Episode #214: Super Gut: Part 2 with Dr. William Davis, MD
In a Nutshell
Dr. William Davis explains SIBO/IMO as microbial overgrowths (e.g., Enterobacteriaceae, methanogens) driving constipation, endotoxemia, neurodegeneration (Parkinson's, Alzheimer's), autism behaviors, and more; eradicate with antimicrobials (zyxicin/neomycin, herbals like Candibactin) if severe, then restore via Super Gut yogurts (*L. reuteri*, *L. gasseri*, *B. coagulans/suis*) that deliver 300 billion CFUs/half-cup, produce bacteriocins, normalize breath tests in ~90%, and yield benefits like smoother skin, muscle gain, oxytocin boost, and waist reduction. Address upstream causes (wheat/grains, magnesium deficiency, PPIs, antibiotics) with grain-free diet, nutrients (Mg, D, omega-3, iodine), prebiotics/polyphenols, and avoid chronic low-FODMAP (harms diversity). Make yogurts via 36-hour fermentation of half-and-half + sterile inulin/starters at body temp; start low for SIBO-sensitive (1-2 tbsp), manage Herx reactions with charcoal, continue lifelong for transient benefits—no monoculture risk. H. pylori often net harmful (eradicate via vitamin C + black seed oil); test SIBO with Aire device + inulin; yogurts safe post-fungals/SIFO for most, transforming gut health beyond antibiotics.
These notes were generated by AI and may contain inaccuracies.
Content is for informational purposes only, not intended to diagnose, treat, or cure any illness or medical condition. Not medical advice; consult personal medical authority for health decisions.
Episode 214 of Better Health Guy Blogcasts with Dr. William Davis on Super Gut (Part 2). Part 1 in episode 213 covered microbiome, beneficial organisms, prebiotics, polyphenols, and mucus layer. Part 2 covers SIBO, IMO, and creating Super Gut yogurts.
SIBO is an umbrella term; methane-dominant SIBO now called IMO (intestinal methanogen overgrowth). Question if Super Gut program yogurts apply to hydrogen, methane, and hydrogen sulfide types.
Dr. Davis: Evolving concept. Hunter-gatherer populations often have more methanogens without constipation. Problem may be context, not overgrowth per se. Methanogens in modern people cause constipation and other issues.
Ways to eradicate/reduce methanogens: zyxicin with neomycin, Candibactin-AR herbal antibiotics. Suggestion: No rush; do basics—fermented foods, L. reuteri, L. gasseri, S. boulardii—let GI tract heal. Methanogen issue may self-correct (anecdotal).
SIBO organisms often in Enterobacteriaceae family (Proteobacteria): fecal microbes like E. coli, Proteus, Morganella morganii, Enterobacter, Citrobacter—very toxic.
Off-the-shelf probiotics won't resolve dominance. Use microbes that colonize small intestine/colon and produce bacteriocins killing those species. With Aire device, ~90% normalize hydrogen breath test.
"If I said the solution is surgical removal of part of your GI tract, you'd say damn it, you better be confident. But if it's yogurt that gives smoother skin, higher testosterone, youthful musculature, amplified immune response, better social behavior—maybe you don't have to be so confident."
Works beyond expectations; will validate in clinical trial (hard due to homemade yogurt). Antibiotics (zyxicin, herbals) better only for severe histamine intolerance or brain fog worsened by L. reuteri/L. gasseri (due to histamine production; histamine is normal signal molecule).
Exceptions: Use antimicrobials first, then introduce yogurts.
25-67% of Parkinson's patients have SIBO; fivefold increase in Alzheimer's. Desulfovibrio linked to Parkinson's via alpha-synuclein impact (produces hydrogen sulfide).
Prevalence of SIBO underestimated; current tests miss many cases (methane/H2S conceals hydrogen; endoscopy/culture unreliable).
Microbiome balancing may reduce risk of Alzheimer's, Parkinson's, MS, ALS. Lack intervention studies. Anecdote: Martha Carlin (BiotiQuest) used glucose-consuming microbes (L. plantarum, L. reuteri, L. rhamnosus) in Sugar Shift—converts sugars to mannitol (in vitro evidence it crosses blood-brain barrier, dissolves alpha-synuclein). Her Parkinson's population saw partial remission (e.g., husband from walker-dependent to walking freely). Not pharma, so clinical trials limited.
Microbiome major player in neurodegenerative conditions, but other factors: omega-3 depletion, heavy metals, glycation.
Martha Carlin has yogurt starter product.
