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It's the Microbiome Stupid
So interesting! I have a yogurt maker, it makes little jars. Why would people start with half and half rather than milk? Do you assume it is a blank slate or do you heat it to pasteurization temp first? I have always used raw milk for kefir, but always pre-pasteurized before yogurt making.
Inulin is a bit scary haha, isn't that the fiber in Jerusalem artichoke? As I'm remembering that stuff hated me. But I can see it might be useful.
Quote from lil chick on January 29, 2026, 5:37 pmSo interesting! I have a yogurt maker, it makes little jars. Why would people start with half and half rather than milk? Do you assume it is a blank slate or do you heat it to pasteurization temp first? I have always used raw milk for kefir, but always pre-pasteurized before yogurt making.
Inulin is a bit scary haha, isn't that the fiber in Jerusalem artichoke? As I'm remembering that stuff hated me. But I can see it might be useful.
from what I have seen from some videos, making long (36 hour) fermented dairy products will create lactic acid, dropping the ph of the milk and causing the proteins to clump, separating into curds and whey, essentially making cheese. You can do that and it will work just fine, it will just be solids and liquids. Some may want the texture of yogurt which is why most stick with half and half.
raw dairy is good in general but we want a blank slate so there is no competition with the microbes in the dairy medium and the ones we are specifically trying to proliferate.
the inulin is used up by the bacteria during the fermentation process so it shouldn't cause any extra issues but ones are free to substitute it for another fermentable fiber if they prefer something different.
On the topic of fiber...
Isn't it interesting how fiber can be wonderful for some and horrible for others?
Or it is wonderful some times and horrible other times?
A certain doctor proclaimed that if one had a poor reaction with soluble fiber that it was an indication that it was causing a bile dump/too big of a bile dump. Frankly, anything that caused a poor reaction was sequestered into this category while anything that gave seemingly positive results most likely was "preventing bile dump".
A pretty basic dichotomy that seemed to explain some things in my experience...until it didn't.
I'm not sure what the mechanism was that was proposed to cause this bile dump when it comes to soluble fiber intake. I think the idea was that the soluble fiber soaked up the bile, excreting the bile from the body and triggering the liver to create fresh new bile to replace the old that was lost. Ok, makes sense I guess.
Insert Activated Charcoal
This compound for sure binds bile. That's well known. No problem. Well, activated charcoal never caused any "bile dump" problems. Why wasn't the fresh bile that was being produced causing a similar reaction as the soluble fiber?
Because it was never about the bile. Insoluble fiber binds bile and that never caused a problem for me either.
There is a reason why it can take people a while to build up a "tolerance" to soluble fiber, especially if you have been on a mostly meat based diet. See Shawn Baker. Years ago after coming off a similar diet, half an apple would send me into another realm. Brain fog, delirium, anxiety, etc. That's not normal. Same thing would happen when I took a tiny sip of coffee. 4 hours of existential crisis. Bacteria consume polyphenols in coffee as a fermentable source.
These events would happen within 30-90 minutes. This is upper digestion. Stomach, small intestines. Was my time on the long term crazy diet the thing that killed off the nice and medium nice microbes, giving the more sinister ones time and space to grow upwards from the large intestine? The very useful microbe called Akkermansia muciniphilia prefers fiber but when fiber isn't available, thrives on eating the mucosal layer of the intestines. Not good. The small intestine/large intestine junction is a very susceptible site for overgrowth btw.
It felt like a war was raging within 30 minutes of eating soluble fiber. Some times it would cause hour long panic attacks. Not fun. Not sure how a bile dump explains this.
Fasting causes a cessation of symptoms. One will say that it is due to no bile being dumped. Ok, I can see that. But it also could be a lack of food for pathogenic bacteria to munch on, reproduce, die, and spew their inflammatory corpses and compounds all about. Funny how symptoms come right back when food is reintroduced.
It's the microbiome stupid and the problem is dysbiosis.
Look up chronic endotoxemia and see just how nasty things can get. Systemic inflammation. Isn't that what most people experience these days? Now, try to love your liver when it's constantly being inundated with toxic waste, directly from the portal vein.
