Small Intestinal Bacterial Overgrowth (SIBO)


In SIBO large numbers of bacteria in the small intestine cause gas, bloating, interrupt nutrient uptake, etc.

Small Intestine Bacterial Overgrowth or SIBO is a chronic condition or infection of bacterial overgrowth in the small intestine. Normally the small intestine has low numbers of bacteria and the large intestine has high numbers of bacteria; however, in SIBO bacteria exist in large numbers in the small intestine which interferes with proper digestion and can lead to nutritional deficiencies.

Bacteria in the small intestine thrive on carbohydrates and produce a lot of gas and endotoxins that can exceed the liver’s detoxifying capacity, creating a state of toxemia. SIBO is associated with damage to the lining or membrane of the small intestine, and is also referred to as Leaky Gut Syndrome.

The symptoms of SIBO include bloating, gas, constipation and/or diarrhea, abdominal pain, nausea, and heartburn. Systemic symptoms include fatigue, sleep disturbances, headaches, brain fog, joint and muscle pain, and food allergies and sensitivities. SIBO is associated with many chronic health conditions, particularly Irritable Bowel Syndrome, and occurs frequently if not always in ME/CFS and FM. Although not the primarily cause of these syndromes, it is a complication that is important to address.


SIBO is diagnosed with a breath test that measures the hydrogen and methane gas produced by bacteria in the small intestine. Patients drink a sugar solution of glucose or lactulose after a 1 or 2 day preparatory diet. Measurements are taken at a baseline (before consuming the solution) and then every 15-20 minutes for 1-3 hours.


The 3-hour lactulose breath tests measures the amount of hydrogen produced in the small intestine

The lactulose breath test diagnoses overgrowth in the distal (lower) end of the small intestine where SIBO is more common. The glucose test can only measure gas in the upper end.

The three hour lactulose breath is considered the gold standard for doctors who specialize in SIBO. Typically patients who produce high levels of hydrogen suffer from diarrhea, and patients who produce high levels of methane suffer from constipation.

Dr. Mark Pimentel’s Protocol

Dr. Mark Pimentel is the pioneering researcher and gastroenterologist who discovered the link between bacterial overgrowth in the small intestine and Irritable Bowel Syndrome. He is director of the Gastrointestinal Motility Program at Cedars-Sinai Medical Center in Los Angeles and author of the book A New IBS Solution Bacteria – The Missing Link in Treating Irritable Bowel Syndrome.[1]

His treatment protocol is three-fold:


First he prescribes a short course of antibiotics to eradicate bacterial overgrowth. If a patient has high levels of hydrogen they take rifaximin (Xifaxan), and if they have high levels of methane they take rifaximin and neomycin. These antibiotics are particularly effective because they are not broad based, and they remain inside the gastrointestinal tract.


Dr. Pimental is the Director of the Gastrointestinal Motility Program at Cedars-Sinai (http://giving.cedars-sinai.edu/page.aspx?pid=2423)

After finishing the antibiotics a breath test is repeated. If gas levels are still abnormally high he prescribes another round of antibiotics. If bacterial overgrowth remains resistant after several rounds of antibiotics, he recommends that patients follow a two week elemental diet where they drink only water and replace meals with a formula (brand name Vivonex Plus) containing protein from free amino acids, carbohydrates in the form of maltodextrin, fat as various oils, vitamins, and minerals.


Second, Pimentel places his patients on a diet of foods that are easily digested, so that most of the food can be absorbed higher up in the intestine–away from the problem bacteria. This means eliminating high fiber foods such as beans, peas, whole grains, nuts, and soy. The diet also avoids all kinds of sugars that feed the bacteria, including lactose found in dairy products.

Prokinetic agents

Third, he places his patients on a prokinetic drug for at least three months to increase small intestine motility with a corresponding decrease in the duration of migrating motor complex cycles.

The most effective prokinetic drug is tegaserod (Zelnorm), but it was withdrawn from the US market in 2007 due to FDA concerns about possible adverse cardiovascular effects.

Alternative prokinetic drugs are low dose naltrexone (LDN) and low dose erythromycin. The body produces the most cleansing wave activity when a person is not eating, which is why the drugs are prescribed to be taken at bedtime. For this same reason Pimentel advises to limit food intake to three meals a day, and to avoid snacking and consume nothing except water between meals.


Possible Autoimmune Connection

According to Pimentel, bacterial overgrowth in the small intestine causes an autoimmune response that damages the nerves that control the migrating motor complex. Eradicating the bacteria alone is not enough to completely heal from SIBO. Patients who take antibiotics and do not follow up with diet recommendations and a prokinetic drug often relapse.

