Undoctored Protocols: Small Intestinal Bacterial Overgrowth (SIBO)

sibo Small intestinal bacterial overgrowth (SIBO) is proving to be more common than previously suspected, occurring in 20% of people with no symptoms, 50-75% of people with irritable bowel syndrome (IBS), as many as 100% with fibromyalgia. SIBO is a form of dysbiosis in which microorganisms are not just disrupted in species composition, but also ascend up the intestinal tract as high as the duodenum and stomach which should nearly be sterile. Because of the challenges in making the diagnosis, the prevalence of SIBO may be even greater than suspected.


SIBO is a common explanation for incomplete response to healthy practices such as grain elimination. A common scenario is someone who has fibromyalgia or rosacea and experiences partial improvement with Undoctored Wild, Naked, Unwashed strategies but does not experience full relief. Typically, SIBO is identified, then corrected, followed by full remission of symptoms. In other words, SIBO permits health conditions to emerge and allows them to perpetuate even after the initial cause or contributing factors have been corrected. Specific correction of SIBO is therefore often required for full recovery of health.
SIBO is caused by a number of factors: grain and sugar consumption, frequent alcohol consumption, reduced stomach acid (achlorhydria, hypochlorhydria) from prior grain consumption (via an autoimmune destruction of stomach parietal cells that produce stomach acid) or from taking stomach acid-blocking drugs (PPI’s, H2 blockers), prior antibiotic use, and factors that reduce intestinal motility such as diabetes, opiate drugs, and uncorrected hypothyroidism.
Several conditions are highly associated with SIBO, suggesting that correcting SIBO may be a necessary step to achieve full remission/response. Such conditions include
  • Fibromyalgia: In one study 100% of people with fibromyalgia had SIBO.
  • Irritable bowel syndrome.
  • Rosacea: Treatment of SIBO is highly correlated with remission.
  • Restless leg syndrome.
  • Vitamin B12and/or folate deficiencies, macrocytic anemia (high MCV value).
  • Joint pain.
  • Chronic prostatitis.
  • Interstitial cystitis.
  • Polyneuropathy.
  • Fatty liver (non-alcoholic steatohepatitis).
  • Deep vein thrombosis.
  • Celiac disease, Crohn’s disease, ulcerative colitis.
  • Colorectal cancer.
SIBO may also result in increased potential for H. pylori colonization of the stomach that increases risk for hypo- or achlorhydria (lack of stomach acid) and stomach cancer, as well as increased potential for colorectal cancer from SIBO alone.

SIBO may also result in increased potential for H. pylori colonization of the stomach that increases risk for hypo- or achlorhydria (lack of stomach acid) and stomach cancer, as well as increased potential for colorectal cancer from SIBO alone.

If a pre-existing gastrointestinal condition is present such as irritable bowel syndrome, celiac disease, Crohn’s disease, or ulcerative colitis, or if metabolic diseases such as type 2 diabetes, obesity, or an autoimmune or neurological condition are present, then the likelihood of SIBO is very high. Type 2 diabetes, hypothyroidism, and opiate drug use are also associated with reduced small intestinal motility, slowing the passage of partially-digested food and thereby contributing to development of SIBO. (The intestinal motility-reducing effect of opiates may also explain one of the means by which wheat and related grains contribute to SIBO, i.e., gliadin-derived opioid peptides that, like prescription opiates, slow intestinal passage of food.)

SIBO is suggested by symptoms that persist even after you have completed your 6-week Undoctored Wild, Naked, Unwashed program, such as:
  • Abnormal bloating and gas, especially upon consuming foods containing prebiotic fibers
  • Diarrhea (occasionally constipation)
  • Malabsorption—i.e., inability to digest some components of diet, most commonly fat and evidenced by fat droplets or an oily film in the toilet with a bowel movement, floating stools
  • Unexplained skin rashes
  • Sensitivity to coffee—with diarrhea
  • Other food sensitivities—e.g., new intolerance to dairy, nuts, coffee, tea, other foods
  • Mood swings—anxiety, depression
  • Sleep disturbances—especially insomnia or inability to enjoy sustained sleep
You can appreciate how far-reaching SIBO can be with consequences for gastrointestinal health, skin health, even emotional and mental health. If uncorrected, potential for colon cancer, diverticular disease, autoimmune conditions, type 2 diabetes, heart disease, emotional disturbances and other conditions increase. Identifying, then correcting, this condition is therefore crucial for long-term health.

