December 2012 Issue

Treatment and Management of SIBO — Taking a Dietary Approach Can Control Intestinal Fermentation and Inflammation
By Aglaée Jacob, MS, RD
Today’s Dietitian
Vol. 14 No. 12 P. 16

Irritable bowel syndrome (IBS) impacts the lives of more than 20% of Americans, yet current treatment options haven’t been successful in relieving the digestive symptoms associated with this disease.1 Emerging research, however, shows that small intestinal bacterial overgrowth (SIBO) could be responsible for up to 84% of IBS cases, paving the way for more effective management of IBS.1

The human gut flora has 10 times more bacteria than the body has cells, but the majority of these bacteria should be located in the colon. Too much bacteria, even of a nonpathogenic nature, overgrowing in the small intestines can lead to various digestive and systemic symptoms as well as nutritional deficiencies.

This article will discuss these symptoms, the common nutritional deficiencies that often result, and successful dietary treatment and management strategies dietitians can employ to treat SIBO and therefore IBS.

Symptoms and Mechanisms
SIBO and IBS symptoms are the same: abdominal distension, flatulence, cramping, diarrhea, and constipation. These digestive symptoms result from both the high osmotic activity and fermentation potential of incompletely digested and unabsorbed carbohydrates present in the small intestines.

Both the gas produced by intestinal fermentation and the water drawn through osmosis can contribute to bloating in SIBO patients. The type of gas produced by the bacteria also seems to impact the motility of the intestines. Hydrogen-producing patients are more likely to suffer from diarrhea, while methane producers are more prone to constipation. Research conducted by Mark Pimentel, MD, director of the gastrointestinal motility program at Cedars-Sinai Medical Center and author of A New IBS Solution, indicates that increased intestinal transit time associated with methane isn’t due to decreased motility but rather to hyperactive reverse peristalsis.1

Two-thirds of celiac disease patients unresponsive to a gluten-free diet and at least one-quarter of acute flares in Crohn’s disease patients can be explained by the presence of SIBO. This chronic bacterial overgrowth also is associated with systemic symptoms such as fatigue, joint pain, headaches, depression, and loss of concentration as well as diverticulitis, hypothyroidism, obesity, and other chronic conditions.1-3 Systemic symptoms are thought to be due to bacterial toxins and abnormal intestinal permeability.2-3

As mentioned, the intestinal fermentation associated with an abnormally high amount of bacteria in the small intestines produces methane and/or hydrogen gas. Humans don’t produce these gases themselves and slowly expel them by diffusion through the lungs. So measuring breath hydrogen and methane levels after giving patients a predetermined amount of lactulose or glucose is the easiest way to diagnose SIBO.1 However, the accuracy of breath tests varies depending on their duration. Dietitians should keep in mind that both hydrogen and methane should be measured for a more accurate diagnosis. Positive breath tests for fructose, lactose, or sorbitol also can indicate SIBO.4

An SIBO diagnosis calls for eradication of excess bacteria living in the small intestines. The treatment can involve using antibiotics to directly kill the bacteria or feeding the patient an elemental diet formula to indirectly starve the bacteria to death.1

Rifaximin is the antibiotic of choice because 99.6% of it stays in the gut without being absorbed into the bloodstream, therefore reducing side effects and enhancing its efficacy within the digestive tract.1 However, recurrence rates reach 43.7% nine months after antibiotic treatment if the underlying causes, such as hypochlorhydria, impaired motility, or certain medications, that can lead to SIBO aren’t addressed.2

Nutritional Deficits
Due to the bacterial overgrowth, patients often experience various nutritional deficiencies. Malabsorption induced by rapid intestinal transit time can lead to the loss of both macronutrients and micronutrients, such as omega-3 fatty acids and liposoluble nutrients, such as vitamins A, D, E, and K.5

Dietitians should be aware that the excess bacteria in the small intestines can deconjugate bile acids and interfere with the absorption of these nutrients as well as coenzyme Q10 and beta-carotene.2,5

SIBO bacteria also can reduce vitamin B12 and iron stores, increasing the risk of anemia. Serum B12 levels aren’t always reliable because vitamin B12 analogues synthesized by the bacteria can mask a deficiency.2,5

Dietary Approach
After following the prescribed treatment plan and confirming the eradication of SIBO with a posttreatment breath test, dietitians can administer nutrition therapy to patients. Besides symptom management, the goals of diet therapy should include repairing the intestinal lining, optimizing nutritional status, and preventing recurrence.

