What is SIBO and is it associated with IBD


If you have been reading my blog, you know that one of the most effective treatments I have used to date for ulcerative colitis is a gluten, dairy, and sugar-free diet. Specifically, I used the specific carbohydrate diet/ GAPS diet as a starting point to get my symptoms under control initially and I still follow an eating style that is very similar to the SCD diet.

When Elaine Gotshall wrote The Specific Carb Diet, Breaking the Vicious Cycle, she described a condition called small intestinal bacterial overgrowth long before it was recognized as a medical condition. This is an excerpt from the official website for the SCD diet.

When the balance in the gut is disturbed, an overgrowth of intestinal flora can result. Microbes migrate to the small intestine and stomach, inhibiting digestion and competing for nutrients. The gut then becomes overloaded with the byproducts of their digestion…….The components of our diet, particularly carbohydrates, play an enormous role in influencing the type and number of our intestinal flora. When carbohydrates are not fully digested and absorbed, they remain in our gut and become nutrition for the microbes we host. The microbes themselves must digest these unused carbohydrates, and they do this through the process of fermentation. The waste products of fermentation are gasses, such as methane, carbon dioxide & hydrogen, and both lactic & acetic acids, as well as toxins. All serve to irritate and damage the gut…Further, lactic acid produced during the fermentation process has been implicated in the abnormal brain function and behavior sometimes associated with intestinal disorders. The overgrowth of bacteria in the small intestine triggers a worsening cycle of gas and acid production, which further inhibits absorption and leads to yet more harmful byproducts of fermentation. The enzymes on the surface of the small intestines are destroyed by the now present bacteria, and this further disrupts the digestion and absorption of carbohydrates, leading to further bacterial overgrowth. As both the microbial flora and their byproducts damage the mucosal layer of the small intestine, it is provoked to produce excessive protective mucus, which further inhibits digestion and absorption.

Elaine Gotshall published the book Food and Gut reaction, in 1987 explaining the condition long before it was given the name small intestinal bacterial overgrowth or SIBO in the early 2000’s.

Since the defining and identification of SIBO in recent years, research has been growing rapidly on the condition, appearing in prestigious journals such as the American Journal of Gastroenterology, Nature, (1, 2). Insurance companies now cover the antibiotic treatment Rifaximin for SIBO and it is being used by gastroenterologists to treat Irritable bowel syndrome (IBS). SIBO is currently being studied in restless leg syndrome, GERD, acne, autism, IBD, CFS, fibromyalgia, Parkinsons etc. It is safe to assume that SIBO is making its way into mainstream medicine and is here to stay. Even still, many Doctors are not trained on the condition or are not even aware that it exists.

What is SIBO?

Simply put, SIBO is a chronic bacterial infection of the small intestines which can interfere with normal digestion and absorption of food which leads to damage of the GI tract. small-intestine

In healthy individuals, a number of bacteria that resides in the small intestines is very low. Unlike the small intestines of ruminant animals such as cows and sheep, which utilize microbes to break down their food, humans have a much more sophisticated digestive tract that secretes digestive enzymes to break down food.

The defining characteristic of SIBO is a higher than normal amount of commensal bacteria in the small intestines. The small intestines are not designed to harbor a great deal of bacteria, unlike large intestines. The higher than normal amounts of commensal bacteria in the small intestines produces gasses such as hydrogen, methane and hydrogen sulfide, which causes abdominal distention or bloating, constipation or diarrhea, and impairs the absorption of nutrients such as vitamin A, D, E, K, and B12, fat malabsorption.

In SIBO the bacteria may produce toxins that damage the mucosa. SIBO is associated with intestinal permeability and inflammation. Incidentally intestinal permeability is almost always present in IBD. (3)

Is IBS all in your head?

The short answer is no. In the past IBS was thought to be a psychosomatic condition, meaning that the symptoms were a result of stress and anxiety, however, research is now showing that notion to be false. It is true that people with IBS feel worse when they are stressed or anxious, but they will often experience IBS symptoms in the absence of stress and anxiety. In other words, IBS is chronic, whereas exacerbations in IBS can occur in acute situations. In addition, studies have shown that mental illness is not higher in folks with IBS as than the rest of the general population. Meaning that IBS is not “all in your head”. (4)

Bacterial overgrowth has given clinicians an objective lab value that can direct treatment and in fact, validates the physiologic presence of digestive dysfunction in IBS. The association of SIBO and IBS is so strong that some researchers suggest a change in the definition of what we consider IBS to be.