Autism complicated. Clinical trials used intranasal oxytocin (3 squirts/nostril every 6 hours)—offensive administration, modest behavior improvement insufficient.
Anecdote: Moms report marked improvement in autistic kids with L. reuteri (provokes endogenous oxytocin release for engagement/sociability)—better socialization, school, jobs. Endogenous oxytocin may differ from intranasal. Just yogurt; dramatic effects reported.
SIBO often downstream from nervous system dysregulation, migrating motor complex, bile flow. Long-term resolution needs addressing root causes beyond killing microbes or yogurts?
Causes: antibiotics, food preservatives, lack of sunlight (infrared on abdomen), hypochlorhydria/PPIs, stress, NSAIDs, possibly EMF.
Programs wheat/grain-free (eliminates gliadin-derived opioid peptides slowing propulsion—worst constipation in wheat/grain eaters; fiber worsens). Opioids like oxycodone/morphine constipate.
Address magnesium deficiency (rampant; low in produce, removed by water filtration)—slows propulsion. Programs restore magnesium, vitamin D, omega-3s, iodine (synergize for propulsion, minimize insulin resistance). No migrating motor complex issues seen.
Dr. Greg Nigh: SIBO response to sulfate deficiency; H2S overgrowth compensates—use Epsom salt baths for magnesium/sulfate.
Probiotic overuse causing SIBO? Blind probiotics can worsen (diarrhea, bloating, brain fog = d-lactic acidosis or die-off). Prep with diet cleanup, nutrients first. Adverse effects signal bad SIBO—use SIBO yogurt or antimicrobials. No evidence probiotics cause SIBO; adverse reaction means address SIBO first.
For SIFO, try yogurts unless histamine/MCAS issues (use herbs first). Fungi invited by bacterial disruption; bacteria suppress fungi.
Exception: Specific antifungal efforts needed (other measures suppress but don't eradicate). Berberine good antifungal (400-500mg 2x/day; e.g., Candibactin-BR)—but indiscriminate, kills L. reuteri/L. gasseri. Use short-term (few weeks), not chronically (reduces glucose/BP via less endotoxemia/SIBO).
Essential oils (allivore, oregano, clove, cinnamon) diluted (3 drops in tbsp olive/avocado oil, 2x/day).
Fungal die-off rough: depression, panic, anger, road rage—reduce dose/frequency, extend over weeks/breaks. Fungi resist, hide in biofilms (hospital nightmare: amphotericin B IV fails; surgical removal needed).
NAC may help biofilms. Oral amphotericin for fungal colonization (less side effects than IV).
Microbiome has limited space (30 feet, couple inches). Overproliferation of Enterobacteriaceae/Proteobacteria (normal 1-2%, sick at 8%) has nasty effects—reduce bad guys to create space for beneficials.
Trio-Smart, Aire device (no H2S yet). False negatives possible (methane/H2S conceals H2), but overlap means imbalanced microbiome often detected.
Prep (avoid false positives from colonic H2): 12-24 hours no fibers, sugars, alcohol. Baseline morning test (low <3-4 ppm, e.g., 1.2). Then 2 tsp inulin (better than lactulose/glucose) with breakfast; test every 30-45 min up to 90-120 min.
Rise ≥4 ppm = positive. Maps overgrowth location/speed.
Judgment needed (e.g., fibromyalgia, fat malabsorption, anxiety = SIBO even if borderline). H2S/methanogen overgrowth (Trio-Smart/stool) implies H2 SIBO.
Post-prep: Eat normally (eggs, bacon, etc.)—won't interfere.
H. pylori has two faces: protects against GERD, acid reflux, weight gain; but causes ulcers, cancers. Research suggests it's educational to
Research suggests H. pylori educates the immune system in a healthy direction, stimulating it positively. However, on balance, unbalanced H. pylori is mostly bad: it reduces asthma in children but risks gastric cancer, Parkinson's disease, SIBO, or colonic dysbiosis. Populations with less H. pylori do better. SIBO yogurt will not eradicate H. pylori but shifts the balance toward benefit. Protocols for eradication exist at drdavisinfinitehealth.com (advanced topic), with high success using easy methods: high-dose vitamin C (1,000 milligrams) combined with black seed oil; multiple agents typically needed. A strain of Lactobacillus reuteri (not the one used in yogurt) eradicates H. pylori by itself; their L. reuteri boosts efficacy of other agents.
Triple antibiotics for H. pylori make little sense: incomplete eradication, reinfection from diet or household, and downside of destroying good microbes being rebuilt.
