Make Your Own Long-Fermented Probiotic Yogurt

If you struggle with digestive issues, mood swings, or gut-brain 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.

What’s New?

Through the Inner Circle, I’ve learned a few key updates. Dr. Davis has swapped out Bacillus coagulans from the original SuperSIBO 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 getting 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): Either take orally or ferment separately at 90–95°F for 24 hours.

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)

• 2 capsules B. subtilis HU58 (FullScript Dispensary by Microbiome Labs)

Instructions:

1. Clean your fermentation vessel thoroughly.

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 106–107°F for 36 hours.

   • For B. subtilis, ferment separately at 90–95°F for 24 hours if desired.

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

The end 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

This yogurt is about much more than digestion, it’s about systemic health. By combining oxytocin-triggering strains with biofilm-busting spore-formers, you create a therapeutic food that supports gut balance, reduces endotoxemia, and even uplifts mood. If you’ve struggled with unexplained fatigue, anxiety, or stubborn gut issues, I encourage you to try this protocol.

You can also explore my functional nutrition programs and dispensary for additional tools to personalize your approach:

👉 Lifetime's Programs (Including Genetic Testing)
👉 Lifetime Health Coaching Fullscript Dispensary