Digestive Symptom Management
Digestive symptoms tend to significantly improve after SIBO treatment, but it’s important for patients, especially in the beginning, to avoid foods that can contribute to intestinal fermentation. Damage to the lining of the small intestines can impair secretion of brush border enzymes, such as lactase, sucrase, and maltase, according to SIBO expert Allison Siebecker, ND.2 Undigested lactose, sucrose, and maltose (starch fragments) aren’t absorbed and can become substrates for intestinal fermentation. Restricting lactose, sugars, and starches can attenuate bloating and normalize bowel movements until the brush border is sufficiently healed to normally produce digestive enzymes again.2

Foods containing FODMAPs (fermentable oligo-, di-, mono-saccharides and polyols) also can ferment in the small intestines and therefore should be limited if they induce symptoms in SIBO patients.2 FODMAPs include fructose (eg, high-fructose corn syrup, agave syrup, honey, apples, pears); lactose (eg, milk and yogurt); fructans (eg, wheat, barley, rye, onions, garlic); galactans (eg, legumes); and polyols (eg, sugar alcohols, mushrooms, cauliflower, avocados, stone fruits).

Customizing patients’ diets according to personal tolerance yields the best results for digestive symptom management.2 An elimination diet supervised by a qualified RD can help identify all problematic foods. In cases of steatorrhea, the presence of excess fat in the stool, the use of medium-chain triglycerides (MCTs) from coconut oil and MCT oil or supplementation with ox bile can facilitate the digestion and absorption of fatty acids and liposoluble nutrients.

Intestinal Lining Repair
Only when digestive symptoms are under control can the abnormal intestinal permeability and inflammation resolve. Optimizing the omega-6 to omega-3 ratio by avoiding high omega-6 seed oils and encouraging cold-water fatty fish consumption can lower inflammation and promote gut healing.

In addition to the high fructan and starch content of wheat, barley, and rye, their gluten can trigger symptoms in some SIBO patients. An Australian study found luminal antigliadin antibodies in 35% of SIBO patients, demonstrating an increased risk of developing celiac disease.6 Gluten is known to increase intestinal permeability through zonulin signaling and may play a role in the development of various autoimmune conditions, including type 1 diabetes, multiple sclerosis, and rheumatoid arthritis.7 Removing gluten as part of an elimination diet is a good precaution for SIBO patients. Those taking supplements such as L-glutamine, zinc, and vitamin A also can improve gut lining integrity.2

Nutritional deficiencies are difficult to correct when digestive symptoms are uncontrolled and the brush border remains damaged, but dietitians can recommend supplements once patients start feeling better. RDs should select supplements without fillers and other inappropriate ingredients, such as starch, lactose, gluten, and sugar, which can contribute to intestinal fermentation or irritation.2
Dietitians also should recommend food sources of nutrients commonly lacking in SIBO patients, such as liver and cold-water fatty fish (eg, salmon, mackeral, sardines). Liver is rich in vitamin B12, iron, and vitamin A, while cold-water fatty fish is rich in omega-3s and vitamin D.