Documenting SIBO

A hydrogen breath test is the preferred method for diagnosing SIBO. While somewhat cumbersome, as it involves 24-hour dietary preparation followed by a 12-hour fast, in-gestion of a sugar such as lactulose or glucose (metabolized by gut flora that release hydrogen gas or methane but not by human digestion), followed by several breath col-lections, it is the most practical and non-invasive means of identifying SIBO with moderate confidence. Because some forms of SIBO, especially those associated with constipation, also increase production of methane gas, a methane gas collection from the breath can also be performed either separately or at the same time as the hydrogen breath collection.

A sample of an abnormal hydrogen/methane breath test can be see here: BioHealth-Sample-Report-900-1

There is also a new product called Aire that is a consumer testing device that can be reused, avoiding the need to purchase H2-testing devices for each testing episode. Our preliminary experience suggests that it is easy to use and does indeed yield positive results that correspond to formal H2-testing. It reports H2 levels on a scale of 0 to 10 and is useful in generating a time-distribution curve, i.e., perform a pre-food test followed by testing every 15 minutes for up to 3 hours: the earlier a positive response is generated, the more likely it is that SIBO is the explanation. (Late responses at 3 hours and later can be due to normal colonic microorganisms.) The Aire device is also useful to assess response to antibiotics if performed daily after a prebiotic fiber challenge, as well as to assess for recurrences after treatment. (Ignore the package description of the applications of this device, as it only discusses its use to identify FODMAP foods for elimination, an approach that does nothing to address the SIBO causing FODMAP intolerance.)

It would also be reasonable to simply embark on a program of treatment if the symptom cluster cannot be explained by any other diagnosis and includes abdominal discomfort, bloating, and gas; an abnormal response to prebiotic fibers; diarrhea; fat malabsorption; and new food intolerances and rashes. The downside to an empiric approach, however, is assessing response and identifying recurrence.

Gastroenterologists prefer to perform endoscopy to retrieve material from the upper jejunum to identify excessive quantities of microorganisms in a location that should be nearly sterile, but this is invasive and, in the great majority of cases, underestimates the condition since there are many “false negatives,” i.e., samples that fail to reveal the extent of the condition since colonizing bacteria must ascend all the way to the duodenum or proximal jejunum to be detected. You can imagine that someone could have, say, only 10 feet of their small intestine colonized but not yet reaching the upper digestive tract and therefore be undetectable by this method. The hydrogen breath test therefore remains the most rational starting test.

The hydrogen breath test is also the easiest way to assess response to some intervention. In other words, if the starting hydrogen breath test proves abnormal, an antibiotic or dietary regimen is followed, then a breath test is repeated to assess response and need for additional therapy. It can also be repeated longer-term, as recurrence is a fairly common issue. But, with each H2 test costing around $150-$300, you can see the appeal of having an Aire device at a current single cost of $159 with unlimited testing ability.

It is also reasonable to treat SIBO empirically, i.e., based on your best judgment without benefit of H2 testing or endoscopy. If, for instance, intolerance to prebiotic fibers is present with lower gas, abdominal discomfort, and diarrhea develop within 60 minutes of ingesting any prebiotic fiber, that is a very confident sign that SIBO is present (or has recurred after treatment). Multiple unexplained food intolerances, especially to foods that you were tolerant to in past, is another reliable sign. Lastly, conditions such as fibromyalgia, irritable bowel syndrome, psoriasis, restless leg syndrome, and autoimmune conditions are highly likely to be associated with SIBO. You will, however, want to make clear note of what signs you are using to presumptively identify SIBO, as you will need to observe for recurrence after a course of treatment.

Reversing Dysbiosis That Has Ascended Up the GI tract

There are four general approaches to killing off the organisms that have ascended up the GI tract:

Probiotics alone: This strategy has not been satisfactorily explored, though preliminary evidence suggests that some people respond to probiotic supplementation alone. This suggests that the probiotic regiment advised in the Undoctored program has potential to reverse SIBO in at least some people. The odds may be stacked in favor of response to probiotics if our L. reuteri yogurt is part of the regimen, as this microorganisms has the unique capacity for colonizing the upper gastrointestinal tract and producing bacteriocins, i.e., natural antibiotics effective against the Bacteriaceae, the species that characterize SIBO.

However, if excessive gas, bloating, abdominal discomfort, or depression symptoms are encountered with addition of prebiotic fibers on the Undoctored program, it is advisable to hold the prebiotic fibers for 4 weeks while continuing the probiotic alone, then reattempt to introduce prebiotics again. If unpleasant symptoms recur, then further efforts, e.g., a hydrogen breath test, should be considered to document SIBO.