Quote from Janelle525 on January 29, 2026, 4:42 pmQuote from Armin on January 29, 2026, 8:07 amIn case anyone is wondering on how to make it and not search through blogs and videos...
3 strains.
-lactobacillus reuteri
-lactobacillus gasseri
-baccillus subtilis
look up the characteristics of these probiotics. They destroy pathogenic microbes and do all kinds of great things.
Fermentation process
ferment the first 2 for 36 hours, the 3rd for 24 hours. I do 3 separate individual batches
temp for first 2 is 100F, temp for 3rd is 95F
I use an instapot with temp customization
1 tablespoon of inulin per quart of product for fermentation
the medium/liquid can be numerous things. most stick with half and half
1 capsule (2 for subtilis product linked below) of probiotic per quart of liquid medium mixed in with inulin.
You can use 2 tablespoons from a batch of yogurt as a starter for a subsequent batch in lieu of a probiotic capsule. I usually add 1 capsule for good measure as I tend to create half gallon and full gallon batches.
sources for microbes
L reuteri: https://www.oxiceutics.com/products/myreuteri?variant=45917346627811
L gasseri: https://www.amazon.com/Dr-Mercola-Probiotic-Supplement-Regularity/dp/B09CSFTM24?th=1
I want to try this. I never had amazing results from yogurt, but maybe this would be different? Also, those probiotics are expensive, I've spent so much money on supplements can we go cheaper on these?
Just out of curiosity, when you say that you have tried yogurt, what kind were you referring to? Store bought? Home fermented? The thing about commercial yogurt is that they suck. lol. They give you some strains that really aren't very special or die during digestion (if they are even alive at all), loaded up with sugar and emulsifiers.
Yogurt requires two essential bacterial strains for fermentation: Streptococcus thermophilus and Lactobacillus bulgaricus
Both are iffy for surviving stomach acid. Depends on the specific strain of each. Not bad but nothing special that can't be had and more with others.
Quote from Ginny on January 29, 2026, 8:18 pmHere is a yogurt maker that requires no electricity.
Similar idea to how we use our crock pot. We only turn it on a few minutes to warm it up. Then when we have heated the milk, stirred in the culture and capped the pint jars, we put the jars in the crock pot, unplug it and put the pot with 5 jars into a warm place to sit.
Quote from Armin on January 29, 2026, 7:08 pmOn the topic of fiber...
Isn't it interesting how fiber can be wonderful for some and horrible for others?
Or it is wonderful some times and horrible other times?
A certain doctor proclaimed that if one had a poor reaction with soluble fiber that it was an indication that it was causing a bile dump/too big of a bile dump. Frankly, anything that caused a poor reaction was sequestered into this category while anything that gave seemingly positive results most likely was "preventing bile dump".
A pretty basic dichotomy that seemed to explain some things in my experience...until it didn't.
I'm not sure what the mechanism was that was proposed to cause this bile dump when it comes to soluble fiber intake. I think the idea was that the soluble fiber soaked up the bile, excreting the bile from the body and triggering the liver to create fresh new bile to replace the old that was lost. Ok, makes sense I guess.
Insert Activated Charcoal
This compound for sure binds bile. That's well known. No problem. Well, activated charcoal never caused any "bile dump" problems. Why wasn't the fresh bile that was being produced causing a similar reaction as the soluble fiber?
Because it was never about the bile. Insoluble fiber binds bile and that never caused a problem for me either.
There is a reason why it can take people a while to build up a "tolerance" to soluble fiber, especially if you have been on a mostly meat based diet. See Shawn Baker. Years ago after coming off a similar diet, half an apple would send me into another realm. Brain fog, delirium, anxiety, etc. That's not normal. Same thing would happen when I took a tiny sip of coffee. 4 hours of existential crisis. Bacteria consume polyphenols in coffee as a fermentable source.
These events would happen within 30-90 minutes. This is upper digestion. Stomach, small intestines. Was my time on the long term crazy diet the thing that killed off the nice and medium nice microbes, giving the more sinister ones time and space to grow upwards from the large intestine? The very useful microbe called Akkermansia muciniphilia prefers fiber but when fiber isn't available, thrives on eating the mucosal layer of the intestines. Not good. The small intestine/large intestine junction is a very susceptible site for overgrowth btw.
