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It's the Microbiome Stupid

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Quote from Joe2 on January 30, 2026, 2:32 pm

@armin

Sounds like you did exactly what Tyler wrote about.  And you are still doing it.

I saved the link.

https://members.nutritiondetective.com/posts/8159193

The Nutrition Detective Network

I want to get Tyler to republish that on a substack.  Or here.  

In the final analysis, I think what we are working toward is versions of what old successful cultures worked out to be optimal.  Probably took generations for them to  come up with it.  Example is kosher laws.  How many bad scenarios did it take to figure out "do not eat pig."  For what it is worth, I ran across someone couple months ago writing about an old family member dedicated to old school probiotics.  Think it was saur kraut they ate daily.  What caught my eye was that they at like a teaspoon daily.  In my saur kraut years, I ate a cup to 2 cups daily.  Used it as a vegetable.  Loved it over steak and eggs.  Smothered.  

Yeh, so I plan on start low, going up slow and hardly going up at all.

What I find interesting from his post was this section - 

As far as my symptoms, within 2.5 months, 80% of them have already disappeared and the remaining 20% have stabilized and are dissipating.

I have a hard time believing that he detoxed that quickly while others spend 5+ years on strict restrictions and are getting nowhere.

If he was really strict and really calculated with his soluble fiber intake and diet in general, I can see how someone can get some pretty good results relatively soon, and I think much is dependent on how your microbiome adapts/shifts. The younger, healthier, and stricter, the more potential bounce back.

I remember years ago when I was 20 years old switching to a more plant based diet and within a week of eating apples and some fiber rich foods, much of my symptoms improved. It plateaued for a few months before everything resolved. I doubt it was vitamin A dependent at the time.

I believe as you get older, the more help you need to undo the decades of gut-busting damage we all take-on on a daily basis. 

Toxins and dysbiosis are compounding variables that just smash you. Toxins (endotoxins and otherwise) damage the liver and creates a compromised microbiome, and a compromised microbiome causes the liver to have to deal with endless endotoxin burden. The cycle is self reinforcing and is a big downward spiral. 

How can you expect to detox Vitamin A when you liver is on overdrive every day using up detox pathways and nutrients on pathogenic endotoxins?

Suggest you read more of Tyler's posts.  The first most important factor I can think of that splains the difference between you and him is severity of symptoms.  I noticed that about Grant, me and a few others.  Usually older males.  So damaged as to quit work inspite of need to work.  Rendered unable to work and head home to put house in order.  

My bounce back was similar to Tylers and took a few months longer.  That said that 20% that was left to fix was no small issue.  The 80% I got back was enough to let me work again.  That was a huge issue.  I am still working on that 20% and am 37 months in.

This all goes nowhere near questioning the import of microbiome and that downward spiral.  

For what it is worth, in last 45 years experimenting on diet, every time I transitioned I felt better fast.  Even got that when I went briefly vegan.  Looking back feels like taking pressure off a vise crushing my right hand feels so good that I hardly notice the new vice crushing my left hand.  Until a few months go by.  Call it the honeymoon period on any new idea?  

Most people I exchange with tell me about deep experience with broad range of diets where they were 100% compliant and zero errors.  Insist that this diet did nothing or that diet did this and not that and oh yeh very familiar with that diet.  More than 90% of the time turns out their deep experience wss 4 months or less.  Every diet I tried took 2 years to work and learn well enough to even claim familiarity let alone compliance.  What happened in following decade became worth studying.

So yeh, I do not count my vegan year for much other than too painful to learn well enough to continue.  We have a few friends who did continue for decades.  They are crippled now.  They still insist their diet is right all others are wrong.

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Armin
Quote from Joe2 on January 30, 2026, 8:42 pm

Suggest you read more of Tyler's posts.  The first most important factor I can think of that splains the difference between you and him is severity of symptoms.  I noticed that about Grant, me and a few others.  Usually older males.  So damaged as to quit work inspite of need to work.  Rendered unable to work and head home to put house in order.  

My bounce back was similar to Tylers and took a few months longer.  That said that 20% that was left to fix was no small issue.  The 80% I got back was enough to let me work again.  That was a huge issue.  I am still working on that 20% and am 37 months in.

