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SIBO—What Causes It and Why It’s So Hard to Treat

on July 5, 2016

by Chris Kresser

While bacteria are an essential part of a healthy small bowel and perform important functions, small intestinal bacterial overgrowth can lead to leaky gut and a number of other symptoms. Learn the risk factors for SIBO.


The normal small bowel, which connects the stomach to the large bowel, is approximately 20 feet long. Bacteria are normally present throughout the entire gastrointestinal tract, but in varied amounts. Relatively few bacteria normally live in the small bowel (less than 10,000 bacteria per milliliter of fluid) when compared with the large bowel, or colon (at least 1,000,000,000 bacteria per milliliter of fluid). And, the types of bacteria normally present in the small bowel are different from those in the colon.

The important role of the small bowel 

The small bowel plays an important role in digesting food and absorbing nutrients. It is also an important part of the immune system, containing an impressive network of lymphoid cells (cells of the immune system that help fight infections and regulate the immune system).

The normal (beneficial) bacteria that are an essential part of the healthy small bowel also perform important functions. These beneficial microorganisms help protect against bad (i.e. pathogenic) bacteria and yeast that are ingested. They help the body absorb nutrients, and also produce several nutrients (such as short chain fatty acids) and vitamins like folate and vitamin K. These bacteria help maintain the normal muscular activity of the small bowel, which creates waves that move the intestinal contents, like food, through the gut.    

What is SIBO?

SIBO, small intestinal bacterial overgrowth, is defined as an increase in the number of bacteria, and/or changes in the types of bacteria present in the small bowel. In most patients, SIBO is not caused by a single type of bacteria, but is an overgrowth of the various types of bacteria that should normally be found in the colon (1). Less commonly, SIBO results from an increase in the otherwise normal bacteria of the small bowel. 

SIBO has been shown to negatively affect both the structure and function of the small bowel. It may significantly interfere with digestion of food and absorption of nutrients, primarily by damaging the cells lining the small bowel (the mucosa). Additionally, this damage to the small bowel mucosa can lead to leaky gut (when the intestinal barrier becomes permeable, allowing large protein molecules to escape into the bloodstream), which is known to have a number of potential complications including immune reactions that cause food allergies or sensitivities, generalized inflammation, and autoimmune diseases (2).

These pathogenic bacteria, whether too many or the wrong types, can lead to nutritional deficiencies on top of those due to poor digestion or absorption. In particular, the bacteria will take up certain B vitamins, such as vitamin B12, before our own cells have a chance to absorb these important nutrients. They may also consume some of the amino acids, or protein, that we’ve ingested, which can lead to both mild protein deficiency and an increase in ammonia production by certain bacteria. (We normally produce some ammonia daily from normal metabolism, but ammonia requires detoxification, so this may add to an already burdened detoxification system.) The bacteria may also decrease fat absorption through their effect on bile acids, leading to deficiencies in fat soluble vitamins like A and D.

What causes SIBO?

The body has several different ways of preventing SIBO. These include gastric acid secretion (maintaining an acidic environment), waves of bowel wall muscular activity, immunoglobulins in the intestinal fluid, and a valve that normally allows the flow of contents into the large bowel but prevents them from refluxing back into the small bowel. (This is called the ileocecal valve because it’s located between the ileum, or terminal end of the small intestine, and the cecum, a pouch forming the first part of the large bowel.)

The cause of SIBO is usually complex, and likely affects more than one of the protective mechanisms listed above.  A number of risk factors for SIBO have been identified, with some of the more common risk factors listed below.  For a more complete discussion of associated diseases and risk factors check out this study and this study.

