As for recs on how to improve your microbiome generally: organic food, at least for anything containing sugar, dairy/eggs, meat, beans/grains/potatoes, and oils apart from olive/avocado/nut oils.
Other than that: Depends what you're trying to do! Lose weight? Build muscle? Poop more? Poop less? I once got pitched a question by a trainer who works with a bunch of NFL teams, being like "Why is like, every player on this one team glycine deficient?? They have the healthiest diet plan of any team out there and their protein intake is the same, but they have to drink crazy amounts of bone broth to stay in the normal range for glycine".
Well, it turns out that their healthy diet plan involves a lot of polyphenols and flavonoids, which—yeah, they're good for your gut bacteria, but the bacteria break down those polyphenols into benzoic acid, which your body clears by sticking a glycine onto it so you can piss it out.
So that kinda thing has me wary of making general recommendations like "eat more polyphenols!" because you need a lot of glycine to build muscle!
They're good! I'm just sayin' organic vs. conventional doesn't matter that much for things harvested live, or harvested in a way where the plant it comes from stays alive. So fruits, nuts, and anything off a tree is usually fine. Rice too :)
The # of age-adjusted deaths due to obesity correlates with amount of roundup in the food with an R of 0.96 and a p value < 10^-8.
I've been meaning to publish a guide of which foods it matters to eat organic for and which it doesn't, but as a general rule, fresh fruits and vegetables are fine to buy conventional. Everything else (except maybe olive oil) get organic (as in "USDA-certified, has the little circular seal on it". Don't be deceived by "all natural" or "non-GMO"). Wish there were an easier (and cheaper) answer, but this is the heart of it for a lot of people.
I lift weights, and at the moment to help get my calories up I drink Dextrose and a lil bit of glutamine, because it seemed to me from the numbers and some arcane looking diagrams I inspected that a) glutamine is the most abundant amino acid in the body b) we need a lot of it c) during exercise levels tank and d) I wanna make sure I don't need to break down muscle to get it.
I tried some BCAAs but they were so bitter I decided against that. Would glycine be a good one to add too? I don't like eating things that taste bad, I prefer to trust my taste buds + instinct. I eat a lot of organic veggies.
In general, getting enough readily available protein is probably the hard part. Do you do fish? Bulk Supplements has a hydrolyzed fish collagen which is very high in glycine (and doesn't taste that bad; a bit like unflavored gelatin but it can be made tasty with some lemon and honey)
Other than that: Beta-alanine.
It's the rate-limiting factor in the biosynthesis of carnosine, which is a big part of your body's natural Muscle Juice. Some people take carnosine directly, but it's way more expensive and the beta-alanine is the part that works.
Be aware: eating large amounts will cause a weird tingling sensation a while later.
Picked up this info from a former olympic athlete (pole vaulting, I think?) which makes me think it's a good tip. The guy now has Parkinson's...I don't think that's why, but figured I'd share in the interest of full disclosure. (There's no evidence that it increases the risk of PD, but I don't think anyone's done the long-term study, and I also don't really understand why it gives you skin-tingles.)
I've also heard that creatine is really worth it. Basic, I know, but there's a reason it's popular!
Ahaha I heard about the tingling, I was already curious about alanine because I thinkI saw it's one of the amino acids most abundant in muscle fibers. I guess beta-alanine is a form of that? I'm a bit cautious about a skin tingling effect and parkinson's because I've had antipsychotic induced akathisia in the past and I'm nervous of doing anything that might tickle those pathways. I do have fish sometimes - but generally trying to minimize my impact there, is getting straight glycine going to be significantly worse?
Also I want to hear more about my body's natural muscle juice...
More so "ethical" reasons - I prefer to avoid eating things where, if I were to think about the whole process of how it came to be on my plate, I would feel dread or horror and repress this knowledge. Slaughterhouses are naturally up at the top. Someone line-fishing a fish might be lower down, but I imagine most fish is more industrial.
So not environmental exactly, a combination of factors, and I'm prone to overlooking a lot and eating lots of cake.
