This article is one core component of my detox strategy. I also recommend checking out the leaky gut fix guide from EndSickness.org.
Previously, I made some posts about dealing with diarrhea and constipation, as well as commenting on the AMD article on DMSO for gut health. But in this article, I will consolidate the most important texts on this topic so that you can directly consult with Gemini (on Flash Extended mode) to extract the top knowledge in the field. On the other hand, I also have some tips which are not found in books or AI.
Keep in mind that Gut health is intimately linked to mental health, as the gut is considered our “second brain.” Some people think their guts are working fine, but they notice other health problems, including mental health, and don’t realize that all disease begins in the gut, to quote Hippocrates, the founder of Western Medicine. Of course, that’s obviously not true, because stress can come from other vectors, but the gut is central to the feedback loop and can cement other stress vectors.
Some Causes of poor gut health
Severe stress/adrenal fatigue/poor sleep: This can cause a lack of mucus to line the stomach, which in turn causes burning, difficulty absorbing nutrients, and so forth. And every other gut issue can also be partly related to this. My mindset page and loveyhuasca protocol can help a lot with this, as well as my deep sleep tips.
Sitting, or lack of exercise and stretching: humans were not designed to be sedentary. Our biology slows down and cramps up when we are. Walk, do yoga, do shaking qi-gong, do bodyweight strength training.
Actually, yoga specifically, and especially Iyengar yoga, which is the most technically anatomical scientific yoga, would be more useful than general exercise:
Years of accumulated shit in your guts: This part isn’t in the gut healing books I read, but even if you fix all of what’s going into you now, if you’re already full and clogged with all of what went in before, that’s gonna be little help. My friend Pooyan got incredibly healthier and happier after getting enough colon hydrotherapy to flush that stuff out, combined with then also doing intense stretches like hanging from one arm, until finally, the most crusted up shit exploded in him which was very painful for a day.
This is likely caused by diverticulosis, a disease that causes herniated pockets to form in the intestines which aren’t supported by smooth muscle. There’s no known cure for this disease, except possibly glutamine, based one one incompleted clinical trial, which found 2 of 9 women had incredible reductions in diverticula. Glutamine an amino acid that’s the fuel for small intestinal cells, so this makes some sense. 10% of people get side effects from it (including constipation). Butyrate is the fuel for the colon cells. I would also suggest diosmin for improving blood vessel integrity.
However, while we don’t know if Pooyan has diverticulosis, what we now do know is that his peak health disappeared 3 days later after eating some bread with A1 dairy.
CAUTION: If you have severe diverticulosis, especially diverticulitis (once the fecal impaction causes intestinal infection & inflammation), you might be at high risk for intestinal wall rupture, and even rejected by the more reputable colonic irrigation clinics. Make sure you get cleared by a gastroenterologist first.
Poor diet now: industrial and processed foods, especially oils, are often empty calories full of countless toxins and oxidation byproducts. Toxins are sequestered in fat cells to prevent them from damaging organs, but this toxic fat (especially visceral fat) becomes a chronic health issue even as it protects us from immediately dying from the sequestered toxins.
Parasites, H. pylori, mold, metals: We are often addicted to junk food due to a vicious cycle in which the junk feeds parasitic organisms and bad bacteria, yeast, etc, which then send signals to our brain to consume more junk. Thus, we have to target the problem from various angles — cleansing out pathogens, repopulating good bacteria, addressing vitamin (especially thiamine), mineral, and enzyme deficiencies, and changing what we eat. I wrote about my detox protocol (which includes the gut) here.
For H. Pylori specifically: if you get heartburn when your stomach is empty only, that’s usually H. Pylori, and it’s easily treated with berberine.
Plant foods: The carnivore diet is trending, as many people are noticing they cannot handle fiber, oxalates, and phytates in plants. It’s certainly a diet worth trying, but it can lead to deficiencies over time, especially with regard vitamins C, E, fiber, magnesium, potassium, calcium, iodine and other trace minerals, and bacteria needed to process plant foods (which already are likely missing in people who need this diet), thus making the carnivore diet sort of hard to get off.
Interestingly, some people have found that when they take a good BPC-157 supplement, they are able to eat plants again because it fixes their gut lining. Note: that company, Barrier, has a good idea and their product may be really ideal, but there are some red flags in their marketing since they say it’s made from plants, which is false.
For the most research-backed recommendations you can check this HRP deep research report. Glutamine seems worth checking into, but plant intolerance is a symptom of a variety of underlying diseases that all have different treatments.
Resistant starch is especially important for leaky gut and a healthy microbiome:
SIBO: Small intestinal bacterial overgrowth is a huge issue underlying a wide range of illnesses. One of the most effective cures for many people is SIBO Yogurt. I also sell these SIBO yogurt bacteria (along with other helpful herbal juices and minerals) in liquid form for vegans.