Risk factors for SIBO

  • Low stomach acid
  • Irritable bowel syndrome
  • Celiac disease (long-standing)
  • Crohn’s disease
  • Prior bowel surgery
  • Diabetes mellitus (type I and type II)
  • Multiple courses of antibiotics
  • Organ system dysfunction, such as liver cirrhosis, chronic pancreatitis, or renal failure

Moderate alcohol consumption and oral contraceptive pills (OCPs) also increase the risk for SIBO

Heavy alcohol use has long been recognized in association with SIBO (3). This study also found an association between SIBO and moderate alcohol consumption, defined as up to one drink per day for women and two drinks per day for men. Alcohol appears to have effects on several of the normal protective mechanisms, including causing injury to the small bowel mucosal cells, contributing to leaky gut, and decreasing the muscular contractions. Additionally, alcohol may “feed” a few specific types of bacteria contributing to overgrowth (4).

Overall there appears to be a moderate association between OCPs and inflammatory bowel disease (IBD) such as Crohn’s disease (5). Though no studies to date specifically correlate the use of OCPs with SIBO, given the known relationship between IBD and SIBO, it is likely that this association holds true for SIBO as well. However, once patients stop taking OCPs, this risk appears to reverse.

SIBO is largely under-diagnosed

The number of people with SIBO in the general population remains unknown. Some studies suggest that between 6 to 15% of healthy, asymptomatic people have SIBO, while up to 80% of people with irritable bowel syndrome (IBS) have SIBO (6). 

SIBO is largely under-diagnosed. This is because many people don’t seek medical care for their SIBO symptoms, and because many doctors aren’t aware of how common SIBO is. Complicating this, the most commonly used tests (breath tests measuring levels of hydrogen and methane gas) still have fairly high rates of false negatives (meaning the test results come back as negative but you actually do have the disease) (7).

The most common symptoms of SIBO include:

  • Abdominal pain/discomfort
  • Bloating and abdominal distention
  • Diarrhea
  • Constipation (generally associated with methanogens)
  • Gas and belching
  • In more severe cases, there may be weight loss and symptoms related to vitamin deficiencies.

Is SIBO contagious?

Unlike many other bacterial infections of the gastrointestinal tract, SIBO is not contagious, and there is no evidence that exposure to any single microorganism increases the risk for developing SIBO. SIBO occurs due to a complex interplay of many different factors and is not passed on between individuals.

Why SIBO can be difficult to treat

Antibiotics are often used to treat SIBO. However, studies show that despite treatment with antibiotics, recurrence develops in almost half of all patients within one year. One study comparing treatment with rifaximin (the most commonly used antibiotic for SIBO) and botanical antimicrobials showed slightly better outcomes with the botanical protocol, but still with successful treatment in close to only half of all patients after one course of treatment.

These finding suggests that treatment of the overgrowth alone is not enough for most people. An additional piece of successful treatment must include addressing the underlying cause, or predisposing factor.

Though there are many identified associations between SIBO and other diseases as described above, abnormalities in gut motility are recognized as one of the most common associations. One study published this month demonstrated that patients with SIBO do have significant delays in small bowel transit time (the amount of time it takes something to move through the small bowel). This finding suggests that patients with SIBO, who do not recover after a standard course of antibiotics, or botanical antimicrobial protocol (which we prefer), may benefit from the addition of a prokinetic agent, which increases the muscular contractions of the small bowel. Octreotide and low dose naltrexone are two such options that are being investigated, and may help treat some cases of SIBO that don’t respond to antimicrobials alone.

As research into SIBO continues, we are increasingly understanding the complexity of this disease, and how treatment must be tailored to each individual to maximize success.

Amy NettAbout Amy:  Amy Nett, MD, graduated from Georgetown University School of Medicine in 2007.  She subsequently completed a year of internal medicine training at Santa Barbara Cottage Hospital, followed by five years of specialty training in radiology at Stanford University Hospital, with additional subspecialty training in pediatric radiology.

Along the course of her medical training and working through her own personal health issues, she found her passion for functional medicine, and began training with Chris in June of 2014.  She has recently joined his clinical practice to work with patients through a functional medicine approach, working to identify and treat the root causes of illness.  Similar to Chris, she uses nutritional therapy, herbal medicine, supplements, stress management, detoxification and lifestyle changes to restore proper function and improve health.