Prescription antibiotics: Rifaximin is the preferred agent, as it is effective against most species of microorganisms in the gut and very little is absorbed outside of the intestinal tract. Rifaximin alone is effective in approximately half of the people who take it. The duration of treatment varies widely from 7 to 30 days with no clear-cut advantage to prolonged therapy.

Effectiveness may be increased by combining it with a prebiotic fiber (e.g., 5 grams per day), presumably because the prebiotic fiber encourages bacterial growth, making microorganisms more susceptible to the antibiotic and keeping them from sporulating, or entering a hibernating spore phase in which they are not susceptible to the antibiotic. Downside: cost (typically around $1200 for a 4-week course) and 3% risk of Clostridium difficile enterocolitis, bloody diarrhea that needs to be treated with another round of antibiotics specific for this organism. Metronidazole and ciprofloxacin have also been used with limited success, though there are few formal clinicals trials examining their use.

Herbal antimicrobials: One study has demonstrated that the mix of herbal antimicrobials in either FC Cidal + Dysbiocide (Biotics Research Laboratories) or Candibactin-AR + Candibactin-BR (Metagenics) slightly outperformed prescription rifaximin with 46% effectiveness in the herbal arm vs. 34% in the rifaximin arm. Each preparation contains a mixture of herbal preparations and it is unclear whether every component is necessary for efficacy. (Berberine, a component of Candibactin-BR, for example, may prove to be effective by itself. There are insufficient data at present, however.) In this study, also, the regimen used was slightly different than that recommended by the manufacturer. (Candibactin-AR labeling recommends one capsule three times per day, while the study used two capsules twice per day.)

Deprive bowel flora of all prebiotic fibers: This approach essentially starves microorganisms of essential prebiotic fibers. Some call this a FODMAPs diet. This approach is of uncertain effectiveness for SIBO (though is known to be effective for IBS with fructose and lactose intolerance), but is extremely restrictive, going beyond elimination of all grains and sugars to also exclude legumes, most fruit, many vegetables, dairy, and liquor. It also requires an extended period of time, typically 8 weeks or longer, to be successful. It also likely not a full solution, as microbial species diversity is reduced (an undesirable effect) and it includes no effort to recultivate healthy bacterial species.

Eliminated foods include nearly all fruit, dairy, starchy vegetables, garlic, onions, mushrooms, and eggs. Permitted foods include meats, poultry, fish, selected non-starchy vegetables such as lettuce and green beans. Note that a carbohydrate limitation is not built into this dietary approach and will be necessary to maintain weight and not incur the health complications of excessive carbohydrate intake.

More details on the diet can be found here: http://www.ibsdiets.org/fodmap-diet/fodmap-food-list/

To date, the greatest success rates have been associated with a combination of strategies, namely:

1)  A course of antibiotic or herbal antibiotic accompanied by prebiotic fiber, followed by

2)  A high-potency probiotic (e.g.,50 billion CFUs or more per day) containing lactobacillus and other species, and

3)  Repeated courses of treatment over several months

In other words, it may require more than one round of treatment to fully eradicate SIBO.

An uncertainty: The success of antibiotics in eradicating stomach populations of H. Pylori (that cause ulcers) are heightened by including a biofilm disrupting agent such as N-acetyl cysteine, i.e., an agent that temporarily dissolves the mucous lining in which bacteria can sequester and be less susceptible to antibiotics. Does this same benefit apply to microorganisms of SIBO that are farther down the intestinal tract, such as the ileum? There are no data, but there is no harm in a course of N-acetyl cysteine, 600-1200 mg twice per day, to accompany the course of antibiotics in the hopes that a more complete response is achieved. 

Preventing Recurrence

Recurrence of SIBO is a common problem, though it is not clear whether this can be blamed on neglecting to address causative factors (as is the rule in clinical trials) or whether response was incomplete and recurrence represents recolonization of resistant or persistent microbes. The same efforts that we institute to prevent and treat dysbiosis are the same that we put to work to prevent recurrence of SIBO. This includes:
  • Avoidance of grains and sugars, minimize alcohol
  • Filtering water to eliminate chlorine/chloramine and fluoride
  • Choosing organic foods whenever possible to minimize herbicides, pesticides, and genetically-modified foods
  • Avoiding emulsifying agents such as polysorbate 80 and carageenan
  • Minimize exposure to prescription antibiotics
  • A course of high-potency, multispecies probiotics after completion of a SIBO therapeutic effort
  • Long-term inclusion of prebiotic fibers
  • Efforts to normalize stomach acid such as stopping stomach acid-blocking drugs, supplemental betaine hydrochloride if hypo- or achlorhydria is identified
  • Supplements to compensate for pancreatic enzyme or bile acid insufficiency, if diagnosed
  • Including fermented foods, e.g., fermented vegetables, yogurt, kefir, etc., in your diet