Yet another fantastic article by you. You have any idea how long we'll need to wait for probiotics to reach the market that handle something like low testosterone or the inability to read a book?
I could have one for you next month lol, but on the market generally? Probably years. There are so many moving parts: relatively few manufacturers who can do anaerobes at industrial scale, shelf life issues since nobody is willing to do the obvious thing and sell 'em frozen as liquid. Hard to muster the "political will" for it in a company, because if you're selling it as a probiotic you can't make substantial claims about this kinda stuff without running expensive clinical trials.
As always, title of the blog applies if you're really desperate: find your healthiest friend, format your hard drive, and do a clean install, so to speak.
You think private microbiome therapies could be on the radar soon? Looking at your answer about having one available next month. I realize that was a joke, still curious if you've seen any interest in that regard.
For precision stuff like this? I know there's plenty of demand, and I can hook you up with a guy in the US who's home-brewing Faecalibacterium prausnitzii and a couple other species that might be helpful. Generally, though, giving someone a new bacterium—even if it should be perfectly safe in theory—is a weird risk, and the institutions where you acquire the knowledge necessary to do this stuff right (i.e. a PhD program) universally select for risk-averse people who are good at following rules and "coloring inside the lines", so there's a shortage of people out there who have both the skill and the will.
I'd love to do it, but it'll probably take a mil in startup cost.
Know anyone who'd be able to fund something like that?
What a great read- thanks! I've just discovered your work and I'm eager to read your other essays. I'm curious: what's the name of the bacteria that prevent your cells from making cortisol? I've never heard of this phenomenon.
Butyricicoccus desmolans! HSDH gets you 11β-Hydroxyandrostenedione, which converts to 11-ketoandrostenedione in the adrenals, which is also known as adrenosterone. Adrenosterone is apparently an inhibitor of human 11βHSDH1, which turns cortisone (inactive) to cortisol.
I recently discovered zbiotics which are probiotics engineered to produce the enzyme that breaks down acetaldehyde, (Alcohol bad bad thing). Your post made me think about Tongkat Ali, which is shown to significantly increase testosterone levels in men. Perhaps Tongkat Ali is a food preferred by the bacteria that produce glucuronidase enzymes?
If I really want to science the shit out of my gut where should I start? I did the Thorne biome poop test and got recommendations and trying them but I want to go deeper. Not some "one size fits all" but hiring a specialist who would be willing to work with me.
Could you offer any advice there? Do you consult? LOVE your blog, only recently discovered it and this was the first notification I got of a new post. I'm so happy you take your time to educate others.
Yeah, I could consult! Shoot me an email, sdskolnick@gmail.com and send me your results—curious to see what Thorne's output looks like. A friend sent me their Viome results and I was appalled to find out they don't give relative abundances.
I think that Abstract 54 in the above document may be the unpublished 'bacteria make allopregnanolone' paper that the author mentions in reference 4. I would like to see a copy of this when it's published.
SUPER SLEUTH! That's the one. I've been in touch with the author but their supervisor is holding up publication on the result for some reason. I'll let you know when it comes out.
Restore your minerals and you can make hormones that work. Nearly 50% of the hormones and neuropeptides require Alpha-amidation for proper functioning. That requires copper and ascorbate. Many minerals are bound by glyphosate but copper is preferentially bound and difficult to access. Without minerals we can’t make enzymes or peptides. Our gut bacteria are key to this process as well.
Extra-interesting to read as someone who, uh, values my estradiol levels. Don't suppose you have any actionable advice for those Bacteroides, or the testosterone-degraders? Asking for a friend.
I've never been to the hospital, so the only intentional exposure to antibiotics I've gotten has been the occasional Strong Stuff for recurring bronchitis...will have to think extra hard in the future if that's worth the potential endocrine risk. The plastics thing is kinda weird too. Like, on the one hand, it shouldn't be a *good* idea to stuff myself full of pseudoestrogens via BPA or whatever the current alarm du jour is. But maybe I can be a little less paranoid about avoiding heating stuff in plastics, etc, if there's some upside too. (At least when taste isn't a factor. Maternal family line can "taste plastic" if something's heated on the wrong kind of plastic the wrong way, and I picked that up too. Or we think we can, anyway.)
