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SIBO/Histamine Bi-Phasic Diet


Dr. Nirala Jacobi,

Heidi Turner,

4-6 week dietary protocol for managing histamine intolerance and SIBO

Health care disclaimer: This treatment protocol is not intended as medical advice and is best used with the guidance of a health care professional. Please ask your doctor if this protocol is appropriate for your condition before starting.


Small intestine bacterial overgrowth is a condition where bacteria, normally found lower in the large intestine, have overgrown in the small intestine instead.

Abnormal amounts of these bacteria cause a number of problems:

  1. They damage the microvilli – the absorptive surface of the small intestine. This can lead to malabsorption of nutrients. Microvilli are also responsible for the digestion of small starch molecules from food. When the microvilli are not working, the bacteria use these small starch molecules to cause fermentation. This bacterial fermentation produces methane and hydrogen gas, which is uncomfortable and causes further damage to the microvilli.

Research has shown that SIBO is a major cause of intestinal permeability, or ‘leaky gut,’ a condition where partially digested food particles are absorbed through the lining of the small intestines, causing an immune reaction. Leaky gut also causes bacterial by-products to be absorbed, triggering inflammation.

  1. Leaky gut can cause malabsorption of nutrients from your food, leading to symptoms such as restless legs at night, fatigue, skin rashes, muscle aching, and various digestive symptoms.
  2. The bacteria cause the motility of the small intestine to slow down or work improperly, causing further fermentation. Restoring proper motility in the small intestines is a major focus of eliminating SIBO. Your practitioner is likely to prescribe a “prokinetic” supplement or medication.
  3. Many people who test positive for SIBO will also have a co-infection with fungal organisms, a condition known as SIFO (small intestine fungal overgrowth) – the SIBO Bi-Phasic diet helps to address this as well.

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Histamine is a substance made inside the body and found in certain foods. In many cases of SIBO, other foods besides fermentable carbohydrates can be problematic. The most common reactions are to foods containing histamine. Histamine is found in certain foods and can cause symptoms in those with severely disrupted mucosal lining of the small intestines. The depletion of the histamine-digesting enzyme, diamine oxidase (DAO), yeast overgrowth, or histamine-producing bacteria are often to blame. As the overgrowth reduces and this lining repairs, histamines typically become less problematic. This food sensitivity is known as Histamine Intolerance, or HIT. Histamine is also made in the body and stored in cells known as Mast cells. Reducing histamine foods can lower the “total load” of histamine.


Not everyone with SIBO has histamine intolerance. Beyond the typical gastrointestinal symptoms, those with HIT often experience symptoms resembling allergies, including runny nose, itchy eyes, sneezing, hives, asthma, and chronic cough, as well as other symptoms like headaches, joint pain, anxiety, and insomnia. Not everyone with these symptoms has HIT, but if you do, eliminating histamines from the diet may provide additional relief during treatment.


Histamines in food typically increase with age and fermentation. Fermented foods (vinegars, 24-hour yogurt, wine/beer/cider, sauerkraut, kombucha, kimchi), aged meats (bacon, sausage, ham, canned meats/fish, smoked salmon, bone broths), tomatoes, spinach, eggplant, spicy foods, and chocolate are typically the most problematic for those with HIT. Histamines also increase as food ages in the refrigerator, so leftovers can be an issue for some. There are other foods considered “histamine liberators” (HL) found in certain vegetables, fruits, nuts, and eggs. Histamine liberators do not necessarily contain histamine but can trigger a histamine response. Tolerance to these foods is dependent on the individual.


This protocol has been developed for those suffering from SIBO and histamine intolerance. It is not intended for long-term use but as a starting point for those with SIBO and food reactions. This diet protocol eliminates histamines and fermentable carbohydrates. Once symptoms are controlled, moving into the SIBO Bi-Phasic Diet is recommended. Please consult with your practitioner before initiating this protocol.


Fermented foods such as cultured vegetables, sauerkraut, kimchi, miso, and yogurt are beneficial for the digestive tract as they contain high amounts of probiotics or beneficial bacteria. However, since these foods are high in histamine, they may not be tolerated and should be eliminated from the diet for now. They can be reintroduced as your symptoms improve and your practitioner allows. Introduce no more than one tablespoon in any given meal and increase only as tolerated.


Alcohol is a known gut irritant and disruptor of the normal microbiome of the intestinal tract. It also reduces the amount of DAO you produce and, if fermented (e.g., beer, cider, wine), contains high amounts of histamine. It is strongly recommended to avoid all alcohol while on the Bi-Phasic Diet. In social situations, clear spirits like vodka and gin are preferred over beer and wine as they do not contain histamine, sulfites, or yeast. Please limit alcohol consumption even in these cases.


Combining a low fermentable diet with a diet low in histamine can be challenging due to the narrow list of foods. While all high-histamine and histamine liberators have been eliminated from the diet in Phase 1, once your symptoms have calmed, you are encouraged to test in histamine liberating foods to expand the variety and balance of the diet. Histamine containing foods are noted with an “H” and should be avoided until later in the treatment process. Histamine liberating foods are noted with an “HL” and should be introduced and maintained in the diet to your personal threshold. A food with an “F/HL” indicates it is both a fermentable carbohydrate and a histamine liberator and should be avoided until you are ready to add more fermentable carbohydrates back into the diet, unless otherwise noted.



