Make Your Own Long-Fermented Probiotic Yogurt

If you struggle with digestive issues, mood swings, or gut-brain-immune symptoms and haven’t read Dr. William Davis' book, Super Gut, I highly recommend it. His Inner Circle membership is also an invaluable resource for staying up-to-date with new protocols, recipe updates, and microbiome research. I'm in the process of creating a new article on SIBO/SIFO to clear up any confusion. In the meantime, I invite you to read my personal story, and you will understand why the gut will continue as a main feature in my virtual functional health practice. 

What’s New?

Through the Inner Circle, I’ve learned a few key updates. Dr. Davis has swapped out Bacillus coagulans from the original Super SIBO recipe and replaced it with Bacillus subtilis for its more reliable fermentation and broader spectrum of benefits. Another important tip: it’s best to refresh your starter after about eight generations to maintain potency. And if you’re taking berberine, avoid consuming it with this yogurt, as berberine can block the benefits. Personally, because I carry the FTO SNP, I follow Dr. Davis’ advice to separate my berberine-based supplement (Code Complex) from my yogurt by at least 6–8 hours. That way, I still get the full effect of both.

A common misconception in the health space is that only spore-forming probiotics can survive stomach acid and bile. While spores like B. subtilis are hardy, research shows that species adapted to the human body, such as L. reuteri and L. gasseri, also survive in significant numbers and can colonize the gut. This is what makes Dr. Davis' long-fermented yogurt so unique: it combines spore-formers with human-adapted strains, each playing a distinct role in gut restoration and helping to get rid of Small Intestinal Bacterial Overgrowth (SIBO).

My Current Protocol

• L. reuteri + L. gasseri: Long-ferment at 107°F for 36 hours.

• B. subtilis (HU58 or DE111): I take 2 capsules orally at night right after dinner; however, you can ferment the B. subtilis with the above two strains together at 100°F (see recipe below) or ferment separately at 90–95°F for 24 hours.

Note from Dr. William Davis' Inner Circle: “… In the updated recipe, we replace B. coagulans with B. subtilis and recommend fermenting B. subtilis separately from the other two microbes, as it requires less fermenting time (24 hours) and prefers a temperature of 90-100°F. …”

Why These Strains Matter

• L. reuteri (LR-DR strain): Considered a keystone species, it stimulates oxytocin release, which explains many of its documented effects: smoother skin, faster healing, reduced appetite, stronger bones, deeper sleep (for some), boosted testosterone/libido, and greater emotional connectedness.

• L. gasseri (BNR-17 strain): Produces bacteriocins that fight gram-negative bacteria linked to SIBO, supports visceral fat reduction, and may persist long-term in the gut.

• B. subtilis (NEW!) (HU58/DE111): B. subtilis has replaced B. coagulans in the new SIBO yogurt recipe as it has proven to produce more consistent bacterial counts during fermentation. A reliable fermenter and powerhouse bacteriocin producer, it helps dismantle pathogen biofilms, reduces endotoxemia by activating intestinal alkaline phosphatase, and produces key B vitamins. This makes it a strong ally against harmful microbes and systemic inflammation.

Together, these strains create a potent anti-SIBO blend that goes far beyond the “yogurt” you’d find at the grocery store.

Dr. Davis’ Super SIBO Yogurt Recipe

Ingredients:

• 1 quart organic half-and-half (or other dairy alternative with modifications)

• 2 tablespoons prebiotic fiber (inulin or raw potato starch)

• Starter: 1 capsule MyReuteri (Oxyceutics) or 2 tablespoons prior batch yogurt

• 2 capsules L. gasseri BNR-17 (Dr. Mercola’s Biothin). See Super SIBO Yogurt in the community plans

• 2 capsules B. subtilis HU58 (FullScript Dispensary by Microbiome Labs) See Super SIBO Yogurt in the community plans

Instructions:

1. Clean your fermentation vessel thoroughly. Dr. William Davis likes the Luvele Brand, and I like the yogurt makers from Amazon with smaller 6-oz glass containers.

2. In a medium bowl, mix the probiotics, prebiotic fiber, and 2 tbsp half-and-half into a smooth slurry (prevents clumping).

3. Add the remaining half-and-half and stir well.

4. Ferment at 100°F for 36 hours.

5. For future batches, use 2 tbsp from your previous batch (curds and/or whey) instead of fresh capsules.

The result is a thick, creamy yogurt packed with tens to hundreds of billions of live probiotics per serving. It tastes rich on its own but also works beautifully as a sour cream substitute on taco salads or fish tacos. Try it with berries, grain-free granola, or a touch of local honey for a probiotic-rich treat at night.

Final Thoughts: TL:DR

This yogurt is about much more than digestion; it’s about systemic health. Long-fermentation efforts can increase probiotic counts from the millions found in many commercial yogurts to tens or hundreds of billions of CFUs. For example, fermenting L. reuteri yogurt using the suggested method can yield 90 billion CFUs, far more than the millions in store-bought yogurts. Extended fermentation times and the addition of prebiotic fibers (potato starch) further amplify bacterial counts, sometimes reaching hundreds of billions or even trillions of CFUs in the final product. Combining oxytocin-triggering strains with biofilm-busting spore-formers, you create a therapeutic food that supports gut balance, reduces endotoxemia (LPS!), and even uplifts mood. If you’ve struggled with unexplained fatigue, anxiety, or stubborn gut issues, I encourage you to try this protocol.

I recommend creating this yogurt over using antibiotics (prescription or herbal) to help eradicate SIBO/IMO, due to the ability of these strains to create bacteriocins (natural antibiotics). The B. subtilis makes 7 bacteriocins, and the L. reuteri and L. Gasseri make two each for a total of 11! This is why it's called SUPER SIBO yogurt:)

If the SIBO yogurt hasn't been enough to resolve your SIBO, or it keeps coming back, the SIBO Help! program is designed to prevent your SIBO from returning. Join the 6-week live coaching program and apply the full $597 investment to the signature program if you want to keep going. Also linked below is my dispensary for additional tools to personalize your approach:

👉 SIBO Help! Program
👉 Order probiotics to make your long-fermented yogurt: Fullscript Dispensary for Super SIBO Yogurt Products

FAQs:

Can I use a different type of milk besides half-and-half?
Yes, but the texture may vary. Half-and-half is recommended for its higher fat content, which creates a thick, custard-like consistency. If you use a dairy alternative like coconut milk, you must ensure it contains no additives (like gums or thickeners), and you will have to boil it and cool it first before use. It also may need to add a bit more prebiotic fiber to support the fermentation process.

Can I ferment all three strains together at once? While you can ferment L. reuteri, L. gasseri, and B. subtilis together at 100°F for 36 hours, Dr. Davis’ updated recommendation is to ferment B. subtilis separately for 24 hours at 90–100°F. This is because B. subtilis is a more aggressive fermenter and can sometimes outpace the others if left for the full 36 hours. I took the B. subtilis form as capsules separately with my yogurt after dinner. You can get HU58 (B. subtilis) from my FullScript account.