This all goes nowhere near questioning the import of microbiome and that downward spiral.  

For what it is worth, in last 45 years experimenting on diet, every time I transitioned I felt better fast.  Even got that when I went briefly vegan.  Looking back feels like taking pressure off a vise crushing my right hand feels so good that I hardly notice the new vice crushing my left hand.  Until a few months go by.  Call it the honeymoon period on any new idea?  

Most people I exchange with tell me about deep experience with broad range of diets where they were 100% compliant and zero errors.  Insist that this diet did nothing or that diet did this and not that and oh yeh very familiar with that diet.  More than 90% of the time turns out their deep experience wss 4 months or less.  Every diet I tried took 2 years to work and learn well enough to even claim familiarity let alone compliance.  What happened in following decade became worth studying.

So yeh, I do not count my vegan year for much other than too painful to learn well enough to continue.  We have a few friends who did continue for decades.  They are crippled now.  They still insist their diet is right all others are wrong.

The only real honeymoon experience I really had in my life when it comes to health was probably the carnivore diet. Long term, it wrecked things. Great elimination diet but it also starved the microbiome, good and bad. A net calming of BS coming from the gut. Long term, total rebuild job. Now when one tries to get off of the carnivore diet, they have to contend with all sorts of new obstacles. If you don't know how to address this, you get lost for years.

Vegan diets start out well for many because it initially addresses the microbiome foundation. However, things go sideways when your body is deprived of nutrients over time and people start to lean of fad foods and vegan slop to try to bind the body together.

Most of my health setbacks seem to have come after periods of terrible microbiome choices. Sugar, tobacco, alcohol, bodybuilding supplements, stress, overexertion from exercise programs, and lastly carnivore.

I feel I finally have a good foundation in which to build and use what I've learned from so much failure. I'm trying to understand how a healthy microbiome could be detrimental down the line. 

We focus so much on top of the skyscraper but fail to invest adequately at the foundation. 

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Joe2

I can relate.  I was lucky in December of 2022 when isotretinoin induced sacroiliitis hit because I had done zone diet a decade earlier.  Felt frantic need to come off 12 years keto fast.  Knew enough not to rip into soluble fiber.  Only ate insoluble fiber those 12 years.  

It was frantic.  Pain had me racked unable to stand, sit, laydown.  Held myself in bent dip on walker or countertop.  Slept 3 naps of 10 to 15 minutes daily.  Woke up full bore bellowing.  Pain directly associated with liver, tallow, butter, coconut oil.  Those were my staples.  Without them I lost weight fast while pain stayed high.  Knew I could not instantly drop the 1500 to 2000 calories a day of fat and pick up difference in fruit and grain I had not eaten in 12 years.  

I trickled in carbohydrates and held steady with my beef.  Started ONE bite of apple.  Worked up to 4oz of apple in a week.  The oats same way.  And on.  I ate each tiny meal the way I knew to in zone.  I matched the amount of carbs I dared to eat with appropriate amount of beef.  Probably lucky to get 500 calories that first day.  Got it up to 1000 in a couple weeks.

Once I got calories up over 1500 in zone proportions weight stopped coming off.  Month or so later got a 90 minute nap.  Knew I was on to something.  Was nice that by then I knew why eating liver ripped my pain levels all the way up in seconds.

I think I was lucky a few ways.  First I had 15 years of zone to fall back on.  Confident if I could transition back to carbs protein fat 40/30/30 that pain would fade and weight would hold.  Luckiest aspect might have been that I felt up against a wall with a gun to my head.  I knew the only help conventional docs could give would be pain killers.  That just made it worse.  Without pain, I could tell that structurally sacroiliac just got worse.  

That is what I mean by saying that a few of us in acute damage are the lucky ones who seem to get the fastest best results.  Not so much a matter of hyper compliance so much as imperative to figure ins and outs of how to safely get to compliance with the idea.

Before he got debanked and flipped out, I think Mercola was on to a good idea.  He started keto a couple years after me.  He was looking at carnivore same time I was in 2022.  He was also focused on learning metabolic adaptability. 