Phase 1 of the Bi-Phasic Diet lasts two-four weeks. You should avoid all fermentable carbohydrates, histamines, and histamine-liberating foods for at least two weeks before considering expanding the histamine liberators (HL) into the diet. Follow the food guide for food choices.


After two weeks on phase 1, and only once symptoms have reduced, you can start testing HL foods. Use the Phase 2 “Allowed” list as a guide. Add in one serving of a new HL food for three consecutive days. If you tolerate it, keep that food in the diet and add another HL food in the same manner. Repeat, as tolerated. If you experience symptoms, reduce to previously tolerated histamine load. If you react to one HL food, wait for symptoms to calm and continue testing another. If you do not tolerate a particular food, avoid it until further into treatment and test it again later. If introducing any HL foods causes a return of symptoms, return to the baseline diet and wait until Phase 2 before testing again.


Your practitioner will advise when you are ready to move to the Phase 2 diet. This involves adding higher histamine and histamine liberating foods, as you are ready. When determining which foods to add first, consider the foods you miss most and what will make the diet more enjoyable. In this phase, you can also expand more fermentable carbohydrates into the diet.


PROTEIN (must be fresh)

Beef (organic, not aged), Lamb, Turkey (organic if available), Skinless chicken (organic), Wild/game meats


Avoid all dairy

VEGETABLES (unlimited)

Alfalfa sprouts, Bamboo shoots, Bok choy, Capsicum/bell peppers (not spicy), Carrot, Chard/Silverbeet, Chives, Cucumber, Ginger, Kale, Lettuce, Parsnip, Radicchio, Radish, Rocket/arugula, Spring onion (green part only), Sunflower sprouts, Witlof

FRUITS (two serves per day)

Blueberries – ½ cup, Cantaloupe/Rockmelon – ½ cup, Grapes – 10 ea, Lime (to flavor, fresh squeezed), Lychee – 4, Honeydew melon – ½ cup, Kiwi – 1 ea, Papaya – ½ cup, Passion fruit – 1 ea


Avoid all, but if practitioner allows, can limit to Quinoa – ½ cup, White rice (basmati, jasmine only) – ½ cup cooked




Freeze large batches in single servings to reduce histamine production. Homemade broths (organic only): chicken, beef, lamb, turkey, 2-hour broths only


Tea (herbal), Water (filtered only)


Dextrose/glucose, Organic honey (clear) – max. 2 tbsp per day, Stevia (100% pure, no inulin)


Coconut flour/shredded – ¼ cup, Coconut milk (no thickeners) – ¼ cup, Coconut cream – 2 tbsp, Macadamias – 20 ea


All fresh and dried herbs and spices except those noted in ‘Avoid’, Green salsa (without onions/garlic) – 1-2 tbsp


Butter, Coconut, Flax (low lignin) Ghee, Grapeseed, Infused (garlic, lemon, onion), Olive, MCT, Sunflower



Eggs (HL), Pork (HL), Seafood (H / HL) (see “Histamines in Food” for info.), Seasons/aged meats (ham, bacon, sausage, canned or smoked fish and meats) (H), Legumes, Meats seasoned with garlic/onion


Avoid all dairy


Capsicum (spicy/chili) (H), Eggplant (H), Olives (H), Spinach (H), Tomato (red) (H) (green or yellow cherry tomato may be OK), Cauliflower, Corn, Garlic, Mushroom, Onion, Sweet Potato, Starch powder: arrowroot, corn, rice, tapioca


Avocado (F/HL) – ¼ fruit (can test in with HL but limited to recommended amount), Banana (H), Kiwi (HL) – 1 ea, Lemon (HL) (fresh squeezed, likely tolerated), Orange (HL), Raspberries (HL), Strawberries (HL), Tangerine (HL)




Bone broth (H/F), Canned soups and soup bouillon (H/F)


Alcohol, Beer, Cider, Club Soda, Coffee, Energy drinks, Fruit juices (H/F), Kombucha, Liqueurs and spirits (dark), Seltzer water, Soft drinks, Tea (black, green), Wine


Artificial sweeteners (avoid completely) (HL), Cane sugar, Chocolate, cocoa, cacao (H/F), Maple syrup, Sugar alcohols (xylitol, mannitol, sorbitol)


All other nuts/seeds (HL) (can introduce upon practitioner’s approval to low FODMAP guideline recommendations)


Capsicum/peppers (spicy): chili, cayenne and their sauces (H), Allspice, Cardamom, Cinnamon, Cloves, Nutmeg (HL), Fermented sauces (such as fish, soy, coconut aminos, oyster, tamari) (H), Fermented foods (such as kimchi, sauerkraut, pickles) (H), Mayonnaise (H), Mustard (H), Vinegar (H), Tomato sauce/ketchup (H), Salsa (H), READ LABELS! No Asafetida, Chicory root, Garlic, Gums/carrageenan/thickeners, Maltodextrin, Starches, Sugar, Onions


Palm, Soybean, Pumpkin, Sesame (HL), Walnut