It may be helpful to view SIBO and dysbiosis like you view the weeds in your garden—just weeding your garden once does not prevent new weeds from taking root a few days later. Surveillance and preventive efforts to keep SIBO and dysbiosis at bay and maintain a healthy bowel flora profile are ongoing efforts that require your long-term awareness.

How to use the AIRE device to identify and manage SIBO


There’s a clever, elegant new consumer health testing device called AIRE made by a company called FoodMarble. The device (pictured above) measures hydrogen gas, H2, in the breath, the same as formal H2 testing used to diagnose small intestinal bacterial overgrowth, SIBO.

Formal H2 breath testing is a hassle. There’s a day-before prep, you drink a sugar solution (lactulose or glucose), then collect breath samples every 30 minutes for 3 hours, then mail the package to a lab. If obtained directly without a doctor, each single-use test kit (glucose only) costs $149. If obtained through a doctor, then additional charges are typically added, especially if the testing is done in a lab or office. Each test kit is useful for only one round of tests. If you want to verify, for instance, that SIBO has been eradicated after a course of antibiotics, then you have to purchase another test kit and go through the process again. The same is true when assessing for all-too-common recurrences: another $149 test kit, another round of testing.

The AIRE device is therefore a game-changer, as it is reusable over and over again. At $159 per device, it can save a lot money over time, as well as cut down considerably on the hassle. It is exceptionally easy to use: turn the device on by pushing a button, open the app on your smartphone. It takes about two minutes for the device to warm-up, then it tells you to blow into the device for about 5 seconds and yields a 0-10 H2 reading within a few seconds.

The real usefulness of this device, however, is to generate a time-course of H2 release. In other words, perform a test prior to eating, consume food containing prebiotic fiber, then test again every 30 minutes for 3 hours; stop if a positive reading is obtained. In other words, you are trying to assess whether prebiotic fibers are converted to H2 gas by bacteria high up in the stomach, duodenum, jejunum, or ileum. If you test positive within the first 90 minutes, you have SIBO. A positive response between 90-180 minutes is equivocal, as it is difficult to distinguish mild SIBO from colonic fermentation, especially in people with rapid “transit time,” i.e., rapid transit of digested food to the colon.

The AIRE device is also useful for assessing response to a course of treatment. On a course of antibiotics, for example, you may begin with consistent H2 levels of 8-10, then reduced to 1-2 on day 6 or 7; this suggests a positive response to the chosen regimen. After successful treatment of SIBO, the AIRE device can be used in future to assess for recurrence.

Note that the device is best used on a day following an overnight fast of at least 8 hours duration to maximize the likelihood of starting with a low H2 level prior to consuming the prebiotic fiber.

To use the AIRE device for H2 breath testing, follow these steps:

Day prior

 For the 24 hours prior to H2 breath testing, only consume foods that contain no prebiotic fibers. You should therefore avoid legumes, hummus, inulin, acacia fiber, fruit, starchy or root vegetables, onions, garlic, sugars or fructose, dairy products. Also avoid any alcohol.

Limit your diet to fat- and protein-rich foods such as eggs, butter, beef, poultry, fish, leafy greens, nuts, oils, seeds, and non-starchy vegetables (e.g., spinach, kale, lettuce, green peppers, cucumbers, green beans, zucchini).

Day of H2 testing

  1. Turn on the AIRE device
  2. Activate the AIRE/FoodMarble app on your smartphone, then follow the instructions in the app
  3. Blow into the device when prompted by the app—this is your baseline H2 value
  4. Consume some food with prebiotic fiber, e.g., 2 teaspoons inulin in coffee or yogurt, 1/4 cup legumes, etc. You can eat other foods of your choosing, also, such as eggs, bacon, sausage, etc.
  5. Test breath H2 every 30 minutes for up to 3 hours.
What the readings mean

Each unit of measure on the AIRE device, from 0 to 10, corresponds to an increase in hydrogen gas of 5 parts per million (ppm) by formal H2-breath testing. A reading of 4 therefore equals 20 ppm H2, while a reading of 8 equals 40 ppm, and 10 is 50 ppm and above. 

