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Dietary Modifications for a Successful SIBO Treatment Plan

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Dietary Modifications for a Successful SIBO Treatment Plan

Small intestinal bacterial overgrowth (SIBO) is a common digestive disorder often mistaken for irritable bowel syndrome. Because SIBO often causes food intolerances and digestive symptoms related to meal times, knowing what and how to eat can be difficult for patients. Successful treatment of SIBO requires a multifaceted approach that includes antimicrobial therapy and dietary modifications, among other interventions, to eradicate bacterial overgrowth, palliate disruptive digestive symptoms, and prevent SIBO recurrence. This article will discuss five therapeutic diets that can be included in a SIBO protocol.


What is Small Intestinal Bacterial Overgrowth (SIBO)?

According to the American College of Gastroenterology, SIBO is the presence of excessive numbers of bacteria in the small intestine, causing gastrointestinal (GI) symptoms (1). In a healthy digestive tract, the small intestine should have little bacterial growth compared to the large intestine. Various factors that prevent bacterial translocation through the small intestine into the large intestine or allow for the migration of bacteria from the colon into the small intestine can contribute to SIBO.

Advances in research have allowed the SIBO diagnosis to become more nuanced, and three distinct SIBO subtypes have been identified. Hydrogen (H2) SIBO is the overgrowth of H2-producing bacteria within the small intestine. Intestinal methanogen overgrowth (IMO), previously called methane (CH4) SIBO, is the overgrowth of methanogens in the small or large intestines. Hydrogen sulfide (H2S) SIBO is the overgrowth of H2S-producing organisms in the small intestine. (2)

Additionally, SIBO research has led to increased knowledge of SIBO's role in the development and progression of other diseases, including irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), systemic sclerosis, intestinal motility disorders, and cirrhosis. (1)

SIBO Symptoms

The signs and symptoms of SIBO arise from bacterial fermentation within the small intestine and pathologic changes to intestinal permeability and immune function caused by the excess numbers of microorganisms within the small intestine. The most common SIBO symptoms, present in more than two-thirds of SIBO patients, include abdominal pain, bloating, gas, abdominal distension, flatulence, and diarrhea. Other common SIBO symptoms include heartburn, reflux, nausea, and constipation. (1)

In more severe cases of SIBO, maldigestion and malabsorption can occur, leading to weight loss, fatty stools (steatorrhea), and evidence of nutrient deficiencies and anemias on lab results. (1, 2)

Increased intestinal permeability and low-grade inflammation can translate to symptoms outside the GI tract. Fatigue, brain fog, skin rashes, changes in mood, headaches, and joint pain can present secondary to SIBO-induced leaky gut. (2)

Certain symptom patterns are indicative of, but not diagnostic for, SIBO. These include:

  • Bloating progressively worsens after meals and throughout the day
  • Digestive symptoms are worse after eating high-fiber foods (e.g., whole grains, bran, beans, raw vegetables), onions, garlic, and apples
  • White bread and rice are better tolerated than whole wheat bread and brown rice
  • GI symptoms begin and persist after a bout of food poisoning, taking a proton pump inhibitor or opiate narcotics, or abdominal surgery
  • Taking antibiotics provides temporary relief and improvement in GI symptoms
  • Probiotics, especially those that contain prebiotics (e.g., FOS, GOS, inulin), worsen digestive symptoms

Who Could Benefit From a SIBO Diet?

While dietary modification is often used in clinical practice for patients with SIBO, research has yet to definitively determine its role in treatment. Dietary strategies predominantly emphasize the reduction of fermentable carbohydrates from the diet; it is unclear if the resulting clinical improvements are due to a reduction of intestinal bacterial concentrations or simply a reduction in fermentation and gas production. Regardless, dietary therapy, even without concurrent antimicrobial treatment, can be enough to provide symptom relief to patients. (3)

Given that SIBO diets can relieve SIBO symptoms, people with confirmed SIBO cases can consider initiating a SIBO diet before or during antibiotic or herbal eradication therapy. Dietary modifications may also be recommended for patients unable to perform diagnostic SIBO testing; improvement in digestive symptoms with the removal of fermentable carbohydrates is indicative and supports clinical suspicion of SIBO.