Association between IBS and SIBO is definite. In fact, controversy exists whether patients presenting with IBS but found to have SIBO on further testing should be diagnosed as IBS. (5)

Conditions SIBO is associated with

Studies show SIBO is associated with:

  • irritable bowel syndrome 30-84% present (5)
  • Crohn’s 20-30% present (6)
  • Ulcerative colitis 15-17% present (7)
  • fibromyalgia patients 100% had SIBO present but only 50% reported gut symptoms (8)
  • celiac disease
  • Chronic fatigue
  • Hypoglycemia (one study by Pimentel showed the higher the methane, the worse the hypoglycemia episodes)
  • chronic pancreatitis
  • diabetes
  • Gastric acid suppression from medication use: bacterial overgrowth was present in 53% of patients who received omeprazole (9)
  • Gastric resection
  • Hypothyroidism
  • Interstitial cystitis
  • Gynecological disorders
  • Nonalcoholic fatty liver (10)
  • Recurrent antibiotic use
  • Renal failure
  • Rosacea
  • Small intestine diverticula
  • Surgical removal of ileocecal valve (11, 12)

SIBO and my experience

My decision to look into testing myself for SIBO came about when I started noticing that my condition improved when I received antibiotics or botanical antimicrobials and diets which restrict fermentable carbohydrates which can feed gut microbes.

I will start from the beginning. Initially, when I was first diagnosed with UC, the docs still weren’t entirely sure if I, in fact, had ulcerative colitis or just a parasite. My physician prescribed me metronidazole and ciprofloxacin. My symptoms improved greatly while on the antibiotic protocol, only to regress significantly after the antibiotics were discontinued.

The next line of evidence is my response to a dietary protocol that involves the removal of fermentable carbohydrates. The specific carb diet (SCD) or gut and psychology diet (gaps) is a dietary approach that was specifically designed to treat SIBO by only allowing foods that are rapidly absorbed in the small intestines and thus “starving” the undesirable bacteria. I experienced great improvements in my UC symptoms from this approach, as have millions of others who have used this protocol.

Next line of evidence arose when I completed fecal transplants, you can read about it here. While doing the pre-FMT prep for this procedure I did a prescription (metronidazole) and botanical antimicrobial protocol. While doing the antimicrobial treatment prior to the FMT, I noticed a significant improvement in my UC symptoms. After FMT I had a complete cessation of all my ulcerative colitis symptoms for 6 months. Somewhere around 7 months later I began to notice mucus in my stool again. In another attempt to bring myself back to perfect digestion I exhibited after my first round of FMT, I did another round of fecal transplants, except this time they did not produce the same effects. The question on my mind, was it the pre-FMT antimicrobial therapy that helped my symptoms?

Lastly, I came down with strep throat at the beginning of this year, which required me to receive antibiotics. The antibiotic I was given was azithromycin, many know it as “z-pack.” This is a broad spectrum antibiotic. An interesting thing happened towards the end of the antibiotic treatment- you guessed it, my symptoms once again improved.

What Causes SIBO

Motility defects:

The migrating motor complex is a coordinated series of events that sweeps materials through the GI tract. Research has shown that defects in the migrating motor complex potentially predisposes to SIBO. The theory is that a defect migrating motor complex results in a failure to transport microbes and other material into the large bowel leading to fermentation in the small intestine. (13)

New research coming out is showing that individuals who get food poisoning will often continue to show symptoms of IBS even after the food poisoning has passed. Another study showed that 1/3rd of patients who get diagnosed with acute gastroenteritis have prolonged and lasting gastrointestinal complaints. (14)

Researchers have termed this condition as “post infectious IBS.” Many researchers believe, including SIBO pioneer researcher, Dr. Pimentel, that SIBO may be propagated by the after-effects of food poisoning by damaging the migrating motor complex.