Nothing I'm comfortable recommending right now; estradiol and testosterone are so similar structurally, AND so similar to e.g. the mineralocorticoids that regulate kidney function, that it's a risky pathway to play with. Also, most of the things that eat 'em are nasty, like Mycobacterium.
BUT, there *is* something to the "soyboys" thing — if you have the right bacteria.
Equol is an estrogen receptor β agonist produced by the microbiome from isoflavones found in soy and red clover, but only some people have the bugs to produce it in substantial quantities. If you have any at all, you can encourage them by eating it regularly (just be sure to get organic, conventional soy is subject to some serious chemical abuses.)
Oh, so it's not just an overblown popsci culture war* meme after all, that's interesting. I actually don't care that much for soy anymore after being raised on it (weird for an Asian, I guess), but this is worth an Experiment For Science. Agreed that a lot of low-quality soy flooded the market back when Westerners were getting really into it, which was inevitable, but I think also counterproductive in that it gave a bad first impression. Keep running into acquaintances who are like "oh I'm soy-sensitive" and I can't help but think it's cause they only ever ate the cheap adulterated stuff. Now they're all off doing...nutmilks or whatever.
I did read that post, and mostly came away thinking it'd probably be extra good for my health to be less poor. The grocer I work for is notorious for plasticizing *everything*, so the stuff's difficult to avoid. Could shop elsewhere, but passing up the hefty employee discount is...not impossible financially, yet a large burden.
At some point a lot of the OG crappy black plastic trays switched over to some kind of supposed plant-based alchemy thing (still wrapped in plastic, ofc), which per your columns I treat with equal distrust. Have to admit some envy for coworkers happily microwaving stuff in the tray without a care though, it sure looks convenient. Oh, to be naive again. (People think I'm weird for always eating out of personal glassware with my own utensils, and it's hard to explain why without sounding a little unhinged. It's not really because the communal sink is disgusting, that's just a plausible cover...)
So fascinating. Everytime you post something I rejoice. Love your writing.
Aside from the Natto post (which has changed my life), do you have other wierd recommendations on how to improve your microbiome?
That's what I like to hear!!
As for recs on how to improve your microbiome generally: organic food, at least for anything containing sugar, dairy/eggs, meat, beans/grains/potatoes, and oils apart from olive/avocado/nut oils.
Other than that: Depends what you're trying to do! Lose weight? Build muscle? Poop more? Poop less? I once got pitched a question by a trainer who works with a bunch of NFL teams, being like "Why is like, every player on this one team glycine deficient?? They have the healthiest diet plan of any team out there and their protein intake is the same, but they have to drink crazy amounts of bone broth to stay in the normal range for glycine".
Well, it turns out that their healthy diet plan involves a lot of polyphenols and flavonoids, which—yeah, they're good for your gut bacteria, but the bacteria break down those polyphenols into benzoic acid, which your body clears by sticking a glycine onto it so you can piss it out.
So that kinda thing has me wary of making general recommendations like "eat more polyphenols!" because you need a lot of glycine to build muscle!
Are you saying olive/avocado/nut oils are good or bad?
That's fascinating about glycine. I like eating vientnamese pho because the good ones get their broth from overnight cooking with bone.
They're good! I'm just sayin' organic vs. conventional doesn't matter that much for things harvested live, or harvested in a way where the plant it comes from stays alive. So fruits, nuts, and anything off a tree is usually fine. Rice too :)
And what would you recommend for someone trying to improve gut while trying to lose weight?
Eat organic.
The # of age-adjusted deaths due to obesity correlates with amount of roundup in the food with an R of 0.96 and a p value < 10^-8.
I've been meaning to publish a guide of which foods it matters to eat organic for and which it doesn't, but as a general rule, fresh fruits and vegetables are fine to buy conventional. Everything else (except maybe olive oil) get organic (as in "USDA-certified, has the little circular seal on it". Don't be deceived by "all natural" or "non-GMO"). Wish there were an easier (and cheaper) answer, but this is the heart of it for a lot of people.
