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DiscussionLet's talk about it: The science of itIt's the Microbiome Stupid

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It's the Microbiome Stupid

#41 · January 31, 2026, 8:10 pm

Interesting thread!

Have you noticed any blackheads/sebaceous filaments on your nose? I think it's related to SIBO. Maybe they've started to reduce in number as your symptoms have improved.

Here's a picture to show what I mean:

Thanks for sharing your experience! SIBO is still something I struggle with for more than a decade. I've tried many things, and they hardly move the needle. I'm glad you've found something with those three probiotics that has improved your symptoms within months. Must be really exciting to finally find something that actually makes a difference.

#42 · January 31, 2026, 8:26 pm

Quote from Hermes on January 31, 2026, 8:10 pm

Interesting thread!

Have you noticed any blackheads/sebaceous filaments on your nose? I think it's related to SIBO. Maybe they've started to reduce in number as your symptoms have improved.

Here's a picture to show what I mean:

Thanks for sharing your experience! SIBO is still something I struggle with for more than a decade. I've tried many things, and they hardly move the needle. I'm glad you've found something with those three probiotics that has improved your symptoms within months. Must be really exciting to finally find something that actually makes a difference.

I've hard black heads like that for years. At least since 2012. I looked in the mirror and they do look fainter but that could just be because I haven't looked at them in a while.

I've tried the herbal SIBO treatments and I don't think I noticed anything even remotely similar to what I've experienced in one month with the "yogurt". Even if you do kill off some overgrowth with herbal/antibiotic treatments, it doesn't bring back these microbes that we've all lost that indigenous peoples and wild animals have. And eventually dysbiosis will most likely creep back.

Again, I have had life changing results in one month.

Die off symptoms happened and I got better. Tangible cause and effect. Not wishful hoping and time/money wasted.

Hermes has reacted to this post.

#43 · February 1, 2026, 2:42 am

Quote from Joe2 on February 1, 2026, 2:42 am

Quote from Armin on January 31, 2026, 8:13 am

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

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.

I think you were not so much into ketosis. On all diets I have tried, the first two years were learning curve, not the diet. Took me months to get past my first mistake on keto. My blood pressure went so low I was almost passing out. Then I learned about salt. Gluconeogenesis was the next mistake. Took more months to recognize it. Then more months to slow my dopamine down to get me under 3 pounds of meat per day. My sweet spot turned out to be 20 to 30 oz of meat per day. It depended on a lot of factors. When I slammed 3 or 4 pounds on special occasions, the meat sweats were the least of my problems. The symptoms were so diabetic, that it reminded me of my sugar slamming days. I learned to back off.

There were other issues I had to learn and navigate during those first few years. After that I was in ketosis and flying.

The next issue I worked with was performance. I had a hard time dialing it back. A lot of folk thought I was a bastard out performing them. Doing 14 plus straight hours where they could barely pull 7. And producing less cognitive mistakes and better dexterity results (driving, phlebotomy, data management and materials transfer). My last few years at the company, another blood center executed hostile takeover. They slowly cleared out rank and file and in the end our mid and upper managers. It was obvious. Any excuses were used to terminate.

I thought new managers wanted me until during my last year, my boss' boss who hired me and was still loyal as I saved her bacon often, called me in. Thought I was done when I saw another manager sitting with her for the meeting. Two managers with one staff in an unannounced meeting is always a sign. She needed to have a witness. She told me I had too much over time and needed to stop. Scolded me. Insane since she was the one who scheduled me. She was the one who called me in on emergencies. Frequently. She kept a serious face and was angry. Creepy as eff since I knew she loved me and would kill many species for me. I routinely did for her. I looked to her partner in crime and she almost busted out laughing. I had a similar and junior relationship with her. But my boss kept straight face.

So I took it straight. Asked:

Who schedules me? How many hours? Who has me stay 2 to 8 extra hours routinely? Who calls me in couple times a week to cover? Who has me train all new drivers? Who has me setting up, working on, tearing down and delivering equipment? It was all her and her assistants. She scheduled me 55 to 60/week. I routinely worked 70 to 90/week. She admitted it all and kept a straight face.

