Announcing:

The Microbiome Renewal Masterclass

Quick Takes

1. Fermented Foods Win the Diversity Game

Head-to-head research shows fermented foods increase gut microbiome diversity while high-fiber diets don't deliver the same results. Furthermore, this improved gut biome results in improved immune system function, including decreased inflammation—the foundation of health from gut to cardiovascular to bone and cognitive wellbeing.

2. The Probiotic Paradox

Taking probiotics alone can be helpful, but the optimal approach likely leverages the ecology of fermented foods. These foods work as an "extended microbiome," providing both beneficial microbes and bioactive compounds that directly interact with receptors in your gut, setting up favorable conditions for a better gut biome.

3. More Fiber Isn't Always Better

Studies show that more fiber can actually backfire. We suspect this happens because "unhelpful" bacteria persist and may even multiply under high-fiber conditions, inhibiting gut biome reorganization. While average US adults consume fairly low fiber (<15 g/day), I've been wondering if my health-conscious patients are consuming more, given the official recommendation, potentially impairing their transition to an ideal gut biome.

4. Disease Changes the Rules

If you have inflammatory conditions, standard gut health advice may not be as helpful. In one study, patients with ulcerative colitis showed impaired metabolism of all fiber types, with fast-fermenting fibers like inulin being particularly problematic. Gut health protocols must consider your individual health status, not just generic recommendations.

ANNOUNCING:

The Microbiome Renewal Masterclass

Yes, Fe-Fo-Fi-yuM… because optimal gut health should be delicious

After reviewing the best studies on gut health interventions, one thing becomes crystal clear: the advice is complex and implementation can be challenging. Many fermented foods are naturally high in fiber, making results unpredictable—some people thrive while others struggle with digestive issues.

That's why I'm launching The Fermented Foods & Fiber Masterclass—a comprehensive program that combines cutting-edge microbiome science with practical, individualized strategies that aim to avoid the pitfalls that have emerged from the studies done so far.

What Makes This Different:

🔬 “Test, Don’t Guess”

• Optional before-and-after microbiome diversity testing so you can actually see your improvements

• For those interested: inflammation markers, insulin resistance, and lipid panels to track broader health impacts

• Using your own symptoms to optimize your approach

📚 Evidence-Based Protocols

Gut bacteria are especially tuned in to food and rhythm. The high-quality studies we have give guidance on effective fiber and fermented food intake levels that can meaningfully improve gut microbiome diversity and immune function. We also have promising insights for improving metabolism, including insulin resistance and cholesterol management. Additional tools we use may include:

• Supplements

• Time-restricted eating

• Approaches that take daily rhythms into account

🥘 Practical Implementation That Actually Works

• Use step-by-step guides for incorporating and enjoying fermented foods while keeping sight of their fiber content

• Learn to use your own goals, digestive symptoms, and other observations to personalize your approach

• Build sustainable habits that enhance your life rather than complicate it

• Be ready for any disruptions such as the need for antibiotics with reliable protocols

👥 Truly Personalized Approach

Small cohort format — we learn together!

The Program Structure:

• 8 sessions over 6 months (allowing real time for microbiome changes to take effect) - starting mid-October 2025

• Front-loaded schedule: More frequent sessions initially when we are making more changes, then spaced out as you build experience

  • Comprehensive resource library with recipes, protocols, and troubleshooting guides

  • Online Group to stay in touch with other participants, share recipes and experiences

• Optional testing at start and finish to track your progress

Early Bird Pricing: $199 (through September 20th) then $399

• Microbiome testing for gut biome diversity adds $200 per test.

• Comprehensive package of blood tests:
  - Advanced lipids, glucose and insulin testing, Hemoglobin A1C, CRP: $100

Interested? Please email me for more details.

We plan to offer either Monday or Tuesday evenings, between 5-8 PM Pacific Time

This will depend on interest and location of participants

Deep Dive:

Fermented Foods, High Fiber Foods, Probiotics and the Gut Microbiome

The human gut microbiome plays a crucial role in everything from immune function to mental and cognitive health, yet many gut health interventions fail to deliver lasting results. In fact most of them only target symptom resolution, when we should be aiming for an optimal, and optimally stable gut microbiome. But new research is providing more and more information on what the gut biome needs to thrive.