What would you recommend I eat if
- I want to build muscle
- I don't eat meat or dairy
I lift weights, and at the moment to help get my calories up I drink Dextrose and a lil bit of glutamine, because it seemed to me from the numbers and some arcane looking diagrams I inspected that a) glutamine is the most abundant amino acid in the body b) we need a lot of it c) during exercise levels tank and d) I wanna make sure I don't need to break down muscle to get it.
I tried some BCAAs but they were so bitter I decided against that. Would glycine be a good one to add too? I don't like eating things that taste bad, I prefer to trust my taste buds + instinct. I eat a lot of organic veggies.
In general, getting enough readily available protein is probably the hard part. Do you do fish? Bulk Supplements has a hydrolyzed fish collagen which is very high in glycine (and doesn't taste that bad; a bit like unflavored gelatin but it can be made tasty with some lemon and honey)
Other than that: Beta-alanine.
It's the rate-limiting factor in the biosynthesis of carnosine, which is a big part of your body's natural Muscle Juice. Some people take carnosine directly, but it's way more expensive and the beta-alanine is the part that works.
Be aware: eating large amounts will cause a weird tingling sensation a while later.
Picked up this info from a former olympic athlete (pole vaulting, I think?) which makes me think it's a good tip. The guy now has Parkinson's...I don't think that's why, but figured I'd share in the interest of full disclosure. (There's no evidence that it increases the risk of PD, but I don't think anyone's done the long-term study, and I also don't really understand why it gives you skin-tingles.)
I've also heard that creatine is really worth it. Basic, I know, but there's a reason it's popular!
Ahaha I heard about the tingling, I was already curious about alanine because I thinkI saw it's one of the amino acids most abundant in muscle fibers. I guess beta-alanine is a form of that? I'm a bit cautious about a skin tingling effect and parkinson's because I've had antipsychotic induced akathisia in the past and I'm nervous of doing anything that might tickle those pathways. I do have fish sometimes - but generally trying to minimize my impact there, is getting straight glycine going to be significantly worse?
Also I want to hear more about my body's natural muscle juice...
When you say "impact", do you mean that you avoid meat+dairy for environmental reasons?
More so "ethical" reasons - I prefer to avoid eating things where, if I were to think about the whole process of how it came to be on my plate, I would feel dread or horror and repress this knowledge. Slaughterhouses are naturally up at the top. Someone line-fishing a fish might be lower down, but I imagine most fish is more industrial.
So not environmental exactly, a combination of factors, and I'm prone to overlooking a lot and eating lots of cake.
Yet another fantastic article by you. You have any idea how long we'll need to wait for probiotics to reach the market that handle something like low testosterone or the inability to read a book?
I could have one for you next month lol, but on the market generally? Probably years. There are so many moving parts: relatively few manufacturers who can do anaerobes at industrial scale, shelf life issues since nobody is willing to do the obvious thing and sell 'em frozen as liquid. Hard to muster the "political will" for it in a company, because if you're selling it as a probiotic you can't make substantial claims about this kinda stuff without running expensive clinical trials.
As always, title of the blog applies if you're really desperate: find your healthiest friend, format your hard drive, and do a clean install, so to speak.
You think private microbiome therapies could be on the radar soon? Looking at your answer about having one available next month. I realize that was a joke, still curious if you've seen any interest in that regard.
For precision stuff like this? I know there's plenty of demand, and I can hook you up with a guy in the US who's home-brewing Faecalibacterium prausnitzii and a couple other species that might be helpful. Generally, though, giving someone a new bacterium—even if it should be perfectly safe in theory—is a weird risk, and the institutions where you acquire the knowledge necessary to do this stuff right (i.e. a PhD program) universally select for risk-averse people who are good at following rules and "coloring inside the lines", so there's a shortage of people out there who have both the skill and the will.
I'd love to do it, but it'll probably take a mil in startup cost.
Know anyone who'd be able to fund something like that?
I wish I knew someone, if I did I would honestly get that person to fund your ideas as this is something that people will buy.
Now, what you're telling about the guy in the US who's growing species on his own. Is he selling?