It felt like a war was raging within 30 minutes of eating soluble fiber. Some times it would cause hour long panic attacks. Not fun. Not sure how a bile dump explains this.
Fasting causes a cessation of symptoms. One will say that it is due to no bile being dumped. Ok, I can see that. But it also could be a lack of food for pathogenic bacteria to munch on, reproduce, die, and spew their inflammatory corpses and compounds all about. Funny how symptoms come right back when food is reintroduced.
It's the microbiome stupid and the problem is dysbiosis.
Look up chronic endotoxemia and see just how nasty things can get. Systemic inflammation. Isn't that what most people experience these days? Now, try to love your liver when it's constantly being inundated with toxic waste, directly from the portal vein.
I think I am familiar with that certain doctor. I pays to scan his site thoroughly. I think his heads I win tails you lose take on bile dumps is because he barely understands who and where he got the idea. I read back through the archives and found Tyler Ginter worth reading more than anyone else on there. Reading back I found his posted article on the virtues of gradual steady approach to all. It looks very much like Tyler wrote that article before lyl g wrote the order of adding stuff list lesson and also before he started using bile dumps to explain everything. Tyler's article was much better stated. There is merit to lyl g's ideas on bile dumps albeit poorly articulated and coached.
Some day I hope to exchange with Tyler more. Genius dude. Want to post his insights all over the internet. Paraphrase it here:
Take an account of life the universe and everything. Symptoms, goals, diet, supplements, sleep, associated issues, theories, problems, whatever. List it and outline it and simplify it. My addition here is to take one page, write down symptoms in one third, diet in another third, supplements and therapies in last third. I like to write a bit on my own on a separate page just generally about goals, theories, whatever. Just to keep the first page shorter and clearer.
Then pick one item that seems the best suspect for change and make a tiny change. Kaizen. The idea is to change that item and tip the balance on the system in the least dramatic way. Getting no change in symptoms is best. After awhile make another tiny change. Maybe more or less of that one item. Keep going. When improvement comes, stop changes. Wait. Keep notes keep tracks.
From experience, big changes usually bring big swings in bile flow. Either big increase or decrease. And everything is capable of going either direction. Bile flow can cause any of a long list of symptoms. The easiest symptom indicating bile flow to track is how fast or slow, solid or liquid colon evacuates. One person had horrific diarrhea he insisted was because his liver cracked open. (Do not ask me to define that term please.)
He insisted he was dumping bile and his theorized cure was to slam charcoal. He had been warned that increasing charcoal too fast usually causes constipation. He got up to 2 cups of charcoal a day and his diarrhea got worse. He was adding a third cup of charcoal at the point he posted a plea for help and advice. I suggested he decrease the dose of charcoal and list all the foods he was eating. Went a few furious rounds with him angry, insulting and claiming I was ignorant and trying to kill him. After a week or so he started slamming vC since that doctor suggests that vC shuts down liver detox. That seemed to work.
Not sure how he came out after that. I do know at the point he got some relief he was slamming like 10g of vC and 2 or 3 cups of charcoal. He never copped to the fact that many people report that charcoal caused diarrhea for them. He was probably playing pushmepullyou with the bile dumping theory of heads I win tails you lose.
My take on it is that he violated Tyler's theory of seeking to maintain whatever balance there currently is in our system and to make tiny changes slowly and infrequently. Pay close attention to results and focus on kaizen. Avoid feeling cornered in need of massive doses of anything. Avoid massive increases or decreases of anything. Recognize that no matter how bad it gets, that there is some balance in the system that is currently working well enough or we would not be here writing long detailed theories about what we KNOW is going on inside us. Because yeh, I was sure when I started taking 10x of item A that I needed that 10x and that after a time I needed 100x of A and then 1000x of A and considering the symptoms I have now and the symptoms I had then I was a genius before and a genius now and,................... and,..........