Leaky gut: a widespread inflammatory condition often intersecting with other categories of illness such as Crohn’s Disease or IBS, and what many alternative health practitioners consider as a root cause of most diseases. Game-changing treatments: Liposomal first-milking colostrum and zinc carnosine, butyrate, glutamine, SIBO yogurt, along with the juices of turmeric, red cabbage, celery, beet greens (not just beet root), and sour fruits for TCAs.
Mitochondrial & Cellular Energy Starvation (Glutamine, Butyrate, TCA Intermediates): Your gut barrier requires massive amounts of immediate, localized energy to maintain tight junction integrity. If your enterocytes (small intestine) or colonocytes (large intestine) lack their preferred mitochondrial fuels, the barrier structurally collapses, allowing lipopolysaccharides (LPS) and endotoxins to leak into systemic circulation.
L-Glutamine (watch Dr. Rhonda vid): The absolute premier energy substrate for enterocytes and activated immune cells. It bypasses complex digestive steps, converting directly into alpha-ketoglutarate (α-KG) inside the mitochondria to power the citric acid cycle. This immediate cellular energy hit actively drives the repair of the gut mucosal barrier and prevents LPS translocation.
Dosing: Use 5g daily as a baseline to counter the gut mucosal breakdown caused by high-intensity or high-volume training (like CrossFit or intense cardio). Titrate up to 10–30g daily during acute immune exposure, high systemic stress, or if you are dealing with active IBD (Crohn’s/Colitis).
The Cancer Caveat: Because hyper-proliferative cancer cells can also hijack glutamine to fuel their rapid replication, avoid high-dose protocol titrations if you have an active, existing colon or liver malignancy (the liver sees it first via portal vein delivery).
Butyrate & SCFAs: While the small intestine runs on glutamine, the large intestine relies on short-chain fatty acids (SCFAs) like butyrate. Getting these via raw resistant starch fermentation or your home-brewed SIBO yogurt fuels colonocytes, locks down the lower gut barrier, and systematically suppresses inflammatory signals.
TCA Cycle Intermediates (Malic & Citric Acid): Organic acids like malate and citrate feed directly into the exact same mitochondrial energy pathways as glutamine. Consuming clean, sour profiles—such as organic malic acid, tart cherries, or green apples—provides rapid, alternative fuel to gut epithelial cells, accelerating mucosal healing from a different biochemical angle.
IBS: While there are many causes and types of irritable bowel syndrome, psychedelics are one promising new avenue of treatment. However, it’s always best to find the root cause of the problem, which requires investigation. A functional medicine gastroenterologist might help.
Low stomach acid, enzymes, and thick bile: which in turn are often due to poor diet, stress, infections. T.C. Hale has a lot of videos on healing digestion issues, which in his experience as a health coach, are often due to these root causes. He’s a bit controversial on some points such as his urine pH testing for anabolic/catabolic state freezes, but he does have some good suggestions he explains in his book.
Concise Recipe for Gut Healing:
I have consolidated the top 9 most effective gut healing books into a customized smart Gemini Pro Gut Health Gem (I think you need Gemini Pro, which is $19/month and highly worth the money). You can ask any questions in that Gem to consult all these 9 experts at once and get far better advice than you’d get from any one of them! If you have any other books you think would be better, lmk in comments!
Text Summary
This protocol is designed to be executed in phases. Do not skip phases. You only move to the next phase if the current one fails to resolve symptoms.
Phase 1: The Pre-Flight Safety Check (The Mechanic & Electrician)
Source: T.C. Hale (Kick Your Fat in the Nuts) & Stanley Rosenberg (Accessing the Healing Power of the Vagus Nerve)
The Logic: Before you add “fuel” (supplements) or “fire” (antimicrobials), you must ensure the engine is mechanically sound.
The Protocol:
Check Autonomic Tone (Hale): Are pupils constantly dilated? Is the gag reflex absent? If yes, you are in “Sympathetic Dominance” (Fight/Flight) and digestion is offline.
The Fix (Rosenberg): Perform the “Basic Exercise” (eye movements) or “The Salamander” to mechanically release the Vagus nerve and switch the body into “Rest and Digest.”
Check Bile Flow (Hale): Do you burp after fatty meals? Do stools float or look clay-colored? If yes, bile is stagnant. Taking antimicrobials now will cause a “herx” reaction you cannot detoxify.
The Fix (Hale): Use Beet Flow or Phosphatidylcholine to thin bile before starting any killing protocol.
Phase 2: The Reset (The Architect & Scientist)
Source: Dr. Michael Ruscio (Healthy Gut, Healthy You) & Dr. Mark Pimentel (The Microbiome Connection)
The Logic: Reduce inflammation and starve overgrowths without harsh chemicals.
The Protocol:
Diet: Adopt a Paleo-Low FODMAP diet (Ruscio) or a Low Fermentation Eating plan (Pimentel). The goal is to stop feeding bacteria in the small intestine.
Meal Spacing (Pimentel): Strictly space meals 4-5 hours apart with no snacking. This allows the Migrating Motor Complex (MMC) to sweep the gut clean.