Functional Medicine Labs to Test That Can Help Support Individualized Dietary Modifications for SIBO Treatment

Functional medicine labs help practitioners personalize treatment options for their patients. Below are some of the most common labs ordered for patients suffering from SIBO.

SIBO Breath Test

The SIBO breath test is a noninvasive testing alternative to small intestinal culture, most commonly used in the clinical setting to diagnose SIBO and IMO. The SIBO breath test helps determine the subtype of SIBO and monitor SIBO treatment progress. Different SIBO breath tests are available, differentiated by their test substrate and duration. Currently, there is no universal standard for SIBO breath testing; the type of test ordered largely depends on the preference of the ordering provider.

The patient can perform the test in the comfort of their home after following a one-day preparatory diet. After the patient collects a baseline breath sample, they drink a solution that contains either glucose or lactulose. The patient continues to collect breath samples at timed intervals for the test duration (two or three hours). While most tests can only measure H2 and CH4 gas levels, the newest test on the market, trio-smart, can measure all three fermented gases associated with SIBO.

Comprehensive Stool Test

A comprehensive stool test cannot diagnose SIBO, but it can provide additional information regarding the health and function of the digestive tract that can guide dietary and other treatment recommendations. Biomarkers included on a comprehensive stool test to pay special attention to regarding SIBO include fecal markers of digestion and absorption, intestinal immunology and inflammation, and dysbiotic patterns.

The information provided on a comprehensive stool test supports a more holistic approach to digestive health and treating SIBO. By identifying the consequences of SIBO, such as maldigestion or leaky gut, therapeutic strategies can be implemented to palliate symptoms and correct imbalances. Additionally, stool results can reveal underlying root causes of SIBO development, like immune dysregulation or digestive enzyme deficiency, so they can be corrected to prevent future SIBO recurrence.


Functional Medicine and Functional Nutrition Treatment Plan For SIBO Patients

Dietary modifications in the setting of SIBO treatment aim to reduce food sources for bacteria while nourishing the patient. Bacteria primarily ferment ("eat") carbohydrates, so you'll note that all diets discussed in this article are similar variations in dietary restrictions of fermentable carbohydrates, including starches, resistant starches, soluble fibers, sugar, and prebiotics.

SIBO Diets for a Successful SIBO Treatment Plan

Many diets can benefit patients with SIBO. The decision on which is used should be based on the patient's health history, lifestyle, preferences, and ability to follow the dietary plan consistently.


The low FODMAP diet is the most notorious and best-studied therapeutic elimination diet for SIBO and IBS. The low FODMAP diet improves digestive symptoms in up to 86% of patients with IBS. The high prevalence of SIBO in IBS patients rationalizes using this diet for SIBO management.

This diet eliminates four troublesome fermentable carbohydrate groups: oligosaccharides, disaccharides, monosaccharides, and polyols. A FODMAP elimination diet is a three-step dietary plan:

Step 1: Low FODMAP Diet

Swap high FODMAP foods for low FODMAP alternatives for 2-6 weeks. MONASH University is a great resource that uses a traffic light system to grade foods from all food groups as high, moderate, or low FODMAP. The elimination diet targets foods high in fructose, lactose, fructans, galactans, and polyols. It allows the consumption of grains, fiber, sugar, and other fermentable carbohydrates, which may trigger patients with SIBO even in low amounts. Because of this, the diet may need to be slightly adapted for those with SIBO.

Source: MONASH University

Step 2: FODMAP Reintroduction

The patient should be advised to reintroduce moderate-to-high FODMAP foods back into the diet. One food should be rechallenged into the diet one at a time over three days to observe for GI/SIBO symptoms and test food tolerance. Reintroductions can be done at the patient's own rate, typically occurring over 8-12 weeks. FODMAP reintroductions allow patients to experiment with how much of a particular food is tolerated to individualize their diet to manage SIBO and digestive symptoms.