A reading of:

  • 4-6 is suggestive of SIBO
  • A rise of 4 units above baseline is also suggestive of SIBO, e.g., 2 increasing to 6.
  • Any value above 6 confidently suggests that SIBO is present. The higher the value, the greater the confidence that SIBO is present.
As elegant as the device is, there a few downsides:
  1. The information provided with the device describe this technology as useful only to identify intolerance to FODMAPs foods. In other words, if you eat an apple and 30 minutes later you test H2-positive, FoodMarble says stop eating apples. You can see the folly in this and with all FODMAP conversations: It does not address the cause, i.e., SIBO or severe dysbiosis. This is why we advise people that a low-FODMAPS diet is nothing more than a symptom reducing maneuver, but does not correct the underlying cause, restore a healthy microbiome, or remove a potent source of inflammation (SIBO). Follow the directions provided on how to use the device, but ignore the advice on avoiding FODMAPs.
  2. This device is for the personal use of one person—The mouthpiece is not disposable, but can be wiped off with a moist cloth or paper towel. The company urges you to not use alcohol because it can damage the silicone mouthpiece. You can share the device, of course, with someone you are intimate with, but it’s a bad idea to share with, say, coworkers or neighbors. In effect, one device for each person or family who wants to engage in testing.
  3. We asked the company if they would share their data correlating their 0-10 H2 scale with formal H2 testing in parts per million H2. As I expected, they said no, claiming that it is proprietary. (This happens virtually every time we ask a company to share validation or reproducibility data, as it may be part of their effort to protect their intellectual property.) We are thus left with a bit of uncertainty on precisely what the 0-10 scale represents. At a practical level, however, the device has yielded credible and meaningful results.

UPDATE: Per Dr. Davis's interview with Aire device inventor Dr. Aonghus Shortt, the following device read-outs were revealed: 2 = 10 PPM H2 Gas, 8 = 40 PPM H2 Gas (this has also been noted in the directions for use above)

Nonetheless, the device is a major step forward for managing SIBO, just as fingerstick blood sugar testing enormously empowered people in managing, and now reversing, type 2 diabetes. It is especially helpful for those of us self-managing SIBO in a world in which physicians do not keep up with issues in health unless they yield rich revenue returns.


Once SIBO is identified and/or confirmed by, for example, high H2 readings on the AIRE device, then we have the option of eradicating overgrowth of unhealthy bacterial species that have ascended up the length of the gastrointestinal tract.

For ideal results, we currently combine at least some efforts at fungal eradication concurrently with SIBO efforts, as fungal overgrowth accompanies SIBO in at least 60% of cases and because eradicating bacterial populations often invites fungal overgrowth.

Herbal antibiotics

We choose from either Candibactin AR + Candibactin BR or FC Cidal + Dysbiocide, the two herbal antibiotic regimens with proven efficacy. We take either regimen for 14 days or until prebiotic fiber challenge yields low values (<4) on AIRE device readings.

Candibactin AR: 1-2 capsules twice per day Candibactin BR: 2 capsules twice per day

Dysbiocide: 2 capsules twice per day FC Cidal: 1 capsule twice per day

Because the Candibactin regimen includes two anti-fungal agents (oil of oregano and berberine), there is no need to add another anti-fungal agent at the start.

If you choose the Dysbiocide/FC Cidal regimen, consider adding curcumin 600-1000 mg per day (divided into 2 or 3 doses) for its anti-fungal properties.

If you are planning to follow an anti-fungal regimen upon completion of the SIBO eradication effort, consider agents such as curcumin 600-1000 mg per day (divided into 2 or 3 doses) + several drops of one or two food-sourced essential oils (oregano, cinnamon, clove, peppermint) diluted in a tablespoon of olive, avocado, or coconut oil twice per day (starting at 2 drops per tablespoon, build gradually up to 6 drops per tablespoon) for minimum 4 weeks or until signs of fungal overgrowth have receded.

Biofilm disruption

Addition of an agent that disrupts the biofilm created by bacteria that makes them less susceptible to antibiotics may increase efficacy.

N-acetyl cysteine 600-1200 mg twice per day with antibiotic

(Efforts to disrupt biofilm are not required during anti-fungal efforts, as the essential oils provide biofilm disruption.)

Prevent sporulation

Some bacteria can enter spore-forming mode and thereby become impervious to antibiotics. After several days of antibiotics (above), you will likely be able to add back prebiotic fibers that you may have been previously intolerant to.

