Healing the Gut Naturally: A Master Gemini Gem
A compilation of what I've learned so far
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 Pro to extract the top knowledge in the field.
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.
Poor diet: 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, 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.
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.
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, along with the juices of turmeric, red cabbage, celery, beet greens juice (not just beet root).
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!
First, I will give a flowchart summary of their combined approach, then the text version:
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:
Herbal Antibiotics (Davis): Use specific herbal combinations like Candibactin AR/BR or FC Cidal/Dysbiocide for 4 weeks.
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.