Phase 3: The Purge (The Restorer)
Source: Dr. William Davis (Super Gut) & Dr. Michael Ruscio
The Logic: If diet didn’t clear the symptoms, active overgrowth (SIBO/SIFO) is likely present.
The Protocol:
AVOID Most Herbal Antibiotics. Davis recommends using specific herbal combinations like Candibactin AR/BR or FC Cidal/Dysbiocide for 4 weeks.
H2O2 actually works better than the herbal antibiotics according to me and orthomolecular drs. My BFF Pooyan tried candibactin actually and it nearly killed him. The H2O2 worked a lot better without side effects. There is one herbal antibiotic that works really well tho for H. pylori: Berberine. If you have an acute infection with something that those don’t help quickly, consider escalating to secnidazole treatment for rapid cure, and paromomycin post-treatment for relapse prevention, with medical supervision.
BIND to the toxins, especially the metals and parasite die of toxins, using Zholy3O.
Triple Probiotic Support (Ruscio): Simultaneously take a blend of Lacto/Bifido, S. boulardii, and Soil-Based organisms to maintain diversity and prevent opportunistic infections (like C. diff) during the kill phase.
Phase 4: The “Nuclear” Option (The Architect)
Source: Dr. Michael Ruscio
The Logic: If herbs failed, the overgrowth is too severe or the gut lining is too damaged for solids.
The Protocol:
The Elemental Diet: A 2-3 week liquid-only diet (predigested nutrients). This starves bacteria completely while nourishing the human host.
Phase 5: The Investigation (The Detective & Hazmat Team)
Source: Benjamin Brown (Digestive Health Solution), Neil Nathan (Toxic), Annie Hopper (Wired for Healing)
The Logic: If the “Nuclear Option” failed, the problem is not the microbiome. It is likely organ failure, environmental toxicity, or brain plasticity.
The Protocol:
Check Organs (Brown): Test for Exocrine Pancreatic Insufficiency (Stool Elastase) or Bile Acid Diarrhea (SeHCAT). Treat with high-dose enzymes or bile binders.
Check Environment (Nathan): Assess for Mold/Mycotoxins or Lyme. If positive, use specific binders (Cholestyramine, Charcoal, Clay).
Check Brain (Hopper): If you react to everything, the issue is Limbic System Impairment. Use “Brain Retraining” (DNRS) to stop the brain from firing false “danger” signals to the gut.
Phase 6: Restoration & Maintenance (The Gardener)
Source: Dr. William Davis & Dr. Will Bulsiewicz (Fiber Fueled)
The Logic: You are clear of infection. Now you must rebuild a diverse ecosystem to prevent relapse.
The Protocol:
Re-Seed (Davis): Introduce high-dose “SIBO Yogurt” (fermented for 36 hours) containing L. reuteri (to heal the lining and boost oxytocin) and L. gasseri (to produce bacteriocins that kill SIBO).
Feed (Bulsiewicz): Slowly titrate plant diversity back into the diet. Aim for 30+ different plants per week to feed the new healthy bacteria.
Maintain (Pimentel): Continue strict meal spacing (4+ hours) forever to keep the MMC cleaning wave active.
Fuel the Mitochondria: Deploy L-Glutamine (5–30g based on inflammatory load), butyrate-producing substrates (resistant starch), and TCA cycle intermediates (malic acid/citrate) to provide immediate cellular energy to enterocytes, cementing tight junction integrity and permanently halting LPS translocation.
Optional Ready-Made Gut Stacks
I do not think there is a universal supplement stack that heals everyone’s gut. The correct order still matters: fix digestion mechanics first, reset diet and motility, then only escalate into antimicrobial or anti-parasite protocols if symptoms persist.
That said, some people want a ready-made starting point rather than buying every ingredient separately. For a general “repair and rebuild” approach, I would look for a stack that covers three categories:
Microbiome support: a well-tolerated probiotic or probiotic system
Prebiotic / butyrate support: something that helps short-chain fatty acid production, especially butyrate
Barrier repair: nutrients that support the gut lining, such as glutamine, zinc carnosine, colostrum, mucosal-support herbs, or similar compounds
The best general commercial stack I have seen so far is Microbiome Labs Total Gut Restoration, because it combines probiotic, prebiotic, and mucosal-support components. For a more leaky-gut-specific stack, Dr. Ruscio’s Leaky Gut Support Kit is a reasonable option. For a single gut-lining repair formula, Designs for Health GI Revive is one of the more complete products, but it should be understood as a repair product, not a complete gut protocol by itself.
I would not recommend general “gut cleanse” stacks built around oregano oil, wormwood, black walnut, berberine, or other antimicrobial herbs as a universal starting point. Those belong later in the decision tree, when there is a stronger reason to suspect overgrowth, parasites, H. pylori, or another specific problem.
Start low, especially with prebiotics, resistant starch, butyrate-support products, and probiotics. People with severe pain, GI bleeding, fever, dehydration, rapid weight loss, active IBD flares, cancer, immune suppression, pregnancy, or complex medical conditions should work with a qualified clinician instead of self-stacking supplements.