17 Comments

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  1. Chris, I read the article a bout SIBO with great interest. I am 68 and have a long history of IBS. About 3 years ago, I had a hydrogen breath test. The results showed an overgrowth of bacteria. After a 2-week treatment with antibiotics (xiafin?), my symptoms abated for about a year. But now the symptoms (bloatedness, gurgling, distention have returned. I am going to ask my GI for another script for the breath test, because I think I might have a chronic case of SIBO. I do take probiotics but they are not that helpful. The more I read, the more I wonder if I have an enzyme deficiency that might be impairing digestion, which, in turn, causes the SIBO. 2 questions. 1) What enzymes should I be tested for to determine a pancreatic enzyme deficiency? What is the best diagnostic to determine enzyme deficiency. Thanks.

    • For me, my probiotic was making it worse! That acidophilus was one of the bacteria that was overgrown in my gut. My doctor said I could use a soil-based one if needed. Did you have a urine test to see what bacteria were overgrown?

      • Amy, my the GI specialist I see in Monterey, CA, has been pretty vague about recommending the right probiotic for my condition. I was diagnosed with SIBO yesterday, and from what you’ve posted here, it sounds like I need to be careful choosing my probiotics. My doctor didn’t ask me to have a urine test to check what bacteria is overgrown. I’m going to inquire about this. Your comments are appreciated.

      • I’ve just done a stool test and discovered that I had overgrowth of some strains. I had a look at my probiotics (I rotate the brands and strains so I had only taken them for 2 months) and to my surprise they contained two of the strains that showed as overgrowth. So a soil-based one would be safer? I am really worried I exarcerbated my dysbiosis (some of my symptoms for Hashimoto’s thyroiditis came back while on this probiotics). Any suggestion would be appreciated.

      • Probiotics gave me more gas, bloating, cramps and diahhrea. I nearly passed out on the floor from the pain. I was sweating so bad I had to quit the Probiotics. Don’t know if this is my problem! Don’t want to rock the boat. People with Fibromyalgia and chronic fatigue, autoimmune thyroiditis seem to be extra sensitive to changes in meds. Antibiotics also cause diahhrea and cramps for me as well!

    • Hello, I just found out yesterday from my GI specialist that my SIBO test was positive. I was 99% sure I had it. What Enzyme testing and diagnostic for Pancreatic Enzyme Deficiency did Chris recommend? I don’t see an answer online here? I’m new to his Blog and learning about SIBO. Any information is appreciated.

  2. Thank you for posting this helpful SIBO article. Are there any natural, non-prescription prokinetic agents to increase muscle contractions in the small bowel?

    • I have the extreme case of SIBO. What I found helped most was eating organic or wholistic. Meaning, no meats that have been Injected with hormone, steroids or antibiotics, only free range, grass fed or organic feed animals. Fruits and vegetables cannot be sprayed with chemicals, only natural deterrents to keep bugs away.
      It’s very costly and I lost all material gain to treat myself wholistically. It’s a long road, but it works.

      Cynthia

  3. Cascara Sagrada helps with colon mobility. Also in addition to taking natural or prescription antibiotics, it is necessary to first start dissolving the biofilm that bacteria make around themselves to protect form destruction. Look up: yeastinfectionadvisor.com and click on bad bacteria. Biofase is the enzyme to use to break down the biofilm.

  4. Thanks for this informative article. I have just been diagnosed with SIBO for the third time! First time was 2015 where I successfully got rid of it with Rifaximin, LDN and SCD diet. It came back in 2016 when I successfully got rid of it with Rifaximin, Neomycin, LDN and a combination of SCD and LowFodmap. It has now come back a third time. I’m in complete dispair and have no idea what to do to prevent it from coming back yet again! I am a Board Certified Health Coach and lead a very heatlhy lifestyle. I’m just at a loss as to why it keeps coming back. Please help direct me to a practitioner that is experienced with recurrent cases. Thanks!