Wait a minute. Is this another example of that 747 scenario where my doc asked me 30 years ago if I thought I could fly a 747 in a storm blindfolded with zero experience? Because really, how well do the smartest, wisest people alive today know what is going on inside us? And how much of what they know do we know? And were they not wrong before they were right with what they currently believe? Are they not likely to be wrong again? Now?
Quote from Armin on January 29, 2026, 7:08 pmOn the topic of fiber...
Isn't it interesting how fiber can be wonderful for some and horrible for others?
Or it is wonderful some times and horrible other times?
A certain doctor proclaimed that if one had a poor reaction with soluble fiber that it was an indication that it was causing a bile dump/too big of a bile dump. Frankly, anything that caused a poor reaction was sequestered into this category while anything that gave seemingly positive results most likely was "preventing bile dump".
A pretty basic dichotomy that seemed to explain some things in my experience...until it didn't.
I'm not sure what the mechanism was that was proposed to cause this bile dump when it comes to soluble fiber intake. I think the idea was that the soluble fiber soaked up the bile, excreting the bile from the body and triggering the liver to create fresh new bile to replace the old that was lost. Ok, makes sense I guess.
Insert Activated Charcoal
This compound for sure binds bile. That's well known. No problem. Well, activated charcoal never caused any "bile dump" problems. Why wasn't the fresh bile that was being produced causing a similar reaction as the soluble fiber?
Because it was never about the bile. Insoluble fiber binds bile and that never caused a problem for me either.
There is a reason why it can take people a while to build up a "tolerance" to soluble fiber, especially if you have been on a mostly meat based diet. See Shawn Baker. Years ago after coming off a similar diet, half an apple would send me into another realm. Brain fog, delirium, anxiety, etc. That's not normal. Same thing would happen when I took a tiny sip of coffee. 4 hours of existential crisis. Bacteria consume polyphenols in coffee as a fermentable source.
These events would happen within 30-90 minutes. This is upper digestion. Stomach, small intestines. Was my time on the long term crazy diet the thing that killed off the nice and medium nice microbes, giving the more sinister ones time and space to grow upwards from the large intestine? The very useful microbe called Akkermansia muciniphilia prefers fiber but when fiber isn't available, thrives on eating the mucosal layer of the intestines. Not good. The small intestine/large intestine junction is a very susceptible site for overgrowth btw.
It felt like a war was raging within 30 minutes of eating soluble fiber. Some times it would cause hour long panic attacks. Not fun. Not sure how a bile dump explains this.
Fasting causes a cessation of symptoms. One will say that it is due to no bile being dumped. Ok, I can see that. But it also could be a lack of food for pathogenic bacteria to munch on, reproduce, die, and spew their inflammatory corpses and compounds all about. Funny how symptoms come right back when food is reintroduced.
It's the microbiome stupid and the problem is dysbiosis.
Look up chronic endotoxemia and see just how nasty things can get. Systemic inflammation. Isn't that what most people experience these days? Now, try to love your liver when it's constantly being inundated with toxic waste, directly from the portal vein.
Thank-you for sharing your experience! We are similar!! I avoided fiber per Ray Peat for yrs and then whenever I'd try to re-introduce it I'd get a panic attack. He had the right idea... prevent endotoxin, but his way of going about it was absolutely wrong. He should have said if you avoid soluble fiber you absolutely must consume the carrot salad (which I did try, but couldn't continue because they taste awful! not to mention the beta carotene, and no way was I going to eat bamboo shoots everyday either!). It got so bad I had to stop drinking milk because that would also cause anxiety. I definitely had dysbiosis. Now I can have milk I just don't want it. I eat beans everyday now and I do get gas still, but Karen Hurd said that's when we are stressed and I have found that to be the case. Stress causes fermentation.
Yeah I would eat store-bought yogurt. It's pretty crappy.
Quote from Joe2 on January 30, 2026, 3:06 amQuote from Armin on January 29, 2026, 7:08 pmOn the topic of fiber...
Isn't it interesting how fiber can be wonderful for some and horrible for others?
Or it is wonderful some times and horrible other times?