Preventing Recurrence
One of the most common underlying causes of SIBO is the impairment of the migrating motor complex (MMC). The MMC corresponds to cleansing waves activated approximately every 90 minutes in the small intestines when fasting to prevent the accumulation of debris and excessive amounts of bacteria. Pimentel found that the MMC is decreased by 70% in SIBO patients.1 Apart from snacking, stress also negatively impacts the MMC. Encourage patients to space their meals every three to five hours and better manage their stress to promote regular MMC activation and prevent SIBO from returning.1

The use of probiotics in SIBO patients is controversial.1,2 Although probiotics may worsen symptoms at first, many patients benefit from trying to rebalance their gut flora. A slow and gradual introduction of probiotics free of lactose, inulin, fructooligosaccharides or prebiotics can facilitate patient tolerance.

Bottom Line
RDs can help SIBO patients optimize their digestion and improve their nutritional status. Customizing the diet and adopting strategies to prevent recurrence make the dietary approach more successful.

— Aglaée Jacob, MS, RD, is a freelance writer who specializes in diabetes education and digestive health.


1. Pimentel M. A New IBS Solution. Sherman Oaks, California: Health Point Press; 2005.

2. Siebecker A. Small intestine bacterial overgrowth: clinical strategies [webinar]. September 17, 2011. Accessed September 25, 2012.

3. Campbell AK, Matthews SB, Vassel N, et al. Bacterial metabolic ‘toxins’: a new mechanism for lactose and food intolerance, and irritable bowel syndrome. Toxicology. 2010;278(3):268-276.

4. Nucera G, Gabrielli M, Lupascu A, et al. Abnormal breath tests to lactose, fructose and sorbitol in irritable bowel syndrome may be explained by small intestinal bacterial overgrowth. Aliment Pharmacol Ther. 2005;21(11):1391-1395.

5. DiBaise JK. Nutritional consequences of small intestinal bacterial overgrowth. Prac Gastroenterol. 2008;69:15-28.

6. Riordan SM, Mclver CJ, Wakefield D, Duncombe VM, Bolin TD, Thomas MC. Luminal antigliadin antibodies in small intestinal bacterial overgrowth. Am J Gastroenterol. 1997;92(8):1335-1338.

7. Fasano A. Zonulin and its regulation of intestinal barrier function: the biological door to inflammation, autoimmunity, and cancer. Physiol Rev. 2011;91(1):151-175.


Table 1: SIBO Symptoms and Associated Conditions

Digestive Symptoms

Systemic Symptoms

Associated Conditions

• Abdominal distension
• Abdominal pain and cramping
• Flatulence
• Belching
• Diarrhea
• Constipation
• Alternating constipation and diarrhea

• Fatigue
• Eczema
• Joint pain
• Headaches
• Mouth ulcers
• Depression
• Increased micturition
• Brain fog
• Concentration loss
• Steatorrhea
• Nutritional deficiencies (vitamin B12, iron, fat-soluble nutrients)

• Celiac disease
• Crohn’s disease
• Fibromyalgia
• Chronic fatigue syndrome
• Interstitial cystitis
• Nonalcoholic steatohepatitis
• Diverticulitis
• Hypothyroidism
• Gastroesophageal reflux disease
• Autism
• Acne rosacea
• Restless legs syndrome


Table 2: Dietary Approaches for SIBO


Dietary Approach

Reduce intestinal fermentation

• Avoid FODMAPs (fructose, lactose, fructans, galactans, and polyols)
• Restrict starches and sugars
• Elimination diet to identify problematic foods (under RD’s supervision)
• Address steatorrhea by using ox bile supplementation or fats rich in medium-chain triglycerides

Repair the intestinal lining

• Lower inflammation
- Decrease the omega-6 to omega-3 ratio
- Eliminate gluten and other problematic foods (identified with an elimination diet)
• Nourish the gut lining as needed
- L-glutamine, vitamin A, and zinc

Correct nutritional deficiencies

• Individualized
- Liposoluble nutrients (omega-3 fats, vitamins A, D, E, K)
- Vitamin B12 and iron

Prevent recurrence

• Promote migrating motor complex
- Space meals every three to five hours, avoid snacking, and fast 12 hours overnight
- Manage stress
• Correct gut dysbiosis
- Probiotics (careful with prebiotics such as inulin and fructo-oligosaccharides)