Appendix Q – Diet

What follows is from Appendix Q of The Gut Health Protocol Book, a lot more information about the diet is included in Chapter 1, Section 2.

Appendix Q – The Gut Health Protocol Diet

(A modified low FODMAP Diet)

Allowed Foods


Artichoke (fm)(low)

Asparagus (fm)(low)

Avocados (HIT)(low)(fm)

Bamboo shoots

Bean Sprouts

Bell Peppers (aip)(low)

Bok choy

Broccoli (low/mod)(fm)

Brussel sprouts (fm)

Butternut squash


Carrots (mod)

Cauliflower (low/mod)(fm)

Celery (low)



Eggplant (mod) (HIT)


Green beans

Green pepper (lg)



Leek leaves

Lettuce, iceberg (low)(IV),?

Lettuce, Spring


Olives (HIT)

Mushrooms (mod)(HIT)



Potato (aip)(lc)(low)

Pumpkin (lc)(HIT)



Sauerkraut (HIT)


Spring onions, green part

Spinach (HIT)


Sweet potato (lc)

Swiss Chard

Tomato (aip)(HIT)


Yam (lc)



Vinegar (HIT)


Any 100% protein /
fat such as beef, chicken, poultry, pork, lamb, seafood. Try for quality, e.g; grass-fed beef, pastured eggs/poultry, wild caught fish.

Limit the amount of chicken (and discard the skin)
due to high omega-6 and low nutrient value. Try for a 1:1 ratio of omega-3 to omega-6 fatty acids and that’s hard to do if you eat a lot of chicken. Remove the skin as that is where most of that Omega-6 fat is located.

Bone broths – healing (HIT)

Fish – eat lots (HIT/R)

Poultry – dark meat is best

Cured Bacon (HIT)

Seafood (HIT)

Eggs (aip)(HIT-R)

Smoked or cured meats (HIT)


Avocado (HIT)

Beef tallow

Butter / Ghee


Lard (non-hydrogenated)

Olive Oil

Palm (but not palm kernel)

Vegetable / Grain Oils (low)


Butter (aip)

Cheese, Hard (hit)

Ghee / Clarified Butter (aip)

Kefir, lactose free (aip?)(HIT)

Milk, lactose free (aip)(HIT)

Sour Cream (HIT)

Yogurt, unsweetened (aip)(HIT)


Bananas (HIT-R) (low)


Cantaloupe (HIT)


Dried Fruits (fm)(HIT)

Honeydew melon (HIT)

Kiwi Fruit

Lemon / lemon juice (HIT)

Lime (HIT)

Orange / Mandarins (HIT)




Strawberry (HIT)



Corn (lc)(aip)(low)

Oats (lc)(aip)

Quinoa (lc)(aip)

Rice (lc)(aip)


almond (aip)(IV)(HIT-R)

cashews (aip)(IV)(HIT)

brazil (aip)(IV)

cocoa (aip)(IV)(HIT-R)

coffee (aip)

hazelnut (aip)(IV)(HIT)

macadamia (aip)(IV)

peanuts (aip)(IV)(HIT)

pecan (aip)(IV)

walnut (aip)(IV)(HIT)

Beans / Legumes

Green Beans

(No other beans unless well fermented)

Fermented Foods / Other

Most any well fermented food is OK. This is because the sugars and starches have been consumed. The more
FODMAP fibers it has the longer it should be fermented. Store bought fermented sauerkraut, pickles, beets, cabbage, radishes, natto, kimchi, kefir, beans, are usually fine for most people. (HIT)

Most Spices are OK other than below. Be careful of
(IV) and (HIT); most fresh herbs are fine for HIT.


Only for cooking while healing. After healing
limit moderate amounts of dry wines, low sugar ciders, limited amounts of hard alcohol with plenty of low sugar mixers (like water, tonic water, soda water, kombucha). Alcohol is not good for the gut (especially inflammation and leaky gut) so use caution. (HIT/R) (AIP)

Many foods contain high salicylate levels that
cause histamine release; may need to cross reference between the histamine and salicylate lists.

All foods on this list are normally safe for people with Fructose
Malabsorption, except for those with the (fm) designator. Very sensitive people may still have issues with some of the fruit.

Abbreviation Key

  • AIP = Autoimmune Protocol, people with leaky gut should avoid foods with the AIP designator
  • IV = Ileocecal Valve issues – May irritate (stick) the IV in sensitive people, avoid these foods if in doubt.
  • lc = avoid these foods if trying to eat low carb or be careful to count these carbs in your daily
  • low = you may be able to eat low amounts of this food, but better to avoid, you can eat more of these after the first 4 weeks.
  • mod = eat in moderation, especially per meal or per day, can eat more of these on maintenance
  • fm = Should always be avoided by people with Fructose Malabsorption. Avoid during the “kill” phase, may be added back in small amounts during the “Repair” and “Maintenance” phase.
  • ? = science is unclear or some people report problems with this food

Only people with Histamine Intolerance need to worry about the following:

  • HIT = Histamine Containing – These are
    reminders only, check other sources to be sure.
  • HIT-R = Histamine Releasing food
  • HIT/R = Histamine Containing and Releasing

Sources for HIT food lists in order of quality/completion. Note these
lists are often at odds with one another and should only be used as a
guide. Each person with HIT has different reactions to high and low
histamine listed foods and histamine liberators. Suggest elimination diet, trialing the lowest hist foods first, one addition at a time to build your own food rotation list:

Avoid These Foods


Beets (low)




Peas, green

Plantain (low)


Spices (HIT)

Garlic (allicin supps OK)(fm)

Onions (fm)

Cayenne pepper (IV)

Paprika (low)

Peppers (black pepper OK)


chicory (fm)

inulin (fm)


Hydrogenated Fats


Old / rancid or over used oils

Fruit (HIT)(fm)
















Dried fruits

Fruit Juices

Canned fruit


Agave (fm)

HFCS (high fructose corn syrup)

Aspartame (blue pkg)

Sucralose (yellow pkg)

Inverted Sugar



Sugar alcohols (maltitol, mannitol, sorbitol,
xylitol, erythritol)

Sucrose (table sugar) (low)

Lactose (fm)

Other high calorie sweeteners







Rice, brown

Rice, Wild


Chocolate (IV)(HIT-R)

Pistachios (IV)

To maintain a low FODMAP diet you will need to avoid the foods on the “Avoid” list above. Anyone with Fructose Malabsorption should not consume any foods on the “Avoid” list and should be careful with foods on the “Allowed” list with the “(fm)” designation.

Most of the foods on the “Avoid” list contain FODMAPs that can cause IBS systems and feed bad gut bacteria. Once on maintenance you can try adding back a little at your own risk, but you will be raising your risk of IBS symptoms and a recurrence of SIBO/SIFO.

34 thoughts on “Appendix Q – Diet”

  1. Hi John,

    I am so glad your book and your website was recommended to me. Thank you so much for reading all these scientific studies and making the information available for the rest of us!

    I got the Monash University low FODMAP app as recommended in your book and have a question. In your list above it says sweet potatoes are allowed and plantains not. In the app it is the other way round (sweet potatoes “red light”, plantains “green light”). Which one is correct, or is there a reason why you chose to exclude plantains and include sweet potatoes? I am underweight, so carbs are important for me and I want to make sure I only eat the right ones…

    1. Even MONASH appears to be confused on Sweet Potatoes. Their app so no, but it is included in many of their recipes ( I have plantains as off limits during the kill phase because they are very high in resistant starch (though that will improve a lot of cooked). I also have plantains listed as “low” meaning a person can eat small amounts of it during the kill phase and more once off the kill phase. Since you need to gain weight, they should be OK if consumed cooked and still hot (with lots of good butter! Assuming you tolerate it well)

  2. Other question, I bought the book, it says on amazon that it’s the 2nd edition, but my kindle only shows it as 1st edition.
    In addition, does it mean that everytime you publish a new edition, I have to buy the book entirely, and parse through it to find the “differences”?


  3. Hello, I believe I have the methane form of SIBO (I have constipation only). I seem to do well with eating fibrous vegetables but don’t do well with fermented foods which I noticed is on the list of allowed foods. Is there a separate list in the book of safe/unsafe foods for constipation sufferers? Thanks.

  4. John, what is the reasons for avoiding cassava? I used cassava flour previously to make tortillas and it didnt seem to bother me. I would really like to eat it again.

    1. For cassava it is simply because it is very high in carbohydrates. It can be consumed within the guidelines of carbohydrates in the diet. If consumed cold it may also have some resistant starch, see Chapter 2 about the benefits (and timing) of RS.

  5. Hi John,

    what is “lg” for green pepper please?

    I am surprised to read that eggplant is not AIP in your list, but it belongs to nightshades family as tomatoes and potatoes do. Is it a mistake?

    I bought Silymarin from Now Foods (milk Thistle extract 150 mg), but it has rice flour inside. Is it ok for the Kill Phase ?

    Thanks for your so amazing book! I begin to fill better after so many years of suffering. Will it be a french translation?

    1. Good question on the “lg” abbreviation, I honestly do not remember and green peppers / Bell Peppers should also be “AIP”. The small amount of rice flour in the capsules should be fine.

      No plans for translations at this time. The cost for technical book translations is just too high, and right now, the demand too low.

      Thank you for the compliments on the book and I’m so glad you’re doing better.

  6. Dear John, I suffer from an autoimmune condition Grave’s disease and i am seriously underweight. What safe carbs are ok during the “kill” phase to maintain my weight? Is buckwheat daily fine? I don’t know whether I have a leaky gut. Thank you.

    1. Evgeny,

      During the kill phase it is recommended to keep fiber to a minimum as we don’t utilize it, but bacteria do. Therefore white rice, and white potato (not eating the skin) are better options. I would try to focus more on consuming fats and proteins and only eat enough carbs to maintain weight.

      After the kill phase the rules change. With SIBO bacteria mostly gone there is a heavy emphasis on soluble fiber and more carbs are allowed.