Increased Risk Factors for Fibromyalgia and Chronic Fatigue Syndrome Patients


Dr. Pimental believes low levels of stomach acid in ME/CFS patients increases their risk of bacterial overgrowth in the small intestine.

Pimentel thinks that food poisoning may initially cause cleaning wave inhibition, setting the scene for SIBO in many patients with IBS. Patients with ME/CFS or FM are particularly susceptible to SIBO because they typically have low levels of stomach acid that reduce bacteria at the onset of digestion, and they have low levels of endorphins that regulate contractions in the intestinal walls.

Pimentel did two studies linking SIBO and FM. In the second study, published in 2004, he found that FM patients had hydrogen levels significantly higher than non-fibromyalgia IBS patients and healthy control patients. [2] These high levels of gas produce exceedingly large amounts of bacterial toxins or endotoxins, which could explain some of the symptomology of FM. Furthermore, he reports a case history of a woman who was diagnosed with FM whose symptoms resolved after completing Pimentel’s treatment.

SIBO Center for Digestive Health

A group of naturopathic physicians associated with the National College of Naturopathic Medicine in Portland, Oregon founded a SIBO specialty called the SIBO Center for Digestive Health.

Their treatments are based on the research of Dr. Pimentel, but they also include herbal antibiotics and various diets.


The SIBO Center for Digestive Health has information on SIBO and SIBO testing

Dr. Allison Siebecker, a founder of the center, has an educational website with information about SIBO including overviews of treatments, diets, studies and resources.   Included on the website are lectures that can be downloaded for a fee from leading clinicians and researchers at the SIBO Symposium that took place in Portland in January of 2014. The physicians at the SIBO Center have found that herbal antibiotics are often as effective as pharmaceutical antibiotics, although the course of treatment is typically longer.

The herbal treatment of choice is Allimed, a high potency, concentrated form of allicin extracted from garlic.

The SIBO Center recommended diets include the Specific Carbohydrate Diet (SCD) described in Elaine Gottschall’s book Breaking the Vicious Cycle; the Gut and Psychology Syndrome Diet (GAPS), an expanded SCD diet and protocol created by Dr. Natasha Campbell-McBridge; the Low Fermentable Oligo-Di-Monosaccharides and Polyols Diet (FODMAPS), a diet low in fermentable carbohydrates that has been shown to be effective in persons with IBS; the Cedars-Sinai Diet (Dr. Pimentel’s diet); and some combination of these diets.

My Story

It took me many years to learn about SIBO and its connection with my health. I began suffering from chronic fatigue in 1973 and initially had no problems with my digestion. Over the first ten years of my condition, however, I became increasingly sensitive to sugar and alcohol, which increased muscle tone and worsened my chronic headaches. Eventually these foods made me hot at night and interrupted my sleep.


First came chronic fatigue, then digestive difficulties, then fibromyalgia then more gut problems

Eliminating them from my diet was one of the most effective ways for me to manage my symptoms, but over time the list of things that I reacted to increased to include food with even a small amount of sugar such as that found in salad dressings, sauces and baked goods, and all kinds of fruit. In retrospect, I think that the diet I arrived at was helpful because it discouraged the overgrowth of bacteria in my small intestine. I knew that I had low stomach acid, and at one point took hydrochloric acid capsules with meals, but that acid supplement did not seem helpful.

In the fall of 2001 my health took a turn for the worse when I developed fibromyalgia muscle pain following physical activity of any kind. This was accompanied by even more disturbed sleep and gastrointestinal problems. Whole grains, beans, and nuts, which I had tolerated well in the past, made me constipated and caused bloating. I passed odorless gas throughout the day and night. My bowel movements consisted of small green or orange/brown balls, which I passed most days. I suspected, however, that I had slow transit because after doing enemas I would not have a bowel movement for a week.

Beginning in 2005 I began a series of breakthroughs in my health. My thyroid function stabilized after taking compounded T3 in incremental doses according to Wilson’s Low Body Syndrome protocol; my cardiovascular function and breathing improved with Oral Systemic Balance, a therapy that improves ease of breathing and restores balance to the autonomic nervous system through specially designed oral appliances; and I reversed years of adrenal exhaustion with LENS neurofeedback. Although I no longer suffered from chronic fatigue my digestion, muscle recovery, and sleep improved only slightly with these therapies. I felt like I had solved the big challenges of my health condition, but I was left with some kind of complication or collateral damage.

I consulted a plethora of medical and alternative doctors about my remaining symptoms. It was clear that I suffered from some aspects of fibromyalgia – muscle pain, sleep disturbances, and gastrointestinal complaints, but my pain was never random and manifested itself as delayed onset muscle soreness that did not improve with conditioning.