In other words get keto and use keto when desired.  Do not stay there.  Go back to carbs and get skill in transitions.  Getting from one to the other was always the big complaint I saw people have.  Keto, carnivore and zone rarely worked for people.  Invariably when asked it turned out they messed up the transition.  They either went too hard or never really restricted whatever needed restricting.

So I already wanted to learn and practice that transition before I was compelled.  Now as I get stronger, get better sleep and weight returns, getting ready to try keto or carnivore again.  BRIEFLY.  

And yeh for sure on microbiome.  I think my bifido went to naught those 12 years.  Between fruit, oats and psyllium husk I am coming back.  

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Armin
Quote from Joe2 on January 31, 2026, 2:08 am

I can relate.  I was lucky in December of 2022 when isotretinoin induced sacroiliitis hit because I had done zone diet a decade earlier.  Felt frantic need to come off 12 years keto fast.  Knew enough not to rip into soluble fiber.  Only ate insoluble fiber those 12 years.  

It was frantic.  Pain had me racked unable to stand, sit, laydown.  Held myself in bent dip on walker or countertop.  Slept 3 naps of 10 to 15 minutes daily.  Woke up full bore bellowing.  Pain directly associated with liver, tallow, butter, coconut oil.  Those were my staples.  Without them I lost weight fast while pain stayed high.  Knew I could not instantly drop the 1500 to 2000 calories a day of fat and pick up difference in fruit and grain I had not eaten in 12 years.  

I trickled in carbohydrates and held steady with my beef.  Started ONE bite of apple.  Worked up to 4oz of apple in a week.  The oats same way.  And on.  I ate each tiny meal the way I knew to in zone.  I matched the amount of carbs I dared to eat with appropriate amount of beef.  Probably lucky to get 500 calories that first day.  Got it up to 1000 in a couple weeks.

Once I got calories up over 1500 in zone proportions weight stopped coming off.  Month or so later got a 90 minute nap.  Knew I was on to something.  Was nice that by then I knew why eating liver ripped my pain levels all the way up in seconds.

I think I was lucky a few ways.  First I had 15 years of zone to fall back on.  Confident if I could transition back to carbs protein fat 40/30/30 that pain would fade and weight would hold.  Luckiest aspect might have been that I felt up against a wall with a gun to my head.  I knew the only help conventional docs could give would be pain killers.  That just made it worse.  Without pain, I could tell that structurally sacroiliac just got worse.  

That is what I mean by saying that a few of us in acute damage are the lucky ones who seem to get the fastest best results.  Not so much a matter of hyper compliance so much as imperative to figure ins and outs of how to safely get to compliance with the idea.

Before he got debanked and flipped out, I think Mercola was on to a good idea.  He started keto a couple years after me.  He was looking at carnivore same time I was in 2022.  He was also focused on learning metabolic adaptability. 

In other words get keto and use keto when desired.  Do not stay there.  Go back to carbs and get skill in transitions.  Getting from one to the other was always the big complaint I saw people have.  Keto, carnivore and zone rarely worked for people.  Invariably when asked it turned out they messed up the transition.  They either went too hard or never really restricted whatever needed restricting.

So I already wanted to learn and practice that transition before I was compelled.  Now as I get stronger, get better sleep and weight returns, getting ready to try keto or carnivore again.  BRIEFLY.  

And yeh for sure on microbiome.  I think my bifido went to naught those 12 years.  Between fruit, oats and psyllium husk I am coming back.  

You were on keto for 12 years? That is a long time. I couldn't last over 2 years with keto/carnivore combined. Just never had energy and my brain was mush. There were always brief moments of mental clarity to reassure me that my brain was not permanently broken. These moments maybe lasted 4 hours during the day and would happen 1 day per month.

So many people said I was too smart for X and I should go to school for Y and I always had to tell them that I couldn't trust my brain to actually invest money into taking courses for months at hand. I look back and think it is wild that I went through highschool as an honor student. How did I do that? What was it like to have a fully functioning brain that didn't "drop connection" dozens of times per day for hours at a time? I honestly couldn't remember until the last couple of weeks where my brain was actually online for days at a time. 

