What Causes SIBO (Small Intestinal Bacterial Overgrowth) and Why It’s so Hard to Treat

This is a guest post written by Amy Nett, MD.

The normal small bowel, which connects the stomach to the large bowel, is approximately 20 feet long. Gut microbiome 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.

Why You Should Thank Your Small Bowel and the Beneficial Bacteria That Live There

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).

Are you at risk for small intestinal bacterial overgrowth? Find out what the most common risk factors and symptoms are.#SIBO #SIBOsymptomps

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 contents of the intestine, 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 malabsorption. 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.

How Do You Know If You Have SIBO?

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). 

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 as Chris discussed in his recent podcast)
• 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. However, some evidence suggests that there is an association between Helicobacter pylori and methane production, suggesting that H. pylori plays a role in gut dysbiosis. (8)

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. Other options may include prucalopride and low-dose erythromycin, as well as lubiprostone. (9)

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.

If you need support in dealing with SIBO, consider working with the California Center for Functional Medicine. CCFM offers a membership-based health transformation service that excels at helping people with chronic conditions make the changes necessary to reclaim their health. Find out more about what CCFM has to offer.

About 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. She works with patients through a Functional Medicine approach, working to identify and treat the root causes of illness. She uses nutritional therapy, herbal medicine, supplements, stress management, detoxification and lifestyle changes to restore proper function and improve health.

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