GAPS Diet for SIBO: Foods, Ferments, and Stomach Acid

The GAPS food route for SIBO begins with the Introduction Diet, fermented foods in their stage-appropriate form, and temporary stomach-acid support while digestion recovers.^[1] The practical work is broader than a list of foods to avoid: it includes the order of Intro, the form and amount of ferments, the HCl and pepsin limits, low-FODMAP distinctions, prebiotic and enema boundaries, fat digestion, and enough food to make the plan livable.

Start With the Introduction Diet

The 2020 SIBO entry calls the GAPS Introduction Diet essential.^[1] Intro begins with easy-to-digest foods and expands through six stages according to stool changes and tolerance:

• Stage 1: fresh meat or fish stock, boiled meat and fish, soups with well-cooked permitted vegetables, natural animal fats, and small amounts of the appropriate probiotic liquid or fermented dairy.
• Stage 2: raw organic egg yolk, then the stage-appropriate whole egg, stews and casseroles, fresh herbs, more probiotic food, homemade ghee, and cod liver oil.
• Stage 3: ripe avocado, the stage pancakes, eggs cooked in fat, cooked onion and fibrous vegetables, and gradually increased fermented vegetables.
• Stage 4: roasted or grilled meat, cold-pressed olive oil, fresh vegetable juice, and bread made with fermented nut or seed flour.
• Stage 5: cooked apple, raw vegetables beginning with lettuce and peeled cucumber, and fruit added to fresh vegetable juice.
• Stage 6: raw permitted fruit, gradually increased honey, and later-stage baked or dried-fruit foods as tolerated.^[2]

Stage movement follows the digestive response rather than a fixed calendar. Return to the last comfortable stage when a new food brings back the symptoms that had settled.

How Fermented Foods Fit

The official GAPS answer keeps fermented foods in the SIBO route. Intro begins with small amounts of probiotic liquid or fermented dairy as appropriate, while fermented vegetable solids arrive later when the gut can manage their fiber.^[2][3]

Record the exact ferment, ingredients, amount, and timing. A teaspoon of sauerkraut juice is a different food exposure from a bowl of fermented cabbage, and homemade kefir is different from a supplement that contains added inulin or FOS.

Temporary Stomach-Acid Support

The 2020 book describes Betaine HCl with pepsin as its most physiological stomach-acid preparation. One capsule typically supplies 200–300 mg of Betaine HCl and 100 mg of pepsin, taken at the beginning of a meal.^[4] The SIBO entry also names Betaine HCl or HCl with pepsin before meals while the stomach is healing.^[1]

The FAQ adds two important limits:

• Long-term HCl and pepsin can irritate the stomach. For children, the source first uses cabbage juice, fresh cabbage salad, or a small helping of sauerkraut five to ten minutes before the meal. When that is not enough, it uses a little HCl and pepsin with larger meals only.^[5]
• Betaine HCl is taken with main meals containing meat and fat, used carefully when needed, and kept temporary rather than permanent. The long-term goal is the person’s own acid production, supported in the source by cabbage juice and fermented cabbage foods.^[6]

The cabbage options above use different food forms. In the ordinary Intro sequence, fermented-vegetable juice begins in Stage 1, uncooked fermented vegetable pieces in Stage 3, and raw salads in Stage 5. The 2020 book also names meat stock mixed with cabbage or sauerkraut juice as an easy option for children. Keep the form and amount with the stage and tolerance already reached.^[2][4]

The sources give no universal number of weeks. The stopping point is tied to recovery of the person’s own digestion, and the irritation limit still applies.

The H. Pylori Branch

The official FAQ says Intro can begin when H. pylori is present. Campbell-McBride reports that most people in her experience remove the related symptoms through the GAPS Nutritional Protocol and says to give the diet one to one and a half years before considering another intervention when symptoms persist.^[7] That is the source’s clinical-experience statement, not a universal outcome promised by this article.

Foods That Remain Out

Across Intro and Full GAPS, the core exclusions remain grains, refined sugar, starchy vegetables, lactose-containing commercial dairy, processed foods, and the other foods on the official avoid list.^[21] After Intro, Full GAPS widens the permitted foods while retaining those exclusions.

Use the WFLI GAPS Diet Food List guide to check general protocol placement. Then apply the SIBO-specific ferment, acid-support, histamine, low-FODMAP, and fat-digestion branches described here.