A variety of organisms is believed to be responsible for causing post infectious IBS. Some specific organisms that have been found to be most responsible for causing are campylobacter, salmonella, and shigella species. (15)

An interesting parallel that relates SIBO to IBD, is that it has been noted that IBD often starts after a bout of food poisoning. One study showed that getting a foodborne infection raises your risk of getting IBD. (16)

Other potential causes of SIBO:

  • history of gastric bypass surgery
  • known gastrointestinal motility disorder
  • collagen vascular disease
  • IBS (association)
  • pancreatic insufficiency
  • chronic proton-pump inhibitor (PPI) use
  • Abnormalities in migrating motor complex
  • Gastroparesis (can result from diabetes)
  • Neurological and neuropathic disease (polymyositis)
  • Disrupted gut microbiome
  • Celiac disease
  • Aging due to low stomach acid production

Interestingly, I had a few of these potential causes of SIBO present throughout my life. Chronic proton pump inhibitor use (acid-blocking drugs), disrupted gut microbiome (antibiotics used for a year to treat acne), and I got food poising just before I received the diagnosis of IBD.

Which test is best for diagnosis of SIBO?

Prior to ordering any tests, one should look for signs and symptoms of SIBO. These include abdominal distention (bloating), constipation dominant IBS, diarrhea-dominant IBS, excess gas, pain, any of the aforementioned associated conditions, vitamin deficiencies, and conditions associated with vitamin deficiencies, carbohydrate malabsorption, fat malabsorption, weight loss and protein malabsorption. Interestingly, elevated serum folate may be present from bacterial synthesis. (17)

There are some criteria that need to be present when selecting a lab to test for SIBO. The test needs to detect both hydrogen and methane, it needs to be at least 3 hours long, should use a Quintron gas analyzer (this is the same gas analyzer used in most all of the SIBO studies) and it should use the same or similar test prep diet as in the studies. Commonwealth labs fit this criteria. In addition, Dr. Pimentel, a pioneer in SIBO research uses this particular lab. (18)

There exist two main methods to diagnose SIBO. The first method uses an endoscopy, in which a biopsy is collected from the small intestines and cultured to detect the presence of SIBO.

A less invasive procedure is a SIBO breath test. This test detects the presence of gasses produced by bacterial fermentation in the small intestines. This is the test I used. IMG_1750.JPG

The SIBO breath test is performed by having the patient drink one of two carbohydrate solutions, either lactulose or glucose, the patient then exhales in a series of glass tubes over a period of 2 to 3 hours. The test measures two different gasses in the breath, hydrogen, and methane. Elevations in hydrogen and or methane over a certain threshold are considered to be a positive finding of SIBO. H pylori infections can cause a false positive on a breath test, so that is something to watch out for. (19)

 Should you use glucose or lactulose SIBO breath test?

Both tests have their advantages and disadvantages. The glucose breath test is more specific but less sensitive and has a greater risk of false negative which can lead to under treatment. (20) The lactulose breath test, although less specific, has greater sensitivity at the expense of being less specific and has a greater risk of false positives which may lead to overtreatment. (21)

These are not hard and fast rules and one must look at the complete picture when interpreting the test results.

In many SIBO studies, both lactulose and hydrogen breath tests are performed. This is the route that I took, so I could get a complete picture and confirm the results. (22)

Methane vs Hydrogen breath tests

Methanogenic organisms (or archaea that produce methane) oxidize (or consume) hydrogen to produce methane gas in the gut. So on a test, if a patient has high levels of methane, typically the hydrogen production will be low because the methanogens will be consuming all the hydrogen. (23)


Methane production on a SIBO breath test is associated with constipation. Treatment and normalization result in relief of constipation. (24)

Studies indicate that methane appears to slow transit time in animal models. In human studies the higher the production of methane in the small intestines, the worse constipation. (25)11f1_L1TT

Treatment differs for SIBO with methane present and that with hydrogen present. Treatment using two antibiotics rifaximin and neomycin was shown to be much more effective at inducing clinical improvements (85% improvement) and reducing methane production on breath test (87% improvement). (26, 27)


In contrast, microbes that produce hydrogen are associated with diarrhea or IBS-D. Patients who test positive for hydrogen alone are typically treated with rifaximin alone. One of the best studies on rifaximin for IBS was a double-blind, placebo controlled trial that showed that the antibiotic improved bloating, abdominal pain and loose watery stools. (28)

How is SIBO Treated?