Although my bowel movements were abnormal, I did not experience any gastrointestinal pain if I adhered to my diet. And I never experienced any kind of brain fog or cognitive difficulties. I also had a positive ANA and low levels of amino acids.


Over the years Darden underwent multiple gut tests

My doctors suspected that I had some kind of infection; however, extensive testing did not turn up anything – no intestinal parasites, candida, Lyme and co-infections, or mycoplasma.  Over a period of ten years I had multiple GI tests used by naturopathic and holistic medical doctors including the Comprehensive Digestive Stool Analysis by Genova Diagnostics and the Expanded GI Panel by Diagnos-Techs.

The tests showed heavy abundance of some nonpathogenic bacteria and the presence of Helicobacter pylori but were otherwise normal.  I consulted for a year with Dan West, an independent scientist in the field of Human Probiotics, but did not experience any improvements in my health from taking his supplements.

Results from the American Gut Project, a crowd funded study that sequences the microbes of thousands of individuals, showed a wide divergence in my microbes from the average person of my age, gender, diet, and body mass index, and found large numbers of a less common phylum of bacteria called Verrucomicrobia that are abundant in the soil and water environments.

In the winter of 2014, my naturopathic physician suggested that I try taking a teaspoon of apple cider vinegar in water before each meal to help my digestion. Introducing apple cider vinegar improved my muscle recovery by 15%, so I suspected I was on to something significant.

Dr. Allison Siebecker's website on SIBO was an important resource

Dr. Allison Siebecker’s website on SIBO was an important resource

Another naturopathic physician suggested that I might have SIBO, a condition that I had never heard of. She recommended a one hour glucose breath test from Metabolic Solutions Incorporated. The test results were negative but I suspected they were inaccurate.

I found Dr. Siebecker’s website and read Dr. Pimentel’s book A New IBS Solution which recommended three hour lactulose breath tests. My doctor ordered three hour tests from two separate labs (Commonwealth Laboratories and NCNM Clinic Lab) simultaneously. The results were similar – high levels of both methane and hydrogen.

In April of 2014 I traveled to Portland, Oregon to see Dr. Melanie Keller, a naturopathic physician at the SIBO Center of Digestive Health. Subsequent appointments were made via Skype, which works well for out of town patients.

Dr. Keller recommended that I take 2 capsules of Allimed three times a day for four weeks. This dose made me constipated and gave me a heavy cramp-like feeling in my abdomen. Then I started taking the magnesium product Homozon that moved my stools and eliminated these symptoms.

Over the course of the treatment I stopped experiencing gas and bloating and my muscle recovery gradually improved to the point where I have now returned to an active lifestyle of gardening, walking, and practicing the piano with no adverse effects. Dr. Keller suggested I take ginger root, a natural prokinetic agent (capsules of 1,100 mg. 2x a day).

This resulted in an improvement in my sleep, an unexpected but welcome outcome that has convinced me that my sleep disturbances are due to problems with the migrating motor complex. My followup SIBO breath test showed a significant reduction of hydrogen and methane gases but still well above normal levels.

Dr. Keller next prescribed a ten day course of rifaximin and neomycin and a pharmaceutical prokinetic drug. In general my health is improving at a steady and sure pace. I know that treating SIBO successfully is a process, but I remain confident that I am on the right path.


Darden’s sleep and gut issues and ability to exercise have all improved as her SIBO has been treated

SIBO is the last piece of the puzzle for me in a long and complex story of chronic illness. I suspect that it plays a significant role in the symptomology of both chronic fatigue and fibromyalgia syndromes. Alternative health practitioners stress the importance of detoxification programs for healing, but my personal experience with these programs, which I pursued extensively, was that they barely made a difference. This makes sense because the bacteria in the small intestine is constantly spewing out endotoxins, which the liver cannot keep abreast of.

The role of the thousands of microorganisms in the gastrointestinal tract referred to as the microbiome is an area of keen interest in medical science today with the prospect of probiotics providing new therapies.

But it turns out that, in the case of SIBO, it is not the particular bacteria that an individual harbors, but the location of the bacteria that is critical. A common theory of CFS is that infections such as Lyme “hide” from the immune system, but I think this theory is flawed.

The infectious agents associated with ME/CFS often fall under the category of “possible pathogens” and are common in the entire population, yet they do not present a problem for healthy individuals. Perhaps it is their presence in the small intestine that is wreaking havoc. I do not think it is a coincidence that magnesium, malic acid found in apple cider vinegar, and low dose Naltrexone (LDN), three of the most effective things that help fibromyalgia patients, are effective in reducing small bacteria overgrowth.

In conclusion, I am relieved to finally understand the role of SIBO in my own health, and I am encouraged by the improvements I have experienced by treating it. I will update this blog post periodically to report my progress.



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