A certain doctor proclaimed that if one had a poor reaction with soluble fiber that it was an indication that it was causing a bile dump/too big of a bile dump. Frankly, anything that caused a poor reaction was sequestered into this category while anything that gave seemingly positive results most likely was "preventing bile dump".
A pretty basic dichotomy that seemed to explain some things in my experience...until it didn't.
I'm not sure what the mechanism was that was proposed to cause this bile dump when it comes to soluble fiber intake. I think the idea was that the soluble fiber soaked up the bile, excreting the bile from the body and triggering the liver to create fresh new bile to replace the old that was lost. Ok, makes sense I guess.
Insert Activated Charcoal
This compound for sure binds bile. That's well known. No problem. Well, activated charcoal never caused any "bile dump" problems. Why wasn't the fresh bile that was being produced causing a similar reaction as the soluble fiber?
Because it was never about the bile. Insoluble fiber binds bile and that never caused a problem for me either.
There is a reason why it can take people a while to build up a "tolerance" to soluble fiber, especially if you have been on a mostly meat based diet. See Shawn Baker. Years ago after coming off a similar diet, half an apple would send me into another realm. Brain fog, delirium, anxiety, etc. That's not normal. Same thing would happen when I took a tiny sip of coffee. 4 hours of existential crisis. Bacteria consume polyphenols in coffee as a fermentable source.
These events would happen within 30-90 minutes. This is upper digestion. Stomach, small intestines. Was my time on the long term crazy diet the thing that killed off the nice and medium nice microbes, giving the more sinister ones time and space to grow upwards from the large intestine? The very useful microbe called Akkermansia muciniphilia prefers fiber but when fiber isn't available, thrives on eating the mucosal layer of the intestines. Not good. The small intestine/large intestine junction is a very susceptible site for overgrowth btw.
It felt like a war was raging within 30 minutes of eating soluble fiber. Some times it would cause hour long panic attacks. Not fun. Not sure how a bile dump explains this.
Fasting causes a cessation of symptoms. One will say that it is due to no bile being dumped. Ok, I can see that. But it also could be a lack of food for pathogenic bacteria to munch on, reproduce, die, and spew their inflammatory corpses and compounds all about. Funny how symptoms come right back when food is reintroduced.
It's the microbiome stupid and the problem is dysbiosis.
Look up chronic endotoxemia and see just how nasty things can get. Systemic inflammation. Isn't that what most people experience these days? Now, try to love your liver when it's constantly being inundated with toxic waste, directly from the portal vein.
I think I am familiar with that certain doctor. I pays to scan his site thoroughly. I think his heads I win tails you lose take on bile dumps is because he barely understands who and where he got the idea. I read back through the archives and found Tyler Ginter worth reading more than anyone else on there. Reading back I found his posted article on the virtues of gradual steady approach to all. It looks very much like Tyler wrote that article before lyl g wrote the order of adding stuff list lesson and also before he started using bile dumps to explain everything. Tyler's article was much better stated. There is merit to lyl g's ideas on bile dumps albeit poorly articulated and coached.
Some day I hope to exchange with Tyler more. Genius dude. Want to post his insights all over the internet. Paraphrase it here:
Take an account of life the universe and everything. Symptoms, goals, diet, supplements, sleep, associated issues, theories, problems, whatever. List it and outline it and simplify it. My addition here is to take one page, write down symptoms in one third, diet in another third, supplements and therapies in last third. I like to write a bit on my own on a separate page just generally about goals, theories, whatever. Just to keep the first page shorter and clearer.
Then pick one item that seems the best suspect for change and make a tiny change. Kaizen. The idea is to change that item and tip the balance on the system in the least dramatic way. Getting no change in symptoms is best. After awhile make another tiny change. Maybe more or less of that one item. Keep going. When improvement comes, stop changes. Wait. Keep notes keep tracks.
From experience, big changes usually bring big swings in bile flow. Either big increase or decrease. And everything is capable of going either direction. Bile flow can cause any of a long list of symptoms. The easiest symptom indicating bile flow to track is how fast or slow, solid or liquid colon evacuates. One person had horrific diarrhea he insisted was because his liver cracked open. (Do not ask me to define that term please.)