SIBO is corrected by using antibiotics which typically results in significant improvements in IBS symptoms and normalize the SIBO breath test results if the treatment was successful.

SIBO with hydrogen production is treated differently than SIBO with methane production. In general, the commonly used antibiotic rifaxamin alone is not sufficient to treat a majority of cases of methane producing SIBO. A combination of the antibiotic neomycin and rifaxamin was shown to more effectively eradicate SIBO than rifaxamin alone. (29)

Prescription antibiotics:

  • Rifaximin: This antibiotic is one of the most commonly used to treat bacterial overgrowth. It is not systemically absorbed, 99.6% stays in the gut. The drug is extremely safe; in studies, the side effects are rare, mild and are similar to that of the placebo group. (30) Studies show it is anywhere from 30-87% effective for SIBO. The high variation may be due to a number of things, including the dose was not high enough, the duration is not long enough and the severity of the SIBO. (31) Rifaximin uniquely acts primarily in the small intestines and has been shown in studied to not adversely affect the gastrointestinal flora, does not contribute to bacterial resistance and does not increase the incidence of C diff. May actually raise the beneficial bifidobacterium and F praznitizii. (32) Dosage: Adults: can be dosed at 400mg TID for 10-14 days or 550mg TID for 10-14 days. (33) Children: 200mg TID for 7 days leads to a 64% lactulose breath test normalization. Children with IBD: 10-30mg per kg of weight achieved a 61% symptom relief. (34) Higher dose and longer duration may be necessary, 1600mg a day lead to a better result than 1200mg a day without increasing bacterial resistance. Another study suggested that up to 16 weeks of rifaximin may be required if hydrogen is more elevated. (35, 36)

Additions for methane:

  • Neomycin: As mentioned earlier, adding this to the treatment of bacterial overgrowth with elevated methane increases the efficacy, inducing clinical improvements (85% improvement) and reducing methane production on breath test (87% improvement) compared to only a 56% clinical improvement with rifaximin alone and 63% with neomycin alone. The drug has been used for 25 years and is generally considered very safe. This drug has a black box warning, but the drug may not be as risky as one might assume. One of the concerning side effects are ototoxicity (ear toxicity), but this side effect is highly rare and are most likely to occur in a patient with a gastrointestinal illness or renal failure. Another review indicates that the drug, when used orally, does not cause ototoxicity. When used orally the drug is not well absorbed. (37, 38)
  • Low-dose erythromycin: increases gastric motility, used at a very low dose decreases risk of side effects. (39)
  • Metronidazole (Flagyl): Pimentel at cedar Sinai is doing a study with some success. Also used to treat IBD. Dose: 250mg BID for 10 days.


  • lactobacillus planetarium have antimicrobial activity against methanogenic archaea. (40) Dosage: 10 billion CFU per day. (41) Brand: Jarrow Ideal Bowel Support
  • Heat treated L acidophilus: effective in reducing symptoms of abdominal pain, bowel frequency, urgency and distension in patients with chronic diarrhea”. (42)
  • Lactobacillus acidophilus, Lactobacillus helveticus, and Bifidobacterium: showed significant improvement in pain and bloating as compared to those who received placebo.” (43)
  • Bacillus subtilis and Streptococcus faecium: effective in reducing abdominal pain as compared to placebo in patients with diarrhea or alternating type of IBS” (44)

Treating SIBO with Antimicrobial Botanical: 

  • One study examined 2 different antimicrobial botanicals and compared them with rifaxamin. The herbal antimicrobials were slightly more effective at normalizing the glucose breath test than the rifaximin. I’m currently using Dysbiocide and FC Cidal manufactured by Biotics Research Laboratories. “2 capsules twice daily of the following commercial herbal preparations; Dysbiocide and FC Cidal (Biotics Research Laboratories, Rosenberg, Texas) or Candibactin-AR and Candibactin-BR (Metagenics, Inc., Aliso Viejo, California” was slightly more effective at normalizing the SIBO breath test……. The response rate for normalizing breath hydrogen testing in patients with SIBO was 46% for herbal therapies vs 34% for Rifaximin.” (45)