Asked more:

When was the last time I missed a day? When was I last late? When did I last refuse a call? When was the last time I said no? Her records (from the new owners' computers) went back 2 years. Had not missed a day. Said I was late one day. Wrong. Her computer was down that day. I was 15 minutes early. That perfect record went back further than 2 years. Everyone in the company knew it.

Told her I wanted to go part time. Schedule me 35 pay no benefits use me up to 45 / week. She did that 10 years earlier for a year when I started a company for a side business of ours. She refused. Told me this all came from new headquarters. They complained since I had the most OT in our new company of 2000 people in 4 states. I also was the only one with perfect attendance. I was covering problems in 2 states. They were asking me to cover 4.

She gave me a gift card in appreciation of my work. She was clearly very happy. Her new bosses were clearly not. I was the senior person not in management making the most money. Never mind the profits I brought in. Two people making half as much as me would do better than me in 6 months. I did not really understand what was going until they early retired her.

So yeh, all that to say my performance after those first 2 years of what I call "almost keto" went wild. I think that the first 2 years of keto were not so keto. This has been the case in every diet I did. Took me the first 2 out of 15 years to work out my mistakes and Barry Sears' bugs in the zone diet. From what I am digging up, Shawn Baker's first year or 2 on carnivore put up some not so good lab results too. I think we are all too unforgiving of our ineptitude and overestimating our knowledge and skills in adopting new disciplines.

To be sure too, even after 12 years, I had other bugs in keto I needed to work out. In my tenth year, I pulled up with hernias. In hindsight, I am confident that was mostly due to constipation. My gut flow was less than optimal. Relying on MCT oil and coconut oil to keep things moving is probably bad idea jeans. I did not know then that 12 cups of cooked crucifers was pretty strictly insoluble fiber and not helping much. That is one aspect of health I think carnivores get wrong. Pooping less than daily is not optimal. Pooping weekly is a pretty obvious problem. After hernia repair I did 2 more years keto. I took better care to avoid constipation.

Still the last bug I needed to work out of keto was organ meats and high vA consumption. It took getting off keto to address that.

After the sacroiliitis compelled I quit keto, I found out another bug in the diet. I almost sure starved out my bifido. I am not so knowledgeable on microbiota. I have read more knowledgeable folk claim that living without bifido is a bad idea. Your notes affirm that principle.

Will see what kind of performance I can repair myself up to. Grant's performance levels do not surprise me that much. They do hearten me. My improvements seem to keep pace with his first 3 years.

Quote from Armin on January 31, 2026, 8:13 am

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

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.

I think you were not so much into ketosis. On all diets I have tried, the first two years were learning curve, not the diet. Took me months to get past my first mistake on keto. My blood pressure went so low I was almost passing out. Then I learned about salt. Gluconeogenesis was the next mistake. Took more months to recognize it. Then more months to slow my dopamine down to get me under 3 pounds of meat per day. My sweet spot turned out to be 20 to 30 oz of meat per day. It depended on a lot of factors. When I slammed 3 or 4 pounds on special occasions, the meat sweats were the least of my problems. The symptoms were so diabetic, that it reminded me of my sugar slamming days. I learned to back off.

There were other issues I had to learn and navigate during those first few years. After that I was in ketosis and flying.

The next issue I worked with was performance. I had a hard time dialing it back. A lot of folk thought I was a bastard out performing them. Doing 14 plus straight hours where they could barely pull 7. And producing less cognitive mistakes and better dexterity results (driving, phlebotomy, data management and materials transfer). My last few years at the company, another blood center executed hostile takeover. They slowly cleared out rank and file and in the end our mid and upper managers. It was obvious. Any excuses were used to terminate.

I thought new managers wanted me until during my last year, my boss' boss who hired me and was still loyal as I saved her bacon often, called me in. Thought I was done when I saw another manager sitting with her for the meeting. Two managers with one staff in an unannounced meeting is always a sign. She needed to have a witness. She told me I had too much over time and needed to stop. Scolded me. Insane since she was the one who scheduled me. She was the one who called me in on emergencies. Frequently. She kept a serious face and was angry. Creepy as eff since I knew she loved me and would kill many species for me. I routinely did for her. I looked to her partner in crime and she almost busted out laughing. I had a similar and junior relationship with her. But my boss kept straight face.

