Is Your Gut Broken? Here's the Reset Button

If you have gut problems like me, maybe you've thought to yourself, "What if I could reset my microbiome?" That's what I want to talk to you about today. But first, let's rewind about 300,000 years. Early humans, we lived in dirt, around animals, in real sunlight, with real darkness. Our food was unprocessed, unsterile, and full of microbes that co-evolved with us. Our guts and our environments were in harmony. But fast forward to today. Today, our microbes are under attack by sugary breakfast cereals, stressful jobs, pesticides, antibiotics, and ingredient lists so long you'd need 3 PhDs to decode them. We live in a world that our biology doesn't recognize, and it's reflected in our health. For me, this story is personal. When I was a newborn, I had a fever of 106, and doctors slammed me with with strong antibiotics. Maybe it was a smart call then, but it scarred my microbiome for life, increasing my risk of inflammatory bowel disease by 500%, which I ultimately did develop. So here's the big question: if your gut ecosystem is broken, can you hit reset?

Let's discuss.

Diversity breeds resilience, induces remission in 60 to 85%, insulin resistance within just 5 days, starve off problematic pathogenic species. This is actually one way to define fitness. These can impair metabolic health through microbiome disruption. It's like playing roulette with your gut. In the rest of this video, I'm going to walk through 4 phases of a microbiome reset: elimination, early repopulation, or repoopulation if you like microbiome puns, advanced repopulation and challenge, and then finally maintenance. We're going to walk through diet specifics, food selection and sequencing, and even go beyond diet. But let's start with Phase 1: Elimination. The concept itself is pretty straightforward. Wipe the slate clean like you're shaking an Etch-a-Sketch and start over. Now, when I say wipe the slate clean, I'm not talking about making your microbiome entirely sterile. That's impossible. And we don't want to hammer you with antibiotics. More on that later. Rather, I mean an elimination diet to, in theory, starve off certain bad bugs—pathogens that may be holding unfavorable niches, corners, in your microbiome. Probably the most effective way to do this is through an animal-based carnivore-style approach sustained for about 8 weeks. You see, by removing plant material, which predominantly feeds gut microbiota, both good and bad, You won't wipe out your entire microbiome, but you can potentially starve off problematic pathogenic species and the worst of the sugar feeders. At least that's the idea. And just to give a little further justification and clarification, this idea does have legs, as revealed by some underrecognized but used clinical practices. For example, treatment-resistant cases of inflammatory bowel disease can actually be treated with fiber elimination diets. This, to quote one paper, induces remission in 60-85% of inflammatory bowel disease cases. Now, this is not to say these diets are sustainable or optimal for your average person, but in situations of microbiome imbalance, so-called dysbiosis, removing components that feed pathogenic species can be therapeutic. Now, during this phase, this elimination phase, it remains important to eat a nutritionally complete diet. This is achievable on a carnivore diet if you include organ meats and whole organisms like liver and heart, which are packed with micronutrients, and whole sardines, which are whole organisms and extremely nutrient-dense. Personally, I've done this and found it to be sustainable because I like beef, eggs, fish, organ meats, and sardines. But if organ meats and whole organisms aren't of interest to you, or even if they are, you can use carefully selected multivitamins for micronutrient coverage. I'll provide some brand suggestions in the associated newsletter, linked in the video notes. And at minimum, I'd highlight keeping your calcium intake up with a calcium supplement before you introduce dairy. It's kind of hard to get calcium just from animal-based foods that aren't dairy.

In fairness, you can also get calcium from mineral water. This is the mineral water I drink, Gerolsteiner. It has 260mg of calcium per bottle, so in theory you could get all the calcium you need from this.

Also, it's high in lithium, which is good for the brain.

See this video for more.

Anyway, a note on fats quickly before we start moving on. On strict carnivore, technically speaking, tallow and ghee, which is clarified butter, would be your staples. That said, even during this phase, I don't think there's any harm in keeping minimally processed high-quality fats that are plant-based, like extra virgin olive oil, avocado oil, and macadamia nut oil in your diet if you prefer these as fat sources. And a note on transitionary symptoms: you may experience GI upset, diarrhea, or more rarely constipation. Or sometimes apparent constipation due to reduction in stool mass rather than retention. Now, if this ends up being you and you're having constipation that's uncomfortable, a light laxative like a magnesium citrate can help. You can start with about 400 to 600 milligrams taken before bed, just during the transition phase.