  • Low FODMAP diet: This diet restricts fermentable carbohydrates, primarily prebiotics and fibers. This diet has been shown to be effective but is extremely difficult to follow. (46)
  • Elemental diet: An elemental diet is a formula, more specifically a nutritionally complete drink that contains all the bodies’ essential vitamins, minerals, and essential fatty acids that the body needs. The protein, carbs, and fats are all in predigested forms that are very easy to digest and absorb, very high up in the small intestines, leaving little to no residue for microbes to ferment and contribute to bacterial overgrowth. Dr. Pimentel’s and his colleagues at Cedar Sinai conducted a study showing that an elemental diet using the product Vivonex, normalized 80% of sibo breath tests after 14 days. (47) These are the best results any study has demonstrated for the treatment of bacterial overgrowth to date. Another argument that IBD may be an associated condition with SIBO is that elemental diets are incredibly effective at putting Crohn’s disease into remission. One study showed that 80-100% of patients with Crohn’s following an elemental diet went into remission in 2-3 weeks. (48) Another study revealed that an elemental diet was as effective as corticosteroids in the treatment of active Crohn’s disease. (49) The SCD diet is modeled after an elemental diet in that the only carbohydrates allowed on the diet are called monosaccharides. Monosaccharides are also called simple sugars which are easily digested in the small intestines. The name of the formula used in the studies is manufactured by Novartis nutrition and called Vivonex. https://www.amazon.com/Vivonex-Plus-2-8-Ounce-Packets-Pack/dp/B001W6RIII/ref=sr_1_1_a_it?ie=UTF8&qid=1471561899&sr=8-1&keywords=vivonex+plus This formula is drunk 2-3 times a day as a meal replacement. Vivonex is expensive and contains a few questionable ingredients. Some healthcare practitioners, such as Dr. Siebecker have designed a homemade elemental diet with higher quality ingredients, however, this exact preparation has not been studied, but makes sense in principal. The downsides are that the elemental diet is very difficult to follow; all of your calories come from unpalatable shakes. An elemental diet should be reserved for the more difficult cases.
  • Specific Carb Diet: you can read about it here

Guar Gum

  • Guar Gum acts as a prebiotic feeding the gut bacteria. Studies show when this is added to the antibiotic treatment for bacterial overgrowth, it is more effective than antibiotics alone. This treatment may seem counterintuitive in that guar gum may actually feed bacteria, however, when you understand how the drug rifaximin works it begins to make more sense. Rifaximin works on replicating bacteria. If bacteria are starved of food (fiber, prebiotics, sugars) then they go into a dormant state and are more difficult to kill. If bacteria are replicating than it is easier for the antibiotics to work. “The combination of rifaximin with partially hydrolysed guar gum seems to be more useful in eradicating SIBO compared with rifaximin” (50)


  • Iberogast (tribute pharmaceuticals in US/Can): It has been used in Europe for quite some time. It has herbal bitters that stimulate the migrating motor complex and has been studied to help with gas, cramping, and constipation. This is a good addition that can be used to prevent SIBO relapse. (51) Dosage: 20 drops TID before meals

Pancreatic enzymes and hydrochloric acid

  • Betaine HCL: Low stomach acid is a risk factor for SIBO and can develop after an H pylori infection, from aging or from chronic use of acid suppressing medication. (52) I couldn’t find many studies on this, but in theory, supplementing with exogenous stomach acid in the form of betaine HCL before meals can be an effective strategy to increase stomach acid and decrease relapses in SIBO after treatment.

Rifaximin and IBD

All good gastroenterologist and IBD researchers know that antibiotics can be used as an effective treatment of IBD. Antibiotics may work by modulation of the gut microbiota, which we know to be the driver in the disease process IBD. (53) Research is not clear as to the exact mechanism by which antibiotics help IBD patients, but there is little disagreement on its efficacy. The question on my mind is, if part of the reason antibiotics are effective at improving IBD is that they are working to kill SIBO.

However, the problem with using antibiotics is that they increase the chances of C diff, they increase antibiotic resistance, can have a rebound effect after therapy, and cause systemic side effects.