I could be talking to someone at work and all of a sudden within 5 minutes it felt like a curtain was being drawn slowly across the front of my face. Like when the blue-light limiter gradually turns on in the evening on my computer screen. That once lively conversation is now in need of an escape hatch. My mind is now drunk and I can't even put on a straight personality. I felt like the main character of Pink Floyd in the Wall when the girl asked "you feeling ok"?

20 years of what could have been but it's time to finally look forward.

 

 

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HermesJoe2

I totally smashed the raw home-made kefir thing hard for several years, but it didn't fix me.   Perhaps I would have had to have both been doing raw kefir hard  AND cut back hard on my vitamin A overload.

I also think that dairy is a good food (I know not everyone here does)-- it helps with calcium and vitamin K and other things.

I would worry that 30 hour yogurt might be inedible for me in that I seem to have issues with anything long-cooked or long-fermented.  (amines, histamines etc).  If I were to try this I'd be doing a regular yogurt timeline.

 

Quote from lil chick on January 31, 2026, 10:54 am

I totally smashed the raw home-made kefir thing hard for several years, but it didn't fix me.   Perhaps I would have had to have both been doing raw kefir hard  AND cut back hard on my vitamin A overload.

I also think that dairy is a good food (I know not everyone here does)-- it helps with calcium and vitamin K and other things.

I would worry that 30 hour yogurt might be inedible for me in that I seem to have issues with anything long-cooked or long-fermented.  (amines, histamines etc).  If I were to try this I'd be doing a regular yogurt timeline.

 

I'm thinking that the strain of probiotics used for fermenting must be very important. Most commercial probiotics and fermented products don't survive the stomach acid or bile acid environment of the small intestine in any decent number. About 95% perish. That is why Dr. Davis chose the 3 he did as well as for their natural antibiotic postbiotics and postbiotics beneficial to the host. 

Dr. Davis believes that amine intolerance is a dysbiosis symptom along with sensitivities to oxalates, etc. 

L Gasseri actually degrades histamine and doesn't produce tyramine so that might be a safe place to start. It helps with reproductive health, especially menopausal symptoms. It reduces visceral fat with no change to diet. It does much more as well.

Do you recall if you had any die off reactions when drinking the kefir?

 

I don't remember, sorry.    Raw kefir would have so many different things in it, including whatever the cow gives to the calf.   I was making it weekly and drinking a half gallon and eating the excess "grains" which are the culture which has been handed down from person to person since the Gods presented it to to man.    :).    So totally not commercial.    The nice thing is, it ferments at room temperature.   The name "kefir" means something like "feel good", I've read.    The "grains" are a blend of different flora (including even yeasts) that live in a self-replicating colony.

Who knows, maybe if I didn't do this all my vitamin A intake would have killed me.   It killed other wapf-ers!

Quote from lil chick on January 31, 2026, 2:53 pm

I don't remember, sorry.    Raw kefir would have so many different things in it, including whatever the cow gives to the calf.   I was making it weekly and drinking a half gallon and eating the excess "grains" which are the culture which has been handed down from person to person since the Gods presented it to to man.    :).    So totally not commercial.    The nice thing is, it ferments at room temperature.   The name "kefir" means something like "feel good", I've read.    The "grains" are a blend of different flora (including even yeasts) that live in a self-replicating colony.

Who knows, maybe if I didn't do this all my vitamin A intake would have killed me.   It killed other wapf-ers!

Interesting. I've had stuff at the store but I doubt it is comparable to raw and fresh fermentation.

Another good thing about long fermented "yogurt" is that the level of vitamin A from the half and half per mega dose of probiotics is negligible. 

Dr. Davis recommends eating a 1/2 cup of "yogurt" daily for 28 days or maybe longer if you have more serious issues. After that, the maintenance phase (forever) is 1/2 a cup 2-3 times per week. 

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Joe2

I was trying to find that video of the person who had psoriasis and taking activated charcoal twice a day kept it under control. The explanation in the video, which I tend to agree with, is that the charcoal absorbed the LPS toxins from pathogenic bacteria and prevented absorption by the the body.

Pretty neat. But is it addressing the problem or is it an unsustainable band-aid? AC absorbs good along with the bad. You would have to time it right and take it away from meds and certain foods. 

Just fix the microbiome and you don't need to this.

AC absorbs bile but that is a red herring IMO.

 

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