Treatment and Management of SIBO — Taking a Dietary
Approach Can Control Intestinal Fermentation and Inflammation

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. Emerging research 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 and other similar GI complaints. SIBO is also known as SBBO (small bowel intestinal overgrowth).

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.


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 intestine.

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.  Increased intestinal transit time associated with methane isn’t due to decreased motility but rather to hyperactive reverse peristalsis.

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.  Systemic symptoms are thought to be due to bacterial toxins and abnormal intestinal permeability.



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. However, the accuracy of breath tests varies depending on their duration.  Positive breath tests for fructose, lactose, or sorbitol also can indicate SIBO.



The 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.

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. 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.


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 (fat soluble) nutrients, such as vitamins A, D, E, and K.

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.

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


Dietary Approach

After following the prescribed treatment plan and confirming the eradication of SIBO with a post-treatment breath test, Nutrition Therapy can be administered 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 SIBOtreatment, 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.  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.

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.  FODMAPs include fructose (e.g., high-fructose corn syrup, agave syrup, honey, apples, pears); lactose (e.g., milk and yogurt); fructans (e.g., wheat, barley, rye, onions, garlic); galactans (e.g., legumes); and polyols (e.g., sugar alcohols, mushrooms, cauliflower, avocados, stone fruits).

Customizing patients’ diets according to personal tolerance yields the best results for digestive symptom management.  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. Antigliadin antibodies may be found in 35% of SIBO patients, demonstrating an increased risk of developing celiac disease. 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.  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.

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. Be sure to select supplements without fillers and other inappropriate ingredients, such as starch, lactose, gluten, and sugar, which can contribute to intestinal fermentation or irritation.

Sources of nutrients commonly lacking in SIBO patients should be emphasized, such as liver and cold-water fatty fish (e.g., salmon, mackerel, and 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. The MMC is decreased by 70% in SIBO patients.  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.

The use of probiotics in SIBO patients is controversial.  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 and offer relief.


Source: Aglaée Jacob, MS, RD


For more information, see the following articles on the website:


Vitamin B12 - Emerging Information