So I took it straight. Asked:

Who schedules me? How many hours? Who has me stay 2 to 8 extra hours routinely? Who calls me in couple times a week to cover? Who has me train all new drivers? Who has me setting up, working on, tearing down and delivering equipment? It was all her and her assistants. She scheduled me 55 to 60/week. I routinely worked 70 to 90/week. She admitted it all and kept a straight face.

Asked more:

When was the last time I missed a day? When was I last late? When did I last refuse a call? When was the last time I said no? Her records (from the new owners' computers) went back 2 years. Had not missed a day. Said I was late one day. Wrong. Her computer was down that day. I was 15 minutes early. That perfect record went back further than 2 years. Everyone in the company knew it.

Told her I wanted to go part time. Schedule me 35 pay no benefits use me up to 45 / week. She did that 10 years earlier for a year when I started a company for a side business of ours. She refused. Told me this all came from new headquarters. They complained since I had the most OT in our new company of 2000 people in 4 states. I also was the only one with perfect attendance. I was covering problems in 2 states. They were asking me to cover 4.

She gave me a gift card in appreciation of my work. She was clearly very happy. Her new bosses were clearly not. I was the senior person not in management making the most money. Never mind the profits I brought in. Two people making half as much as me would do better than me in 6 months. I did not really understand what was going until they early retired her.

So yeh, all that to say my performance after those first 2 years of what I call "almost keto" went wild. I think that the first 2 years of keto were not so keto. This has been the case in every diet I did. Took me the first 2 out of 15 years to work out my mistakes and Barry Sears' bugs in the zone diet. From what I am digging up, Shawn Baker's first year or 2 on carnivore put up some not so good lab results too. I think we are all too unforgiving of our ineptitude and overestimating our knowledge and skills in adopting new disciplines.

To be sure too, even after 12 years, I had other bugs in keto I needed to work out. In my tenth year, I pulled up with hernias. In hindsight, I am confident that was mostly due to constipation. My gut flow was less than optimal. Relying on MCT oil and coconut oil to keep things moving is probably bad idea jeans. I did not know then that 12 cups of cooked crucifers was pretty strictly insoluble fiber and not helping much. That is one aspect of health I think carnivores get wrong. Pooping less than daily is not optimal. Pooping weekly is a pretty obvious problem. After hernia repair I did 2 more years keto. I took better care to avoid constipation.

Still the last bug I needed to work out of keto was organ meats and high vA consumption. It took getting off keto to address that.

After the sacroiliitis compelled I quit keto, I found out another bug in the diet. I almost sure starved out my bifido. I am not so knowledgeable on microbiota. I have read more knowledgeable folk claim that living without bifido is a bad idea. Your notes affirm that principle.

Will see what kind of performance I can repair myself up to. Grant's performance levels do not surprise me that much. They do hearten me. My improvements seem to keep pace with his first 3 years.

Armin has reacted to this post.

#44 · February 1, 2026, 2:55 am

Quote from Armin on January 31, 2026, 6:39 pm

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.

Charcoal intake for 37 months now. First 35 months were 1/4 cup to 1/2 cup per day. Have zero first hand evidence of charcoal absorbing nutrients in me, spouse, 4 dogs and 7 chickens. Also have seen zero evidence in literature of it happening. In fact quite the opposite. Most farmers using charcoal mix it in with the feed. We do and have for 3 years.

Your theory on LPS makes sense.

#45 · February 1, 2026, 2:59 am

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!

Sounds like you went too hard on the kefir. You were a kefirniac. Please keep in mind, I am the guy who goes too hard on every new thing that comes along. I catch flack routinely around here for it. Before you join those making such wildly flawed claims about me, be forewarned of my replies to criticism of mey extremism now.

I am now EXTREMELY MODERATE in all I do.

And yeh, I used to eat 2 cups plus of homemade yogurt daily. My next experiment with yogurt, I plan on a couple tablespoons a day. Maybe charcoal flavored yogurt?

lil chick and Armin have reacted to this post.

#46 · February 1, 2026, 3:57 am

I keep forgetting to raise this question and it is another thing that fell out of the wapf, and it is this: Fat's don't ferment, they go rancid.

The fermented cod liver oil rancidity question broke the wapf in half.