He insisted he was dumping bile and his theorized cure was to slam charcoal. He had been warned that increasing charcoal too fast usually causes constipation. He got up to 2 cups of charcoal a day and his diarrhea got worse. He was adding a third cup of charcoal at the point he posted a plea for help and advice. I suggested he decrease the dose of charcoal and list all the foods he was eating. Went a few furious rounds with him angry, insulting and claiming I was ignorant and trying to kill him. After a week or so he started slamming vC since that doctor suggests that vC shuts down liver detox. That seemed to work.
Not sure how he came out after that. I do know at the point he got some relief he was slamming like 10g of vC and 2 or 3 cups of charcoal. He never copped to the fact that many people report that charcoal caused diarrhea for them. He was probably playing pushmepullyou with the bile dumping theory of heads I win tails you lose.
My take on it is that he violated Tyler's theory of seeking to maintain whatever balance there currently is in our system and to make tiny changes slowly and infrequently. Pay close attention to results and focus on kaizen. Avoid feeling cornered in need of massive doses of anything. Avoid massive increases or decreases of anything. Recognize that no matter how bad it gets, that there is some balance in the system that is currently working well enough or we would not be here writing long detailed theories about what we KNOW is going on inside us. Because yeh, I was sure when I started taking 10x of item A that I needed that 10x and that after a time I needed 100x of A and then 1000x of A and considering the symptoms I have now and the symptoms I had then I was a genius before and a genius now and,................... and,..........
Wait a minute. Is this another example of that 747 scenario where my doc asked me 30 years ago if I thought I could fly a 747 in a storm blindfolded with zero experience? Because really, how well do the smartest, wisest people alive today know what is going on inside us? And how much of what they know do we know? And were they not wrong before they were right with what they currently believe? Are they not likely to be wrong again? Now?
Thanks for the reply Joe.
I'm a member of that certain doctor's forum and I tune in every now and then and I guess the new idea is to take MSG for liver health. Before that was Nicotinic Acid. Before that was chlorine dioxide. It just seems from a casual onlooker that everyone is on a boat without a sail, flailing around, hoping that their terrible symptoms are indicators of future success to come. Maybe they are but I have reservations.
I understand and respect the small/slow change approach but also think testing the waters needs to be at times.
Week 1 -My first few days of eating yogurt I took the smallest amount I could. I didn't know what to expect. I started with L gasseri. The other 2 hadn't come in the mail yet. I did fine. Day 3 I took a few tablespoons of both L gasseri and L reuteri. Felt pretty good. Then I started going a little more aggressive. I had gallons of this stuff and didn't know how long it would last before spoilage so I was up to a few cups a day. Not a mistake but definitely elicited some acute changes. Nothing unbearable or life threatening. Just very noticeable. In hindsight, it was good to know that something was happening and it was definitely in the right direction. Main symptoms were extreme fatigue, weakness, despair, general malaise. Nothing I can't handle, just not good for being awake at work. lol
Week 2 - I backed off, took a tablespoon or so per day and gradually upped to a cup or 2 a day. By now I was eating all 3 strains. My first batches of reuteri and gasseri were now starters for my 2nd batch.
Week 3/4 - The whole thing changes. Those 2nd batches are now super tart and super potent. I wasn't ready for this jump. Another herx, while at work. I backed it back down to a tablespoon or 2 and I continued that until week 5. Main symptoms were hip pain and small flare in eczema and irritability. My wife took 2 cups of this stuff a few nights ago (she's on week 3) and it completely wrecked her. Again, nothing life threatening. Mainly headache, joint/muscle pain she hadn't felt in years, etc. She's ok now. lol
Week 5 - I am at the end of week 5 and continued to take a few tablespoons of the tart product (all 3 mixed together) in the morning and little more at night. I'm going to push the envelope this evening as it is the weekend.
In a month I went from chronic inflammation making daily activities a struggle (joint pain, fatigue, anxiety) to waking up every morning excited to go to work and see what each day brings. Really makes me think about how many peoples' lives could so easily be fixed.
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.