And on the topic of pooping, I do have a constipation masterclass for you. You can check it out at the newsletter.

Okay, so elimination clears the slate. But our reset isn't complete until you repopulate— carefully. So Phase 2 is thoughtful repopulation. This can last between 6 and 12 weeks. Before we hit the how-to, I just want to flesh out a little bit more the why. Imagine now a flourishing coral reef. It's flourishing with incredible color and diversity of life, and it's this diversity that makes the coral reef resilient. The same is true of a rainforest or your microbiome. Diversity breeds resilience. And on balance, a more diverse ecosystem is more resilient to stressors. This is actually one way to define fitness—how tolerant a system is to challenge. And parallels, they do exist in the human data. As in N=1, recall from our prior content the 117-year-old superager Maria, her microbiome was remarkably youthful and diverse, and that might have contributed to her incredible healthspan and lifespan. That said, I will caveat, diversity isn't the be-all and end-all. I can come up with counterexamples when an intervention does improve metabolic health while actually decreasing microbiome diversity. Still, in my view, in all else being equal, I think if you can, cultivating a diverse microbiome composed of health- favoring species as the foundation is your best bet for long-term health. And that brings us to the how of repopulation. Begin by reintroducing probiotics and prebiotics. Start with more bland fermented foods like kimchi and pickles and consider some probiotic supplements. Now, before we get to the rest of our microbiome reset protocol, I want to tell you about the only probiotic that I take and the sponsor of this video, Winnow. Now, if you're like me, you're probably skeptical of probiotics by default. I get that. But Winnow is different because it's not just a best-in-class probiotic, it's been specifically engineered to address the very real and urgent problem of microplastics. You see, microplastics and nanoplastics, they're everywhere in our environment, in our water, even the air we breathe. And they're not just gross, they're incredibly dangerous. A major New England Journal of Medicine study— I don't know why I had trouble saying that— major New England Journal of Medicine study found last year that microplastics in your blood vessels can increase your risk of heart attack, stroke, and death by 350%. They get in your immune cells, your macrophages, and irritate them, causing inflammation. So how do we defend ourselves? Well, from the inside out. That's the genius of Winnow. The team screened thousands of bacterial strains to find the few that can bind up microplastics and nanoplastics So your body just flushes them out before they enter your bloodstream. And I was so impressed by the science that I joined the company as a scientific advisor. So yes, I have a conflict of interest, but because I want to be part of developing this product, if you want to try it for yourself, what I'm using, you can use the code STAYCURIOUS for 15% off. I really can't speak today. STAYCURIOUS for 15% off. Links below. And I also will provide more information to break down the science so you can see it for yourself. This isn't just probiotic puffery, it's practical evidence-backed innovations. Now, back to repopulation and the rest of this protocol.

I also want to highlight you definitely want to check out the letter on this paper about microplastics in the brain and my conversation with Dr. Matthew Dunn, PhD, CEO of Winnow Labs, and really nice guy.

And during this phase, it's important to keep your volume of plant intake low overall during this early phase. And with the exception of fermented foods, cook your fruits and vegetables for digestibility. Introducing new foods slowly and in small amounts. Some specific starter foods I could recommend are cooked zucchini and summer squash, avocado, olives, sauerkraut and pickles.

And while we're on brand recommendations, this is the kimchi I like, Real Pickles.