Step 3: FODMAP Personalization

Long-term dietary customization is determined through the patient's reintroduction challenges. Understanding tolerance of FODMAP foods helps to add and maintain variety in the diet by incorporating tolerated amounts of some high-FODMAP foods and avoiding others.

Specific Carbohydrate Diet (SCD)

Dr. Sidney Haas developed the SCD to treat celiac disease in the pediatric population, as explained in his book published in 1951, The Management of Celiac Disease. The SCD eliminates select carbohydrates (disaccharides and polysaccharides) that are more difficult for the digestive tract to break down, contributing to intestinal inflammation, dysbiosis, and digestive symptoms. For patients with SIBO, eliminating these carbohydrates reduces bacterial fermentation contributing to SIBO symptoms. (4)

The following foods are allowed on the SCD:

  • Meats, poultry, fish, shellfish, and eggs without additives
  • Legumes, including but not limited to dried navy beans, lentils, peas, split peas, and lima beans
  • Dairy: cheddar, Colby, Swiss, and dry curd cottage cheese; homemade 24-hour fermented yogurt
  • Most fresh, frozen, raw, or cooked vegetables
  • Fresh, raw, cooked, frozen, or dried fruits without added sugar
  • Most nuts and nut flours
  • Most oils
  • Mustard, cider, and white vinegar
  • Plain tea and coffee
  • Juices without additives or sugars
  • Honey

The following foods are not allowed on the SCD:

  • Sugar, molasses, maple syrup, sucrose, fructose (including high-fructose corn syrup)
  • All grains
  • Canned fruits and vegetables
  • Some legumes, like soybeans and chickpeas
  • Seaweed and its byproducts, like carrageenan
  • Starchy vegetables, including potatoes, sweet potatoes, and turnips
  • Canned and processed meats
  • Canola oil and mayonnaise
  • High-lactose dairy: milk, mild cheddar cheese, store-bought yogurt, cream, sour cream, ice cream
  • Candy and chocolate
  • Food products that contain fructooligosaccharides (FOS)

SIBO Bi-Phasic Diet (SIBO B-PD)

Developed by Dr. Nirala Jacobi, the SIBO B-PD combines principles of the low FODMAP and SCD diets to implement a phased dietary approach to treating SIBO that is timed in conjunction with antimicrobial therapy. The three-month SIBO B-PD protocol can be accessed here.

Phase 1: Reduce and Repair

The first phase of the B-PD is performed before antimicrobial therapy. This more restrictive phase focuses on eliminating all fermentable starches (grains, legumes, dairy, sugar, and certain fruits and vegetables) for 4-6 weeks or until digestive symptoms improve. Examples of approved Phase 1 foods include:

  • Unlimited vegetables: alfalfa sprouts, bamboo shoots, Bok choy, bell pepper, carrot, cucumber, eggplant, kale, lettuce, radicchio, radish, arugula, tomatoes
  • Limited vegetables: asparagus, artichoke hearts, beet, broccoli, Brussels sprouts, cabbage, celery, fennel, green beans, pumpkin, zucchini
  • Fruits (2 servings per day): lemons, limes
  • Homemade beef or lamb bone broths, chicken meat broths
  • Nuts and seeds (in limited amounts): almonds, coconut, hazelnuts, macadamia nuts, pecans, pine nuts, pumpkin seeds, sesame seeds, sunflower seeds, walnuts
  • Most oils
  • All fresh and dried herbs and spices
  • Condiments: sugar-free mayonnaise, garlic-free mustard, vinegar

Phase 2: Remove and Restore

The second phase of the B-PD is followed for 4-6 weeks during prescription or herbal antibiotic SIBO therapy. Phase 2, while still a low-fiber diet, allows the reintroduction of dairy, legumes, and grains per patient tolerance to nourish the microbiome and augment antimicrobial SIBO treatment.