Increase prebiotic fiber intake, as tolerated, up to our long-term target intake of 20 or more grams per day from sources such as legumes, garlic, asparagus, leeks, dandelion greens, jicama, raw white potato, green unripe banana, inulin powder, pectin, acacia fiber.

L. reuteri yogurt

While L. reuteri yogurt likely provide advantages in eradicating or preventing recurrences of SIBO, it also generates positive H2 readings by the AIRE device, making it impossible to distinguish SIBO from H2-generation by L. reuteri. If you plan to use the AIRE device to track H2 readings during or immediate following a course of herbal antibiotics, you should stop consuming L. reuteri yogurt for at least 2 weeks until negative H2 readings are obtained, then resume. The upper gastrointestinal colonizing capacity of L. reuteri where it takes up residence and produces bacteriocins effective against the species of SIBO likely provides further advantage in preventing recurrent SIBO.

Efforts to prevent SIBO recurrence

Once the course of herbal antibiotics has been completed, we also stop N-acetyl cysteine but continue prebiotic fibers. We add a high-potency, multi-species probiotic; fermented foods such as kombucha, fermented sauerkraut, kefir, and fermented vegetables; add L. reuteri yogurt. If the AIRE device is available, monitor/assess potential recurrences with H2 readings after prebiotic fiber challenge. Note that L. reuteri yogurt will need to be stopped for 2 weeks prior to any AIRE readings.


Hydrogen breath test: Your healthcare provider submits your mailing address and a test kit is mailed to your home or your provider provides a test kit to you. You are billed for the test that you can, if desired, submit to your healthcare insurer.

You can ask your healthcare provider to obtain a test kit through:

Genova Diagnostics

BioHealth Laboratory

Aire device: https://foodmarble.com Just bear in mind that this company seems to not understand what their device accomplishes, as they only discuss use of the device for low-FODMAPs diet adherence.

Candibactin: While Candibactin can be obtained through the primary source, Metagenics (www.metagenics.com), it is only sold to healthcare practitioners. You can also obtain without a healthcare provider through retailers such as Amazon and others. (Search for Candibactin-AR and Candibactin-BR), though the price is sometimes higher.

FC Cidal + Dysbiocide:
As with Metagenics, Biotics Research (www.bioticsresearch.com) only provides their products to healthcare practitioners. Search online for retailers such as Amazon who provide these products directly.


Role of probiotics in treatment for SIBO Chen WC, Quigley EM.Probiotics, prebiotics & synbiotics in small intestinal bacterial overgrowth: opening up a new therapeutic horizon! Indian J Med Res 2014 Nov;140(5):582-4.

SIBO and other health conditions

Pimentel M, Wallace D, Hallegua D et al. A link between irritable bowel syndrome and fibromyalgia may be related to findings on lactulose breath testing. Ann Rheum Dis. 2004;63(4):450–2 .

Jacobs C, Coss Adame E, Attaluri A et al. Dysmotility and proton pump inhibitor use are independent risk factors for small intestinal bacterial and/or fungal overgrowth. Aliment Pharmacol Ther. 2013;37(11):1103–11.

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):759–64.

Weinstock LB, Fern SE, Duntley SP. Restless legs syndrome in patients with irritable bowel syndrome: response to small intestinal bacterial overgrowth therapy. Dig Dis Sci 2008;53(5):1252–6.

Antibiotic followed by probiotic may increase successful eradication of SIBO

Cuoco L, Salvagnini M. Small intestine bacterial overgrowth in irritable bowel syndrome: a retrospective study with rifaximin. Minerva Gastroenterol Dietol 2006;52:89–95.

Khalighi AR, Khalighi MR, Behdani R et al. Evaluating the efficacy of probiotic on treatment in patients with small intestinal bacterial overgrowth (SIBO)--a pilot study. Indian J Med Res 2014 Nov;140(5):604-8.

Rosania R, Giorgio F, Principi M et al. Effect of probiotic or prebiotic supplementation on antibiotic therapy in the small intestinal bacterial overgrowth: a comparative evaluation. Curr Clin Pharmacol 2013;8:169–72.

Co-administration of antibiotic with prebiotic may increase efficacy

Furnari M, Parodi A, Gemignani L et al. Clinical trial: the combination of rifaximin with partially hydrolysed guar gum is more effective than rifaximin alone in eradicating small intestinal bacterial overgrowth. Aliment Pharmacol Ther. 2010;32:1000–6.
Herbal antimicrobials

Dysbiocide and FC Cidal (Biotics Research Laboratories) or Candibactin-AR and Candibactin-BR (Metagenics) may be equivalent or modestly superior to rifaximin

Chedid V, Dhalla S, Clarke JO et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med 2014 May;3(3):16-24.