It's really good. And Jerusalem artichokes, or globe artichokes if you can't find Jerusalem. These all tend to be rather digestible at lower doses and/or have particular prebiotic or probiotic properties. And to the best of your ability, it's really important to track your intake and symptoms rigorously. Use a food log. This is essential in observing relationships between symptoms and intake in the context of your n=1. You should make it your own. You can use a handwritten notebook or a Word document or an Excel sheet. Do what works for you. And phase 2 is also when you can introduce dairy. This isn't a must, but I really think it could be beneficial. Focus on A2 dairy sources, that means A2 casein, coming from sheep, goat, or buffalo, or when specified, labeled A2 if it's a cow dairy source. This is because the A1 casein, their alternative, is more likely to cause inflammation, GI upset, and autoimmune issues. Actually, early humans were never exposed to A1 casein. That's an evolutionarily new development that came with the domestication of cattle. And as for specific dairy, goat milk kefir and blue cheeses from sheep or goat sources probably rank at the top of my list, kind of like Roquefort cheese, which is my number one favorite. That said, I do have one carve-out for the A1 vs. A2 casein divide, and that is low-sugar, high-protein yogurts, which may be hard to find as A2 sources but can offer live cultures that support gut health. So, I'll list a few brands to consider. There's Siggi's Plain, Skyr yogurt, Alexandre A2 A2, this is A2, plain yogurt, and Wallaby Organic Aussie Style Plain Greek Yogurt and Fage 5%. I don't know if I pronounced all that right, but those are 5 good brands that are high protein, low sugar, and probiotic. Anyway, that brings us to Phase 3, which is advanced expansion of your microbiome and repopulation. Phase 3 extends Phase 2 by increasing the variety and dose and challenge of your foods. So here you can start with more challenge foods that are harder to digest. And if you do, expect mild or moderate symptoms. These may resolve over time. But if you experience serious GI discomfort, it's fine to scale back. Here are some foods to try. These are the challenge foods: cruciferous vegetables like broccoli, cauliflower, and Brussels sprouts, nuts and seeds. Ideally, you want to intake these raw. Start with macadamia, which are easier to digest, and follow it up with things like walnuts, sesame, and tahini. Raw vegetables you can introduce in this phase, like simple salads with an extra virgin olive oil dressing. Make sure to keep your probiotic and fermented food intake up and continue food and symptom logging to track patterns that are unique to your system. And finally, we get to phase 4, which is maintenance. This is the final step. Find a pattern that's sustainable and enjoyable that supports your microbiome. And it's always reasonable to cycle back to an earlier phase if you feel it helps, if you need another little micro reset. That said, even in maintenance mode and throughout, there are certain things I'd focus on avoiding completely and forever, at least as much as possible. Number 1 on this list is artificial sweeteners. Avoid aspartame, saccharin, and sucralose. Human studies show these can impair metabolic health through microbiome disruption. For example, this graph shows the human response on an oral glucose tolerance challenge after consuming artificial sweeteners. Now, in the 7-day trial, 4 out of 7 participants developed insulin resistance within just 5 days of modest artificial sweetener intake. This isn't a one-off. In general, artificial sweeteners can disrupt the microbiome. And even more striking actually in this study, when microbiomes from the responders, those who consumed the artificial sweeteners and had insulin resistance, when these microbiomes were transplanted to germ-free mice, mice without microbiomes, the mice also developed insulin resistance. The TL;DR on this is artificial sweeteners in humans can promote insulin resistance and do so by disrupting the microbiome. So avoid artificial sweeteners to keep your microbiome healthy. That said, natural alternative sweeteners like allulose, stevia, and monk fruit are likely safer and I think they're fine. Moving on, artificial food colorants. Avoid dyes like Yellow 6 and Red 3. These can disrupt the microbiome as well and have been linked to inflammatory conditions in preclinical models. Moving on, oral and intravenous antibiotics. These are necessary at times, perhaps for baby Nick, but they can be extremely disruptive. So always consult your doctor and use caution. Only use the antibiotics if you really need them. And finally, those mysterious additives. If you don't recognize something on an ingredient list, Avoid it. Consuming a food with an ingredient list you don't fully understand is like playing roulette with your gut, and you don't want to do that. Variables outside of diet also shape the microbiome. For example, meal timing. Aim for an eating window under 12 hours and avoid meals too close to bedtime. This can disrupt your circadian rhythm and your microbiome. Also, light exposure. Get natural sunlight daily to help regulate your circadian rhythms. Your microbiome has its own clock and it needs input both from light and routine meal timing. Also, stress disrupts the microbiome directly via the vagus nerve. So when you're stressed, a signal goes from your brain via the 10th cranial nerve, the vagus nerve, to your gut. And this changes secretions in your gut, something called Brunner's glands, that feed gut bacteria. So literally, there's a direct line from your brain to your gut whereby stress can change your microbiome, feed or starve it. Therefore, stress management practices like meditation, Deep breathing, hot baths, or even just relaxing and watching TV with a loved one can improve your microbiome. So yeah, your favorite trashy reality TV show can be a microbiome hack. Now, finally, as a closing note, this is just a self-experimental framework. This is not medical advice. Everyone's microbiome is different, and science today lacks precise protocols. However, I believe through community engagement, through thoughtful questioning and safe personal experimentation exploring your n=1 we can all make everlasting progress on our health journeys sometimes we need to just try to hit reset! Reset— Thank you.