Rifaximin on the other hand may be a safer alternative, without many of the other negative consequences associated with the most commonly used antibiotics used to treat IBD such as metronidazole, ciprofloxacin, and clofazimine. This is due to the fact that rifaximin poorly absorbed, acting primarily locally and excreted unchanged in the stool and thus devoid of systemic effects.

One study showed that percentage of SIBO was higher in patients with ulcerative colitis than the general population.

Occurrence of SIBO was significantly higher in IBD patients as compared to controls. The occurrence of SIBO in CD (45.2%) was significantly higher as compared to patients with UC (17.8%) group. (54)

In addition, rifaximin has been shown to improve IBD.


  • Studies show that using rifaximin, the most commonly used drug to treat SIBO resulted in 59% to 65% remission in Crohn’s and a 76% remission rate in Ulcerative colitis. (55)

Rifaximin and Ulcerative colitis

Rifaximin used in ulcerative colitis trails revealed that the rifaximin group had a significant reduction in rectal bleeding, suggesting that rifaximin appears to be beneficial even in distal ulcerative colitis.

The other two studies demonstrated a 76-100% remission rate in the rifaximin group. These impressive results speak for themselves.

Another interesting tid-bit I pulled from the ulcerative colitis studies is that all 3 studies make no mention of testing patients for SIBO prior to the trail, and presumably did not exclude patients who tested negative for SIBO. In other studies, only 17% of patients with UC test positive for SIBO.

In spite of not monitoring for SIBO test results in IBD, rifaximin has some very promising results in IBD trails. (56) This suggest rifaximin may work in ways other than just killing methane and hydrogen producing microbes, but also by potentially killing hydrogen sulfide producing organisms and pathobioant microbes such as certain types of toxic E coli that has been identified to be in higher numbers in IBD.

An additional potential explanation is that rifaximin is eradicating sulfate reducing bacteria in the small intestines, which has been shown to be elevated in ulcerative colitis patients. Several studies show that the production of highly toxic sulfur containing gases, such hydrogen sulfide correlates with the severity of ulcerative colitis. (57)

This alternative explanation would explain my negative test results for my SIBO breath test.

The Hydrogen Sulfide Connection

On the SIBO breath test I took, my hydrogen and methane came back suspiciously low.

My glucose breath test results

My glucose breath test results

This would suggest that I do not, in fact, have SIBO. However, a second potential interpretation is that I have an elevation of sulfate reducing bacteria in my gut that is competing with methanogenic bacteria (organisms that produce methane gas) and producing hydrogen sulfide gas instead of hydrogen or methane. My methane levels on my test were almost zero across the board. Furthermore, sulfate reducing bacteria, consume hydrogen for energy, as mentioned my hydrogen levels on the test were extremely low as well.

Sulfate reducing bacteria produce toxic hydrogen sulfide, which SIBO breath tests do not measure. Elevated production of highly toxic hydrogen sulfide, and its producer, sulfate reducing bacteria correlates strongly with IBD. (58)

The higher the sulfite reducing bacteria in UC correlates with higher disease severity. (59) Hydrogen sulfide is damaging to the intestinal epithelium. (60)

So it stands to reason that if you have a mass amount of sulfite reducing bacteria in your gut, competing with methane producing organisms and consuming hydrogen as a food source, you would have extremely low methane and hydrogen production. I believe this is the case for me.

Let’s go through this one more time: methane is consumed by sulfite reducing bacteria, potentially causing methane to be low on the breath test in UC patients.  The sulfite reducing bacteria produce hydrogen sulfide in the gut, which we have no commercially available way of measuring in the breath. Hydrogen is consumed by sulfite reducing bacteria as well, potentially causing hydrogen to be low on a breath test. So both methane gases and hydrogen gases will feed the sulfate reducing bacteria to produce more toxic hydrogen sulfide gas.

During bacterial fermentation, hydrogen is converted to either methane by methanogenic microbes or hydrogen sulfide by sulfate-reducing bacteria in the right colon. (61)

As you can see on the far left, hydrogen (H2) producing bacteria are oxidized (consumed) by sulfate reducing bacteria and then produce hydrogen sulfide (H2S) gas and which are then broken down by the liver. If there is an excess in hydrogen sulfide it may overload the liver and cause symptoms.

