeability, Fecal Microbiome, and Organic Acid Excretion in Irritable Bowel Syndrome

Andrés Acosta, Michael Camilleri, Andrea Shin, Sara Linker Nord, Jessica O’Neill, Amber V Gray, Alan J Lueke, Leslie J Donato, Duane D Burton, Lawrence A Szarka, Alan R Zinsmeister, Pamela L Golden, and Anthony Fodor
. 2017 Mar; 11(2): 196–208.
Published online 2017 Mar 15. doi:  10.5009/gnl16126
PMCID: PMC5347643
PMID: 28274108

Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy

Uday C. Ghoshal, Ratnakar Shukla, and Ujjala Ghoshal
 2014 Nov;17(6):605-9. doi: 10.1097/MCO.0000000000000116.

The role of FODMAPs in irritable bowel syndrome.

Shepherd SJ, Halmos E, Glance S.
. 2017 Jun; 18(6): 1283.
Published online 2017 Jun 16. doi:  10.3390/ijms18061283
PMCID: PMC5486105
PMID: 28621716

Antibacterial and Antifungal Activities of Spices

Qing Liu, Xiao Meng, Ya Li, Cai-Ning Zhao, Guo-Yi Tang and Hua-Bin Li
 2017 Mar 28;27(3):429-438. doi: 10.4014/jmb.1608.08024.

Antimicrobial Activity of Basil, Oregano, and Thyme Essential Oils.

Sakkas H, Papadopoulou C

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