Gut and Psychology Syndrome Diet (GAPS)

The GAPS diet was adapted from the SCD by Dr. Natasha Campbell-McBride. The diet's premise is that numerous neurologic and mental health disorders are caused by leaky gut. The GAPS diet is an elimination diet aimed to decrease intestinal permeability and heal the gut; because it significantly reduces total carbohydrate intake, patients with SIBO often will see improvements in digestive symptoms.

The GAPS diet is the SCD with a few modifications. The GAPS diet emphasizes more fat, broth, juicing, and cultured vegetables than the SCD. It also highlights incorporating some highly fermentable foods, like avocado and onion, so it may need to be modified for patients with SIBO. Because it emphasizes more home cooking, the GAPS diet may be more challenging to follow than the SCD.

The GAPS diet calls for a structured six-stage introduction diet. The patient progresses through each stage as they can tolerate newly introduced foods into the diet. After completing all six stages, the patient can continue to the full GAPS diet. The phases of the GAPS diet are summarized below.

Introduction Diet

  • Stage 1: homemade meat or fish stock; homemade soups with meat or fish stock; dairy- or vegetable-based probiotic foods; ginger tea
  • Stage 2: Addition of raw organic egg yolks; stews and casseroles with meats and vegetables; homemade yogurt or kefir; juice from sauerkraut or vegetables; fermented fish; homemade ghee
  • Stage 3: Addition of avocado, scrambled eggs, sauerkraut, and other fermented vegetables
  • Stage 4: Addition of roasted and grilled meats; cold-pressed olive oil; freshly pressed juices; baked bread with ground nuts or seeds
  • Stage 5: Addition of cooked apple puree and raw vegetables
  • Stage 6: Addition of peeled raw apple, other fruits, and honey

Full GAPS Diet

The full GAPS diet introduces more foods into the diet that are intended to heal the gut. The diet guidelines recommend that 85% of consumed foods come from meat, fish, broth, eggs, fermented foods, and vegetables. A complete list of foods to be eaten and avoided on the full GAPS diet can be viewed here.

Elemental Diet

The elemental diet (ED) is the only diet at this time that has data to support its ability to treat SIBO, not just improve symptoms. The ED is a liquid, hypoallergenic formula of predigested nutrients mixed with water. It fulfills all human caloric and nutritional needs while being devoid of all nutrients needed to sustain bacterial life. As such, a 14-day course of ED is 80% effective in treating SIBO, and up to 85% effective when extended to 21 days (5).



Many different diets can be used for SIBO management. Dietary modifications can be an integral aspect of a SIBO treatment plan for short- and long-term management of symptoms. Restrictive elimination diets are not intended to be followed forever; the goal instead should be to implement therapeutic dietary modifications for as little time as possible while SIBO is being eradicated and the underlying causes are being corrected to prevent SIBO relapse. Working with a functional nutritionist can help patients navigate the many SIBO therapeutic diets and implement challenging dietary modifications.

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1. Pimentel, M., Saad, R.J., Long, M.D., et al. (2020). ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. The American Journal of Gastroenterology, 115(2), 165–178.

2. Cloyd, J. (2023, March 30). An In-Depth Overview of the Three Types of SIBO: Hydrogen, Methane, Hydrogen Sulfide. Rupa Health.

3. Souza, C., Rocha, R., & Cotrim, H.P. (2022). Diet and intestinal bacterial overgrowth: Is there evidence? World Journal of Clinical Cases, 10(15), 4713–4716.

4. Specific Carbohydrate Diet (SCD). (2022, July 19). Cleveland Clinic.

5. Pimentel, M., Constantino, T., Kong, Y.,et al. (2004). A 14-Day Elemental Diet Is Highly Effective in Normalizing the Lactulose Breath Test. Digestive Diseases and Sciences, 49(1), 73–77.

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