Hydrogen sulfide is also removed by first pass metabolism in the liver. If there is a location and volume shift in the sulfate-reducing bacteria to the small intestine, then hydrogen sulfide excess may predominate and cause symptoms. (62)

Hydrogen sulfide identification and eradication maybe the next piece of the puzzle in SIBO research, but sadly the labs have not identified an effective test to measure hydrogen sulfide in the breath. It is encouraging to see that SIBO researchers are talking about the future direction of measuring hydrogen sulfide.

Another line of evidence to support the hydrogen sulfide connection to IBD, is that studies show that low sulfur diets may be beneficial in ulcerative colitis. (63)

Understanding the potential hydrogen sulfide connections adds to the argument to treat SIBO in IBD, even with a negative SIBO breath test.

The SIBO protocol I used

Given that I personally have some risk factors associated with bacterial overgrowth: history of chronic proton pump inhibitor use (acid-blocking drugs), disrupted gut microbiome and food poising, in addition to the fact that I started noticing that my condition improved when I received antibiotics, I decided to follow a SIBO eradication protocol. Unfortunately I have to treat this empirically because we cannot measure hydrogen sulfide.

I decided to use the herbal antimicrobials instead of the prescription antibiotics. I chose this route because herbal antimicrobials actually were shown to be slightly more effective at normalizing SIBO, the herbal preparation was 46% effective and rifaximin was only 34% effective at normalizing the breath test.

Additionally, herbal antimicrobials contain a broad spectrum of coverage against many different types of bacteria. (64)

Wormwood, contained in one of the two antimicrobials used, is a potent anti-inflammatory and has been shown to successfully induce remission of crohns disease.

In an attempt to replicate the study in myself, I used the exact preparation used in the study.

Here is the current protocol I’m currently using:


  • Gluten, dairy and egg free, traditional diet or paleo diet. I eat starchy tubers such as yams, sweet potatoes, plantains, occasionally white potatoes. I do not limit fermentable carbohydrates because if you remember from earlier that if bacteria are starved of food (fiber, prebiotics, sugars), they go into a dormant state and are more difficult to kill. If bacteria are replicating than it is easier for antibiotics to work.

Botanical antimicrobials:

  • FC Cidal: This is one of the two herbal antimicrobials used in the comparison study.
  • Dysbiocide: The second herbal antimicrobial used in the comparison study.

-Dosages: 2 capsules twice a day (64)


  • VSL#3 Double strength: VSL#3 is the most well studied probiotic available, and has specifically shown to be an effective treatment for ulcerative colitis.The double strength must be prescribed by a physician but the regular VSL#3 can be ordered from amazon.
  • S boulardi 

The main lingering problem I have been experiencing and my motivation to go down this road is, I still tend to see a bit of mucus in my stool early in the day and a bit of excessive flatulence and fatigue in the afternoon. Upon starting the aforementioned protocol I have noticed improvements in all of those lingering symptoms. Sadly I am not able to do a post test to see if I cleared the suspected hydrogen sulfide.


The link between IBS and bacterial overgrowth is well established. The link between IBD and SIBO is not quite as clear. I presented multiple lines of evidence that SIBO and IBD may be linked. These include: the empirical and scientific literature showing the specific carb diet to benefit both bacterial overgrowth and IBD, the ability SIBO has to produce intestinal inflammation and permeability, the onset of both bacterial overgrowth and post infectious IBS commonly occurring after food poisoning as does IBD, the research showing rifaximin to be an effective treatment for IBD, the hydrogen sulfide link to ulcerative colitis and the higher than average population of IBD patients who test positive on SIBO breath tests.

The point of this blog post was to give an overview of what SIBO is and how it is connected to IBS, diarrhea, constipation and IBD. The discovery of the link between IBD and SIBO demanded quite a bit of inquiry and research which not a great deal of folks are talking about. I hope that this information can help to serve as another tool that helps people to get to the root of their digestive problems.

I would like to add, there are a lot of moving parts to treating bacterial overgrowth and patients should have an overseeing physician during the whole process.



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