GAPS and Low FODMAP Are Different Food Lists

GAPS decides whether a food belongs in the protocol and which stage introduces it. A low-FODMAP plan limits particular fermentable carbohydrates according to serving size, then uses reintroduction and personalization. Monash describes the stricter first step as a two-to-six-week phase, followed by structured reintroduction and a wider personalized diet.^[8]

The lists do not match. Rice and potato can fit low-FODMAP choices while remaining outside GAPS. Onion, garlic, apple, and honey can fit GAPS while carrying FODMAP limits. If both plans are being used, write one positive list of complete meals and portions that meets both sets of rules instead of assuming either list automatically covers the other.

Onion and Garlic in Stock

Onion and garlic fructans are water soluble. Monash explains that when either cooks in soup or stock, fructans move into the liquid; removing the pieces afterward does not remove what has already leached into the water.^[9] If an individual low-FODMAP plan limits them, make that batch without onion or garlic from the beginning and label the container clearly.

Use Meat Stock Before Bone Broth

The current 2020 GAPS rule uses fresh meat stock first and waits at least one year before bone broth, longer for some people.^[10] Rachael Mamane’s Mastering Stocks and Broths is our source for the culinary stock technique; the GAPS book sets when meat stock and bone broth belong in the protocol.^[11]

Meat stock includes raw meaty joints, connective tissue, fat, skin, and other soft tissues and cooks for a few hours. It is not the same preparation as a long-cooked broth made from bare bones.

An Elemental Diet Is Not Meat Stock

An elemental diet uses specialized enteral formulas designed for high passive absorption. Research has studied elemental formulas in SIBO and other gastrointestinal conditions.^[12] Homemade meat stock is a GAPS food and cooking foundation. It is not an elemental formula or a nutritionally complete substitute for one.

Prebiotics and Enema Limits

The official FAQ does not authorize a prebiotic-powder enema for SIBO. Its answer says prebiotics feed beneficial and pathogenic organisms, and that people who tried them in enemas commonly reported heavy gas for several days afterward.^[13] The source supplies no preparation, amount, frequency, duration, or SIBO eligibility schedule, so none belongs here.

The 2020 book separately says prebiotic foods can be tried later after the microbial balance and gut function improve.^[14] That later oral food trial is not permission to put prebiotic powder into an enema.

The Histamine Food Branch

When histamine-type reactions occur beside SIBO, the GAPS FAQ gives a temporary food branch. It initially removes alcohol, black tea, canned and smoked foods, leftovers, beans and lentils, fermented vegetables, mature cheeses, cocoa, and nuts, while allowing freshly made homemade yogurt and kefir.^[15] That is a specific histamine branch, not a general rule to remove every ferment from every SIBO plan.

The Poor-Fat-Digestion Branch

The GAPS FAQ connects poor fat digestion in this question with bile stones and gives a specific sequence:

1. Make a GAPS milkshake from fruit-and-vegetable juice, one to two raw whole eggs, and a large dollop of raw sour cream. Use coconut oil when sour cream has not been introduced.^[16]
2. Start with a few tablespoons a day and build gradually to two glasses a day, first thing in the morning on an empty stomach and again in the middle of the afternoon.^[16]
3. Introduce animal fats from the amount tolerated and increase gradually. The source uses one to two ox-bile capsules with every meal temporarily, then stops the supplement gradually once a good amount of fat is digested without it.^[17]
4. The source also names regular coffee enemas for adults.^[17]

Adult Coffee-Enema Method and Limits

The 2020 book first empties the bowel with its basic solution: one liter of filtered warm water with one teaspoon of natural salt and one teaspoon of bicarbonate of soda. It repeats the cleansing step two to four times until no solids remain.^[18]

For the coffee solution, it boils one liter of water with three heaped tablespoons of organic medium-roast ground coffee for two minutes, then covers and simmers it for ten minutes. The liquid is cooled to 40–42°C (104–108°F) and strained. The book says a quarter cup of homemade whey or sour cream may be added, or about ten billion live cells of a commercial probiotic when there is an anaphylactic dairy allergy.^[18]

The adult frequency in the source is as needed: once a day, once every few days, or occasionally. It aims to hold the coffee for about fifteen minutes, though the procedure still counts if it must be released earlier. The book says the whole cleansing-and-coffee sequence takes about two hours.^[18]

This branch stops when diarrhea includes active blood and mucus. The book says no enemas in that situation until the intestinal wall has had about a year to heal and only when enough healing has occurred.^[19] It also says pregnant and nursing women should use only water with a little salt for constipation, not coffee enemas.^[20]

Build Meals You Can Keep Making

Build a short rotation from a suitable protein, the vegetables and ferments that fit the current stage, natural fat the person can digest, and enough food for the meal. Treat stock, vegetables, seasonings, and ferments as separate parts so one ingredient can change without losing the entire meal.