  5. I like all the others above was treated for SIBO with Xifaxin and now am worse that I’ve every been. Not sure where to go from here as my body is now rejecting everything doctors are giving me. Please someone help with some insight.

    • I suggest you look into Ajwan seeds. It has multiple spellings and is grown mostly in India. You can buy the seeds for fairly cheap online or at any Indian/Pakistani/Persian grocery store. It is used in Indian cooking and I think some Indian restaurants put it by the front door like breath mints, but they’re small seeds.

      The seeds have more thymol (the organic oil with the antibiotic and antifungal properties) than thyme itself so it is basically a Indian Herbal Medicine treatment for dysentery including bloody dysentery. Even though this is in analogy “nuking” my gut flora I have found it to be incredibly helpful for both constipation and diarrhea, and I also have Crohn’s disease with a possible SIBO due to having had prior surgeries. When I drink Ajowan I may have increased gas temporarily but overall it is anti-gas, and as I said anti-bacterial, anti-fungal, and it probably has some other health properties too. You could always try Oregano oi, but unlike Oregano oil Ajowan is cheaper and much more gentle on the stomach. oregano oil is perhaps stronger but in my experience it stimulates the immune system more and thus causes more symptoms like bleeding or increased crohn’s symptoms. I know there is the die-off effect but if you’re making ajowan tea (I rush half a teaspoon of seeds in a coffee grinder, electric, or actually I grind it in bulk for the week, then do about half a tea spoon 2-3 times a day, and I strain the water once to get out the larger pieces of seeds, making it more drinkable. there is a tiny bit of sediment which I drink but I suppose it doesn’t matter.

      I have found thymol from ajowan in hot water (cold water might work fine too, but i make it with hot water like a tea) works great for dysbiosis or just crohn’s in general.

      Good luck.

  6. Red flags waving all around! All evidence seems to be pointing to my having SIBO. I have suffered with life altering IBS for 43 years. It began when I first started taking OCPs. I stopped taking OCPs after 1 year, but the IBS persisted. I have read about Rifaxamin and asked my doctor if we could try it. The answer was no b/c it was “off label”. I inquired why it is that I feel better than ever while I am on a course of Keflex for something unrelated. The doctor has no clue. Could it be that for the I am taking Keflex the bacteria in my small intestine is under control? Additionally, I was diagnosed with very low Vitamin B12 levels last December, just above the level that would have indicated I would have needed Vitamin B12 injections. I started taking Align about a week ago and thought I had noticed some improvement, but felt more bloated than usual. I ran across a remark made by someone who said do not take Align if you have SIBO. Looking up SIBO led me to you. Please advise me. I am desperate for answers.

  7. I have malabsorption and intestinal sound symptoms since 2006 on and off. Recently from March 2018 started getting intestinal sounds again, lost 15 pounds within 6months and stool is getting seperated like a particles in commode within couple of min. Gastroenterologist told that I have IBS and Bacterial Overgrowth and prescribed Rifaximin for a month and Mebeverine ( for 3 months. When I used Rifaximin I did not have intesinal sounds and stool is also well formed. After this course again seeing the same symptoms. It is very difficult for me to put on weight in last 15 years irrespective of food I take. Is it really Bacterial overgrowth problem or any other disease like Tropical Sprue or Whipple disease or something else. weight loss is concerning more as I am already have less weight 118 pounds and 39 years old. I do not have any other symptoms except the mentioned above.

  8. Hi,
    Thanks for your informative article. I have been diagnosed with h pylori in the past and now I have systems back again only worse! I don’t know who to see at this point. My systems are everything that was mentioned in the other comments; bloating, cronic gas, bleching, acid reflex, constipation, and it is hard keeping weight on. Suspect of yeast over load went on yeast free diets and did feel better. I have experienced die off not fun.At this point not sure what to do.

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