Eradication of SIBO may correlate with symptom improvement

Pimentel M, Chow EJ, Lin HC. Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome. a double-blind, randomized, placebo-controlled study. Am J Gastroenterol 2003;98(2):412–9

Go to Forum discussion.


This is an Undoctored protocol for small intestinal bacterial overgrowth, a form of dysbiosis in which the disrupted bowel flora organisms ascend, up through the 20-some feet of the small intestine, all the way up into the duodenum, and even into the stomach, and colonizing parts of the gastrointestinal tract that should not be colonized.

This is a very very big problem. It's becoming clear that it's far more common that we ever thought, and it can account for many health conditions. It can also account for your partial response to the basic Undoctored program. For instance, if you have rheumatoid arthritis, or fibromyalgia, and you do the Undoctored Wild-Naked-Unwashed program, and you only have maybe 70-80% improvement, and you're still left with some flare-ups and problems, consider, strongly consider small intestinal bacterial overgrowth.

There's a separate video on recognizing the telltale signs, that can make you suspicious that you have it. I urge you see that video. In a nutshell, it involves:

  • …looking for an intolerance to fats: that is if you have fat in your toilet, or your stools float, it may be due to small intestinal bacterial overgrowth causing fat malabsorption.
  • If you have new food intolerances — out of the blue you seem to be intolerant to peanuts, or other nuts, and you don't know why, think about this process.
  • If you have an excessively gaseous or uncomfortable response to prebiotic fibers, particularly if it occurs rapidly, say within the first half hour of taking them, think about small intestinal bacterial overgrowth.
  • If you've had a lot of antibiotics in your life, think about that.

Think about small intestinal bacterial overgrowth whenever you have any of those situations, and take some of the steps that we discuss in the Undoctored protocol. As always, this Undoctored protocol is over and above all the steps that you begin in the Undoctored Wild-Naked-Unwashed program, because those basic steps play a big role. You just can't do this protocol without having done the basic program. You must do the basic program first.

It helps to assess, conduct your own assessment for your small intestinal bacterial overgrowth. There's only a handful of ways to do that.

Hydrogen breath test

NOTE: The following opinion was offered prior to the release of the Aire device (see above) which replaces hydrogen breath testing in most cases.

I think the best way is what's called a hydrogen breath test. It's not very costly; it's about $150. Insurance can sometimes pay for it. You do have to get it through a doctor, so you have to find a healthcare practitioner who's open to this conversation. Most gastroenterologists will have no idea what you're talking about, because they're interested more in scoping you, not in making a diagnosis. You may have to go to a functional medicine practitioner, an integrative health practitioner, or a chiropractor, naturopath — somebody truly interested in health. They can get the hydrogen breath test.

It's a bit cumbersome. It involves a period of fasting, and manipulation of diet before you do it. In a nutshell it just means drinking a solution of sugar, such as lactulose or glucose, and then obtaining breath samples over about three hours, and seeing what the curve of hydrogen or methane release is in the breath. That's because microorganisms will produce hydrogen or methane that's captured in the breath, and it show you whether you have organisms that release it quickly, that is, small intestinal bacterial colonization.

Endoscopy for a duodenal or upper jejunal aspirate

Gastroenterologists like to do endoscopies (in fact that's about all they do), but they can make a diagnosis by obtaining a sample, an aspirate, of the liquid material, or partially digested food material in your duodenum or proximal jejunum, the upper part of the small intestine — it's invasive, though. They like it because they can charge a lot of money for it.

The problem with that is (1) it's invasive, and (2) it commonly yields false negatives, that is it typically shows no organisms, or too few, even when you do have small intestinal bacterial overgrowth. It could be due to that they do this as a sample, or it could be that the organisms haven't ascended all the way to where the scope can reach. The scope really can't reach very far, right. If the small intestine is 24 feet long, and the scope can only reach the first inch, two, three, something like that — you see the problem here, that lots and lots of small intestinal bacterial overgrowth is not reachable by an endoscope. But, if you need an endoscopy for another reason, it would be a good opportunity to at least get a sample, and see if it proves positive. If it's positive, you know you have it. If it's negative, you still may have it.

Empirical therapy

Lastly, some people choose to pursue a course of therapy empirically, that is, just a best guess — they think they have it. I think that's reasonable, if you have pretty good evidence, such as malabsorption. If you have fat and oils in the toilet, there's a good chance you have small intestinal bacterial overgrowth. If you have unexplained skin rashes, and that peculiar response to prebiotic fibers, those are pretty solid signs that you have small intestinal bacterial overgrowth, and you can proceed to treating it or having it treated.