A soup is easier to troubleshoot when the container lists the stock ingredients, vegetables, seasonings, date, and portion. If onion or garlic is being limited, make a separate batch from the beginning. If leftovers are excluded in the histamine branch, plan smaller fresh batches rather than several days of refrigerated meals.

Continue Through the SIBO Guides

• Return to the complete SIBO and GAPS guide for the definition, testing boundary, source overview, and starting route.
• Read what causes SIBO in the GAPS framework for the low-acid, overgrowth, motility, histamine, food-reaction, and malnutrition mechanisms.
• Use the SIBO symptoms and gut-signs guide to organize the pattern without diagnosing from a checklist.

For help organizing the everyday work of Intro, my First 30 Days on Intro GAPS: Stages 1–6 course is in the WFLI shop catalog. The 90-Day Family Food Diary gives you one place for meal, ferment, supplement, bowel, and stage notes.

Frequently Asked Questions

Is GAPS the Same as Low FODMAP?

No. The two food systems answer different questions and contain different foods. Low FODMAP uses a short restriction phase followed by reintroduction and personalization; GAPS uses its own Intro stages and Full GAPS rules.^[8]

Does Straining Remove Onion and Garlic Fructans?

No. Monash explains that the fructans are water soluble and move into soup or stock while cooking.^[9]

How Long Does GAPS Use Betaine HCl?

The source calls it temporary and gives no universal number of weeks. It is taken with main meals while the person’s own acid production is being restored, and long-term HCl and pepsin can irritate the stomach.^[5][6]

Is Meat Stock an Elemental Diet?

No. Meat stock is a GAPS food. Elemental diets use specialized enteral formulas and are a different intervention.^[12]

References

1. Campbell-McBride, N. Gut and Physiology Syndrome (2020), “Small intestinal bacterial overgrowth,” pp. 445–446.
2. Campbell-McBride, N. Gut and Physiology Syndrome (2020), “GAPS Introduction Diet,” pp. 177–184.
3. Campbell-McBride, N. “Probiotics,” Q5, GAPS FAQs.
4. Campbell-McBride, N. Gut and Physiology Syndrome (2020), “Digestive enzymes,” stomach-acid booster and natural cabbage-food options; p. 340 for the HCl and pepsin formulation.
5. Campbell-McBride, N. “Stomach,” Q2, GAPS FAQs.
6. Campbell-McBride, N. “Supplements,” Q13, GAPS FAQs.
7. Campbell-McBride, N. “Stomach,” Q3, GAPS FAQs.
8. Monash University. “Starting the Low FODMAP Diet.” Accessed October 7, 2026.
9. Monash FODMAP Team. “Cooking With Onion and Garlic: Myths and Facts.” Accessed October 7, 2026.
10. Campbell-McBride, N. Gut and Physiology Syndrome (2020), “Meat stock and bone broth,” p. 223.
11. Mamane, R. Mastering Stocks and Broths, Part Two, chapters 8 and 9.
12. Nasser, J., et al. “Elemental Diet as a Therapeutic Modality: A Comprehensive Review.” Digestive Diseases and Sciences, 2024.
13. Campbell-McBride, N. “Stool,” Q8, GAPS FAQs.
14. Campbell-McBride, N. Gut and Physiology Syndrome (2020), “Prebiotics,” p. 23.
15. Campbell-McBride, N. “Diseases and symptoms,” Q29, GAPS FAQs.
16. Campbell-McBride, N. “Gallbladder,” Q3, GAPS FAQs.
17. Campbell-McBride, N. Gut and Physiology Syndrome (2020), “GAPS shake and fat digestion,” Liver and Lungs chapter, p. 90.
18. Campbell-McBride, N. Gut and Physiology Syndrome (2020), “Coffee enema recipe and procedure,” Bowel Management chapter, pp. 378–380.
19. Campbell-McBride, N. Gut and Physiology Syndrome (2020), “Enemas,” p. 375.
20. Campbell-McBride, N. “Pregnancy and breastfeeding,” Q5, GAPS FAQs.
21. Campbell-McBride, N. Full GAPS Diet: Recommended Food List and Foods to Avoid List.