Herbal Antimicrobials and Microbiome Impact
Berberine is potentially indiscriminate, affecting healthy microbiome. Herbal antimicrobials (e.g., black seed oil), ozonated/oxygenated magnesium for constipation, iodine: effects on beneficial flora unknown due to lack of clinical trials and microbiome analyses. Insufficient validation plagues non-pharma approaches, unlike pharma's $122,000/month drugs.
Colloidal silver: unknown impact on beneficial microbiome; not truly selective as claimed.
SIBO more common than type 2 diabetes and pre-diabetes combined. SIBO patients have 10x more lipopolysaccharide (LPS) or endotoxin, contributing to health issues including neurodegenerative conditions.
Beneficial bacteria produce some endotoxins, but not meaningfully pathogenic. Mitigate endotoxins primarily by reducing Enterobacteriaceae/Proteobacteria (esp. from small intestine), eradicating endotoxemia. Dr. R. Cano's trial with Sugar Shift (commercial product: Lactobacillus reuteri, L. gasseri, L. rhamnosus, maybe Bifidobacterium helveticum, others) achieved ~100% endotoxin reduction via microbiome restoration (confirmed by analysis), without mucus barrier interventions or shifting Firmicutes:Bacteroidetes ratio. Transient microbes like L. reuteri suffice.
LPS endotoxin assay unavailable clinically (used in research like Rao's study). No clinical test because LPS varies (e.g., E. coli vs. Proteus vs. Bacteroides); no single test identifies all.
Low-level colonic endotoxin likely normal/necessary (e.g., E. coli, Salmonella ok in colon if not overproliferated or ascending).
Alkaline phosphatase (ALP): intestinal enzyme detoxifies LPS/endotoxins. Chronically low serum ALP common despite zinc, curcumin, omega-3s. Unknown how to increase it or if serum ALP reflects intestinal levels. Low serum ALP generally good (no biliary/gallbladder/bone disease).
Low-FODMAP (or elemental, specific carbohydrate diets) starves SIBO bacteria, reducing symptoms (bloating, diarrhea, panic attacks from FODMAPs, nightshades, fructose, legumes), but problem is SIBO, not food. Chronic use worsens dysbiosis irreversibly: starves beneficial species (e.g., Faecalibacterium prausnitzii, key butyrate producer), reduces diversity (lose hundreds of species permanently).
Brief use ok for relief; chronic = bad idea.
SIBO (bacterial), SIFO (fungal), SIPO (protozoan/parasitic). Fungal overgrowth (small bowel/colon) likely seeds systemic sites: airways, sinuses, throat, skin, brain. Dementia brains filled with fungi (e.g., Ruth Alonso in Spain: brain sections from deceased dementia patients). Unclear cause/effect; type 2 diabetics show multi-site fungal overgrowth (GI, ear, scalp, neck, breast, groin, nails). Systemic antifungals (crossing blood-brain barrier) untested for preventing dementia.
Organic acids test shows fungal metabolites as marker.
Sinus/oral fungal/bacterial overgrowth constantly reseeds gut SIBO/SIFO; address holistically.
For SIBO/SIFO: address separately (die-off reactions nasty: nightmares, anxiety, fevers, aches, depression). Bacterial first (L. reuteri gassei/coagulans/suis yogurts) for weak grain elimination, skin/muscle/strength/happiness benefits.
Should anyone really be eating wheat? Convincing themselves they're okay is one of the most destructive things.
Wheat issues beyond gluten: gliadin yields appetite-stimulating opioid peptides, massively increases permeability (lethal with SIBO); amylopectin A provokes small LDL particles (heart disease; bagel = week's risk, persists 5-7 days); wheat germ agglutinin inflames GI, denudes villi; phytic acid binds minerals (Ca, Mg, Fe, Zn), amplifies deficiencies. Grains unfit for humans despite USDA. Plus glyphosate contamination.
External mold exposure (home/school/work) colonizes with fungi (e.g., Aspergillus); optimize environment for internal success. Factor in minority; remediation helps, but unclear protocols.
Four-week process:
- Week 1: Prepare garden – remove artificial sweeteners, emulsifiers, glyphosate, NSAIDs, PPIs.
- Week 2: Plant seeds – probiotics, fermented foods.
- Week 3: Water/fertilize – prebiotics, fibers, polyphenols; super fertilizers: eugenol (clove), oleic acid, capsaicin.
- Week 4: Grow super gut – yogurts.
Capsaicin (hot sauces, peppers) modestly helpful super fertilizer; prefer as food, not capsules.
Super Gut yogurts: 1,000x beneficial organisms vs. probiotics/store yogurt (~300 billion per 1/2 cup/120ml). Not true yogurt (lacks qualifying organisms).