Downside? What if you have only a partial response after the treatment, or, what if you have recurrence of some of the symptoms, but not all? You won't have a test to rely on to tell you whether or not you have it, whether there's recurrence, whether you've gotten rid of it. So there is a downside to the empiric therapy, but it is one of your choices, particularly if you or your healthcare provider feel that the symptoms or signs present at the start are so persuasively indicative of small intestinal bacterial overgrowth.


Treatment choices, likewise, are not bad. There's only a few.


There are prescription antibiotics. The most popular is rifaximin. Downside: very costly; about $1200 for a month's worth of pills. It also carries a risk (about 3%) of clostridium difficile enterocolitis. It only occurs in about 3% of people, but it's a very very bad complication, of this and other antibiotics. So that's a downside. And it only works about 50% of the time — a little better if you combine it with a prebiotic fiber. That's discussed in the Undoctored protocol below [below the video on the Protocol page; above this transcript].

Herbal antibiotics --e.g. Candibactin-AR®/-BR®

I believe there's some evidence to suggest that the best solution are herbal antibiotics or antimicrobials, and those are discussed below [below the video], such as Candibactin AR and BR. Anecdotal evidence suggests they work. One study compared the herbal antimicrobials/antibiotics to rifaximin, and the herbal preparations were somewhat superior, and did not come with risk for clostridium difficile. So I think that should be your first choice if you want to go the antibiotic route.

It's not clear how long you do these things, but I think two weeks is probably a pretty good time line. Longer periods have been tried with the antibiotic rifaximin, and it doesn't seem to yield any further benefit. Shorter courses yield less effect, like seven days, so I think a good compromise is 14 days, maybe as short as 10 days.

Eliminate prebiotic fibers, e.g. FODMAPs diet

Lastly follow a diet in which you eliminate all prebiotic fibers. You are, in effect, starving your bowel organisms, and they die, over time, although some sporulate. That's a downside. They go into a quiescent hibernating spore form. That may be the reason why this doesn't always work.

There's something called the FODMAPs diet. It's a very restrictive diet. That's the problem with it — extremely restrictive: no eggs, very few vegetables, very few fruits, no legumes, no alcohol. So you'll find more detail in the discussion below [below the video] and the links provided.

It's not quite clear how long you have to do this. It could start to yield benefits in just a few weeks, but sometimes it requires months or years, and that's risky, because if you deprive your bowel flora of prebiotic fibers forever, you incur risk for colon cancer, diverticular disease and inflammatory diseases. So be careful. The data on FODMAPs is better for treatment of irritable bowel syndrome symptoms, particularly associated with fructose intolerance. There's no a lot of data for use on small intestinal bacterial overgrowth, but it does work in some people, and it's among your choices.

Repeated courses of treatment are usually necessary

Keep in mind that rarely does one course of treatment, whether it's FODMAPs diet, or antibiotics like rifaximin, or the herbal antibiotics like Candibactin. Rarely is only once course of treatment effective. Typically, people have to go through repeated cycles of treatments. A common way to do this would be take Candibactin-AR® and -BR®, say for two weeks. Then go off for two weeks. Do it again for two weeks. Go off for two weeks; or something like that. No one's worked out the perfect schedule for this. You might have to do that 3, 4, 5 or more times. You can see where having that hydrogen breath test might be better, in this instance, or at least watching for recurrence of some of the signs and symptoms of small intestinal bacterial overgrowth.

And then lastly, you want to prevent recurrence. Do all you can to prevent recurrence, and encourage a positive response to whatever therapy you choose. So those are also listed below [below the video], and these will be familiar to anyone engaged in the Undoctored basic program. It involves such things as avoiding antibiotics whenever possible, eating organic foods to avoid the herbicides and pesticides and GMOs, filtering your water, avoiding emulsifying agents like polysorbate 80 and some of the gums and other emulsifying agents because they also emulsify your mucus intestinal lining, and that disrupts bowel flora. There's a few other steps you can take to help prevent recurrences.

Small intestinal bacterial overgrowth is something that you don't just treat once, walk away, and be done with it. It's something you have to work at, continually chip away at, over time, until you reverse this process that took many years to become established. But keep at it, because it's such a good thing to do, to get rid of small intestinal bacterial overgrowth, because if you don't there's bad things ahead in health. So take this very seriously, and you can have success over time