The Extended Microbiome Concept

We suspect that a healthy microbiome has ways to keep itself stable. However, how do you get there if you don’t have some of the substances made by a healthy microbiome? The answer might be to borrow these substances by consuming fermented foods.

Recent studies introduce the concept of fermented foods as an "extended microbiome"—sources of bioactive metabolites and microbes that influence health through pathways similar to our gut bacteria, but with some unique advantages.

Unlike isolated probiotic strains, fermented foods provide multiple benefits:

• Antimicrobial protection: Organic acids create environments hostile to pathogens

• Enhanced nutrition: Increased vitamins (C, B2, B12, K, folate) and improved bioavailability

• Metabolite diversity: Compounds that interact with receptors throughout your GI tract, influencing hormone secretion

Why Fermented Foods Outperform Fiber

A landmark randomized controlled trial directly compared high-fermented food consumption to high-fiber diets in healthy adults. The results were striking:

• Fermented foods in patients on an “average American” fairly low fiber content diet, increased gut microbiome diversity compared to baseline

• High-fiber diets with nearly no fermented foods, showed no significant diversity improvement

• Participants who focused on fermented food intake had decreased inflammation markers

• Some high-fiber participants saw increased inflammatory makers

• Effects persisted beyond the intervention period

The mechanism involves unique metabolite-host interactions. For example, D-phenyllactic acid from fermented foods activates the HCA3 receptor—found only in great apes and humans—suggesting our evolutionary adaptation to fermented foods.

The Personalization Problem

Perhaps most importantly, research reveals that individual responses to gut interventions are highly variable and predictable:

Baseline Microbiome Matters: Studies show that initial bacterial composition significantly influences intervention success. What works for your neighbor might not work for you.

Disease State Considerations: People with inflammatory conditions like ulcerative colitis show impaired fiber metabolism across all types, with fast-fermenting fibers being particularly problematic.

Probiotic Response Patterns: Clinical trials identify distinct "responder" and "non-responder" groups, with responders often having different dietary patterns and baseline lipid levels.

The Synbiotic Advantage

The most promising approach combines probiotics with prebiotics (synbiotics) or fermented foods with fiber-rich diets. A 12-week study using Bifidobacterium animalis with inulin showed:

• Better reduction in visceral fat area in just a few weeks (vs. placebo)

• Significant triglyceride improvements

• Better metabolic outcomes than either intervention alone

Practical Implications

This research suggests several key principles for effective gut health interventions:

1. Start with fermented foods rather than isolated probiotics but perhaps limit fiber intake

2. Consider your baseline health status when choosing interventions

3. Monitor your individual response rather than following generic protocols

4. At some point, combine approaches for synergistic effects

5. Think long-term as microbiome changes take months to stabilize

The Future of Personalized Gut Health

As our understanding grows, successful microbiome interventions will likely require:

• Individual microbiome analysis to predict responses

• Targeted recommendations based on health status

• Combined approaches leveraging both foods and supplements

• Long-term monitoring to optimize protocols

We are not there yet! But we can start carefully incorporating some of the available findings.

There's no universal solution for gut health. But with the right approach—one that considers your individual microbiome, health status, and response patterns—significant improvements are not only possible but predictable.

References

Caffrey, E. B., Sonnenburg, J. L., & Devkota, S. (2024). Our extended microbiome: The human-relevant metabolites and biology of fermented foods. Cell Metabolism, 39(4), 684-701.

Wastyk, H. C., Fragiadakis, G. K., Perelman, D., et al. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell, 184(16), 4137-4153.

Wastyk, H. C., Perelman, D., Topf, M., et al. (2023). Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet. Gut Microbes, 15(1), 2178794.

Baba, Y., Saito, Y., Kadowaki, M., et al. (2023). Effect of continuous ingestion of bifidobacteria and inulin on reducing body fat: A randomized, double-blind, placebo-controlled study. Nutrients, 15(3), 741.

Fu, J., Zheng, Y., Gao, Y., & Xu, W. (2022). Dietary fiber intake and gut microbiota in human health. Microorganisms, 10(12), 2507.