Developed from MIT-studied L. reuteri ATCC 6475 (Biogaia Gastrus for babies: reduced colic, antibiotic diarrhea; 100 million dose trivial for adults). Amplified via 36-hour fermentation at body temp (12 doublings) + prebiotic fiber. Quantified by flow cytometry: 300 billion/1/2 cup. Company claimed impossible, blacklisted him.
Extended to Bifidobacterium infantis, Lactobacillus brevis, L. gasseri, B. longum: unique flavors/effects, crowd-sourced discoveries.
SIBO yogurt (L. reuteri gasseri/coagulans, now suis): eradicates SIBO in ~90% (H2 breath test); no device needed (benign, improves skin/muscle).
Dairy-reactive: prolonged fermentation minimizes issues – converts lactose to lactic acid (pH 3.5 vs. 4.5 conventional), denatures beta-casein A1/immunogenic sequences; pour off whey (insulinotropic). Half-cup rare intolerance.
Prebiotics in Yogurt
First batch thin/separates (subsequent thick). Bad batches (stinky, separated) due to non-sterile inulin: Bacillus species (<900 CFU/g per COAs), but thousands vs. billions starter microbes. In a tablespoon or two of inulin
They no longer use BioGaia Gastrus due to lower counts; developed their own product with 10-20 billion per capsule (can use more than one). Sent a bad batch for analysis; likely Bacillus species from the inulin. Agonized over solutions for months: ultraviolet light won't penetrate properly (requires thin layer, 3 hours in sterile hood, impractical); gamma rays possible but people object despite no radioactivity. Found a source of sterile inulin; will verify via lab analysis for no Bacillus species.
Workarounds for Contamination
- Use higher starting numbers: 10-20 billion per capsule from their product (e.g., MyReuteri), or 2-3 capsules.
- For first or second batch, save whey, freeze as ice cubes (cover in plastic), use 2 ice cubes as starter for next batch. This avoids propagating Bacillus contamination since initial batch had minimal, and subsequent batches use whey without adding new inulin (though still adding inulin, not amplifying via fermentation).
- Preheating inulin to 180°F before adding microbes won't kill Bacillus (spore-formers).
95% of batches fine; occasional issues. Friend David Worth (PhD, patent attorney) pointed out inulin not sterile. Boiling inulin with liquid before adding microbes ineffective against Bacillus spores (tough: pounding, baking, boiling doesn't kill).
If original microbe capsule not alive (common), yogurt won't form; results in soured milk (disgusting, inedible, stinks). Happened with BioGaia Gastrus in hot summer shipping. Their preparation uses higher numbers, ships on ice; during summer, still risks if delivered in extreme heat (e.g., Coachella Valley 114°F, left on step for days).
Most yogurts in book use 36-hour fermentation. No need for pH check; methods listed in Super Gut book and davis infinitehealth.com.
- Lactobacillus species (brevis, acidophilus, reuteri): 24-36 hours (24 enough for some, 36 better for slow growers like reuteri; over-fermenting fast growers fine).
- Bifidobacterium similar.
- Exceptions: L. plantarum ferments at any temperature.
Detailed methods in book/website; not critical unless fermenting many microbes. Hopes for product line with majority needed strains for confidence in sourcing.
Reject limiting fat/saturated fat; fat healthiest dairy part. Use half-and-half (18% fat) for best thick, rich results.
- Whole milk: thinner, preheat for better mouthfeel.
- Cream: too thick like cream cheese.
- A1 milk fine unless immune response to beta A1 casein; fermentation denatures much casein via acidic pH. Use A2, goat, sheep, or human milk (A2) if casein issue.
Coconut milk: canned without emulsifiers (except guar gum); add 1 tsp guar gum per can, blend with stick blender ≥1 min to prevent separation.
Raw milk risky: beneficial microbes but possible Listeria or Staph aureus; fermentation amplifies pathogens (e.g., dozens of child deaths yearly in Minnesota from family farm raw milk). Avoid.
Non-dairy (e.g., coconut): optional to boil 2 min for safety (rare contaminant can make you very sick, <1% risk, higher if from places like Malaysia). Pasteurized/ultra-pasteurized unlikely contaminated.
Fermented foods (SFO, kimchi, kefir, yogurts, fermented veggies, pickles) increase diversity (per Sonnenburg study at Stanford: enthusiastic intake best for diversity). No evidence of dominance by one microbe (e.g., L. reuteri, B. longum) unless pathogen like C. diff. Even trillion L. reuteri doesn't dominate (hundreds of trillions total GI microbes). Numbers small; most don't colonize long-term.