Perhaps a person could make this yogurt skim. Of course, skim milk has vitamin A added here. So a person would want to buy raw skim and home pasturize it. Or maybe buy non-homogenized and take the fat off?

btw: I do wonder what the effect of fermentation is on vitamin A. Does it become more or less problematic?

Anyways, your good results do matter and should not be downplayed. Just musing here.

The milk cure (which is an historical cure for TB and other things that the wapf has written about) was skim and raw if I'm not mistaken.

Milk can make a whole cow. It's much like eggs in that it is a complete food. Taking away the fat might not actually be the best idea. So maybe I'd just make the thing in less hours for less rancidity?

Or, I know! take the fats separately!

Armin has reacted to this post.

#47 · February 1, 2026, 7:00 am

Quote from Joe2 on February 1, 2026, 2:55 am

Quote from Armin on January 31, 2026, 6:39 pm

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.

Charcoal intake for 37 months now. First 35 months were 1/4 cup to 1/2 cup per day. Have zero first hand evidence of charcoal absorbing nutrients in me, spouse, 4 dogs and 7 chickens. Also have seen zero evidence in literature of it happening. In fact quite the opposite. Most farmers using charcoal mix it in with the feed. We do and have for 3 years.

Your theory on LPS makes sense.

Dr. Davis has his patients/followers/yogurt eaters take some AC if they get too much die off early on. I used it once or twice the 3 week when I spiked things a bit hard. I think it took the edge off but that was a while now in retrospect.

I used AC a lot a few years ago and it feels like it kept the worse symptoms at bay. My wife complained about the black soot everywhere so I kind of backed off and then forgot about it.

Joe2 has reacted to this post.

#48 · February 1, 2026, 7:13 am

Quote from Joe2 on February 1, 2026, 2:59 am

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!

Sounds like you went too hard on the kefir. You were a kefirniac. Please keep in mind, I am the guy who goes too hard on every new thing that comes along. I catch flack routinely around here for it. Before you join those making such wildly flawed claims about me, be forewarned of my replies to criticism of mey extremism now.

I am now EXTREMELY MODERATE in all I do.

And yeh, I used to eat 2 cups plus of homemade yogurt daily. My next experiment with yogurt, I plan on a couple tablespoons a day. Maybe charcoal flavored yogurt?

I also have that all or none mindset. It's a blessing and a curse.

Charcoal yogurt would be a great idea to address preemptive die off reactions during the early stages.

#49 · February 1, 2026, 7:19 am

One interesting potential unseen occurrences of keto and other high fat diets is that the increases in bile production/excretion can promote the present of a bacterium called Bilophila wadsworthia.

Bilophila wadsworthia can have negative effects, particularly in excess, by promoting gut inflammation, damaging the intestinal barrier, disrupting bile acid metabolism, and worsening metabolic issues like fatty liver (hepatic steatosis) and glucose intolerance, often linked to high saturated fat diets and its hydrogen sulfide byproduct, but it's also part of the normal microbiome in small amounts.

#50 · February 1, 2026, 8:21 am

Quote from lil chick on February 1, 2026, 3:57 am

I keep forgetting to raise this question and it is another thing that fell out of the wapf, and it is this: Fat's don't ferment, they go rancid.

The fermented cod liver oil rancidity question broke the wapf in half.

Perhaps a person could make this yogurt skim. Of course, skim milk has vitamin A added here. So a person would want to buy raw skim and home pasturize it. Or maybe buy non-homogenized and take the fat off?

btw: I do wonder what the effect of fermentation is on vitamin A. Does it become more or less problematic?

Anyways, your good results do matter and should not be downplayed. Just musing here.

The milk cure (which is an historical cure for TB and other things that the wapf has written about) was skim and raw if I'm not mistaken.

Milk can make a whole cow. It's much like eggs in that it is a complete food. Taking away the fat might not actually be the best idea. So maybe I'd just make the thing in less hours for less rancidity?

Or, I know! take the fats separately!

Apparently there is a thing called water kefir that uses water as the medium and inulin or some other fiber to ferment the kefir grains.

You can use coconut milk instead of half and half as well. I'm sure many mediums could work just fine. Just the consistency may be a little different that yogurt.

It's the Microbiome Stupid

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