  7. I was diagnosed with severe SIBO through Genova Diagnostic lactulose breath test. I am currently nursing a 7 month old but would like to do the protocol hoping to feel better, have more energy, gain weight, absorb my nutrients and hopefully give my baby better milk. Is there any supplements I should not take since I am nursing? I did find that wormwood could be harmful to my baby. Any thoughts or suggestions?

    1. I would write down what you plan on taking and ask your MD or lactation specialist. I think most will pose no problem, they’re food based and won’t cross over in to the blood/breast milk. I would avoid wormwood, I know that crosses over. NAC might. Pure cinnamomum zeylanicum (Ceylon) is suppose to be fine, but Cassia should not be used due to the amount of courmarin that it contains (Ceylon is very low in this).

      Milk thistle increases milk production (its been used for that for thousands of years), but you should still ask if it is OK (it isn’t strictly needed anyway). In addition to your doctor, this is a very good source of information

  8. I am 2 weeks into kill phase and have a couple questions. Can organic expeller pressed REFINED coconut oil be used in place of the EVCO? Does the green, peas on avoid list include home grown sugar snap peas? Are cultured onions, garlic, and peppers okay if following the (aip) not allowed foods? Is Dandy Blend (coffee substitute) okay? And how will I know if I should continue kill phase for 6 weeks versus 4 weeks? Also I have been getting calf/ foot cramps during the night. I drink lots of water due to nursing, but am not taking any minerals or vitamins other than the kill, parasite and yeast supplements according to your book.

    1. Yes, we use refined coconut oil for cooking all the time. Onions, garlic, and peppers are OK after the kill phase (due to the fiber content). If they bother you the body will get better at breaking down the inulin in them over time. I would limit the kill phase to 4 weeks as the healing phase now includes two weeks of cinnamon oil, this is enough for most people.

      1. I Just received Phage Complete in the mail. You suggest limiting cultured foods to once a day. Does that include during the kill phase? Also you mention avoiding Kombucha?! Always? Does Phage Complete replace Advanced Orthomecular Probiotic 3?
        Thanks for answering my questions, Marie

        1. Marie,

          This is for “Best Results”. You just won’t need as much fermented food with phages as the phages amplify the other probiotics, throughout the gut. This is a good thing, but if you start off with a lot of beneficial bacteria (from the fermented food), you can end up with too much. The type of bacteria is beneficial, and the gas they produce is CO2 (the good one). But it could get uncomfortable. So, yes, I would recommend limiting fermented foods, during all phases, to 4 ounces / day if you are you taking Phage Complete.

          Yes, IMHO, it will replace AOR3. However, you can keep taking it after a 2 week break. This will allow your gut to adjust to Phage Complete and allow you to see if adding AOR3 causes problems for you.

  9. Just finished reading the book. I am about to start fermenting the vegetables. Do i have to wait four weeks till my vegetables are fermented before i begin the ‘kill phase’ ?
    Also, the diet is low carb, high protein. You suggested that the total carbohydrates should be no more than 50 grams from vegetables; that’s about 2 ounces right? Is that per serving or total amount of carbohydrates allowed each day?
    I am about to start working full time. Can i warm up lunch in a microwave?
    I am also confused, is this the low FODmap diet or the Paleo diet?

    1. You do not have to wait for the fermented vegetables to be ready. In fact if you are using a an anaerobic jar to ferment you can start sneaking a little each day after 7 days. Yes, this is a very low carb diet for the first month, many strains of bad bacteria are very heavy carbohydrate consumers. When these strains are in the small intestine they get first dibs! More carbs can be added after the first month. Yes, microwaving the foods is fine (just don’t microwave the fermented vegetables!) This diet is basically a combination of low FODMAP and low carb Paleo. You can find a lot of great recipes on Paleo and low carb websites, just make sure they meet the other requirements.

      After two weeks you will need to add soluble fiber, preferably larch tree fiber, in order to feed the good bacteria in the colon.

    1. Not during the kill phase. Shallots (and onions) are very high in inulin / fructans. This type of fiber ferments very quickly, therefore if there is an overgrowth of bacteria in the small intestine it will feed it. The green part of green onions (scallions) is OK, but the white part is also high in inulin. I know they have a very different flavor profile, but in some situations they may work to add that onion like flavor.

    1. Yes, Spore / Soil based probiotics can be used, they’re recommended in the book (Chapter 1, Section 8). Though some can be helpful they usually don’t flourish in numbers high enough to push out unwanted bacteria. Using it with fermented foods and/or Phage Complete is a great option to make up for this.

  10. Another question about raw food. For collagenous colitis I have been juicing raw veggies to remove insoluble fiber. Does juicing make the veggies any more digestible?

    1. Juicing raw vegetables can be a very good way to get more nutrition. It not only removes the insoluble fiber, but much of the soluble fiber remains (which is great after the first two weeks of the kill phase). You are correct in that it makes raw vegetables more digestible.

  11. I am a vegan and so trying to see what I can eat on the kill phase. Since Tofu is fermented soy, I am hoping it is allowed? Thank you!

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