Bacillus spores as keystone strains aid diversity (per Kiran Krishnan).
Anecdote: Dream from L. reuteri
Took L. reuteri; dreamed of woman (auburn hair, hazel eyes, big smile, first/last name), overwhelming affection persisted into day. Tested trillion reuteri etc., no recurrence. Possible oxytocin amplification?
For sensitive/ultra-sensitive/SIBO: reasonable to start individually (L. reuteri, L. gasseri, B. coagulans or subtilis), but prefer trio or 2/3 for benefits (small intestinal colonization, bacteriocin production). If diarrhea from gasseri (½ cup/day), cut to 1-2 tbsp, build up. Not drugs with nasty effects; yogurt with benefits like gasseri shrinks waist 1-2 inches (no diet/exercise change, likely via reduced endotoxemia).
L. reuteri strains: ATCC PTA 6475, DSM 7938 (different strains vary). New product OxxyMyut (LRDR strain); equivalent to 6475 in animals/humans (tested 5/200+ strains; no better found yet due to cost). LRDR proprietary (patent risk if disclosed). Repeating animal work, more human data; hopes to find superior strain (e.g., 40% better oxytocin, better adhesion, more bacteriocins).
Effective for broad Bifidobacterium (e.g., B. infantis, often missing in adults). Commercial B. infantis probiotic used. Caveat: subsequent batches may shift (one dominant?); predict roughly equal if starting ⅓ each same genus, unconfirmed (analysis $2k/run).
No histamine intolerance after remediating SIBO (reverts to grandparents' era, no 37-food avoidances). No persistence with B. coagulans yogurt (spore-based).
Commercial B. coagulans products have maltodextrin, titanium dioxide, carrageenan, magnesium stearate, silicon dioxide (avoid); found clean BC30 from GlutenFree Remedies (CA).
L. plantarum PS128 (for Parkinson's): fermentation-friendly (room temp, 85-90°F, body temp); good for skin, GI; per Martha Carlin, converts sugars to mannitol (dissolves alpha-synuclein?).
Freezing yogurt: no negative effect (microbes tolerate cold; shipped frozen on dry ice/liquid nitrogen, lyophilized). Freeze in ice cube trays; eat as frozen yogurt (chocolate, berry).
Flavoring: add post-fermentation (some antimicrobials if added earlier). Papaya (pureed, ¼-½ cup pre-fermentation): vigorous fermentation, flavor, high vitamin C (topical/oral dermal collagen); prebiotic. Ladies love for skin (vs. $120-180 serums).
Herbal antimicrobials (e.g., berberine) kill yogurt microbes; take together safe but no benefits. Finish herbals, then yogurt. Iodine antimicrobial; separate by ~4 hours.
Luvel and Ultimate: adjustable temp/timing, reliable. Anova sous vide (with basin): works well, loud. Avoid basin sous vides (overheated to 180°F, smoking). Newer Instant Pots with yogurt setting good (104°F; older cycled 90-120°F, killed microbes).
Mold contamination from HVAC: obvious (pink, orange, green, black discoloration); scrape off, eat rest. Use as home mold test.
Common: anxiety, depression, dark/suicidal thoughts, panic, racing heartbeat, low-grade fever, muscle aches, sleep disruption (insomnia, nightmares), hatred, anger, violence. Reduce ferments (e.g., ½ cup to 1-2 tbsp). Activated charcoal (1000 mg capsules, as needed; binds nutrients, works 15 min). Avoid diatomaceous earth (lead contamination).
Microbes transient; continue lifelong (70 years?) until permanent colonization figured out. Benefits persist even transient.
FMT: only for C. diff in US; potential but risks (adverse events from poor screening, e.g., no SIBO screen). Not necessary for most (need keystone restoration, ferments, lifestyle). Hopes for lessons, better "crapsules/poop-sicles".
Probiotic 1.0: haphazard (e.g., double encapsulation for colon release ignores small intestine issues). Future: microbe combos with synergistics; encapsulate Akkermansia/obligate anaerobes (e.g., Faecalibacterium lost in keto/carnivore/low-FODMAP). Site-specific microbes (mouth, vaginal, prostate, endometrial). Early stages.
L. reuteri every other day; Gut Glow (hyaluronic acid, carotenoids); sloppy collagen coffee (big scoop bovine collagen); unlimited fat, loves eggs; fermented food every meal; eats 2x/day (late breakfast, early dinner; not hungry otherwise). No probiotics.
Importance of hyaluronic acid as a fiber.
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