Friends & family right now, I'm trying to convince him to take it commercial. Shoot me an email if you're in the US
Hey Stephen, I'm interested in this as well and also in the US. Could I get in the loop as well?
What a great read- thanks! I've just discovered your work and I'm eager to read your other essays. I'm curious: what's the name of the bacteria that prevent your cells from making cortisol? I've never heard of this phenomenon.
https://pubmed.ncbi.nlm.nih.gov/28314858
https://ars.els-cdn.com/content/image/1-s2.0-S0303720721000332-fx1_lrg.jpg
Butyricicoccus desmolans! HSDH gets you 11β-Hydroxyandrostenedione, which converts to 11-ketoandrostenedione in the adrenals, which is also known as adrenosterone. Adrenosterone is apparently an inhibitor of human 11βHSDH1, which turns cortisone (inactive) to cortisol.
Thanks! That is the craziest thing I've read today! Wow.
I recently discovered zbiotics which are probiotics engineered to produce the enzyme that breaks down acetaldehyde, (Alcohol bad bad thing). Your post made me think about Tongkat Ali, which is shown to significantly increase testosterone levels in men. Perhaps Tongkat Ali is a food preferred by the bacteria that produce glucuronidase enzymes?
If I really want to science the shit out of my gut where should I start? I did the Thorne biome poop test and got recommendations and trying them but I want to go deeper. Not some "one size fits all" but hiring a specialist who would be willing to work with me.
Could you offer any advice there? Do you consult? LOVE your blog, only recently discovered it and this was the first notification I got of a new post. I'm so happy you take your time to educate others.
Yeah, I could consult! Shoot me an email, sdskolnick@gmail.com and send me your results—curious to see what Thorne's output looks like. A friend sent me their Viome results and I was appalled to find out they don't give relative abundances.
I am interested in a consult too! Your blog is fascinating. Just got my mapping done with a lab in Australia.
are you still posting? got here via ACX
Yes!! I've been unbelievably busy for the past year but in an interval now where I should have more time to write.
https://bostonbacterial.org/wp-content/uploads/BBM2022_Abstract_Book_v5.pdf
I think that Abstract 54 in the above document may be the unpublished 'bacteria make allopregnanolone' paper that the author mentions in reference 4. I would like to see a copy of this when it's published.
SUPER SLEUTH! That's the one. I've been in touch with the author but their supervisor is holding up publication on the result for some reason. I'll let you know when it comes out.
https://www.sciencedirect.com/science/article/abs/pii/S0092867424005142
Restore your minerals and you can make hormones that work. Nearly 50% of the hormones and neuropeptides require Alpha-amidation for proper functioning. That requires copper and ascorbate. Many minerals are bound by glyphosate but copper is preferentially bound and difficult to access. Without minerals we can’t make enzymes or peptides. Our gut bacteria are key to this process as well.
I spent time looking at Aldercreutzia equolificians a while back when i spotted in our Parkinson’s samples.
Extra-interesting to read as someone who, uh, values my estradiol levels. Don't suppose you have any actionable advice for those Bacteroides, or the testosterone-degraders? Asking for a friend.
I've never been to the hospital, so the only intentional exposure to antibiotics I've gotten has been the occasional Strong Stuff for recurring bronchitis...will have to think extra hard in the future if that's worth the potential endocrine risk. The plastics thing is kinda weird too. Like, on the one hand, it shouldn't be a *good* idea to stuff myself full of pseudoestrogens via BPA or whatever the current alarm du jour is. But maybe I can be a little less paranoid about avoiding heating stuff in plastics, etc, if there's some upside too. (At least when taste isn't a factor. Maternal family line can "taste plastic" if something's heated on the wrong kind of plastic the wrong way, and I picked that up too. Or we think we can, anyway.)
Nothing I'm comfortable recommending right now; estradiol and testosterone are so similar structurally, AND so similar to e.g. the mineralocorticoids that regulate kidney function, that it's a risky pathway to play with. Also, most of the things that eat 'em are nasty, like Mycobacterium.
BUT, there *is* something to the "soyboys" thing — if you have the right bacteria.
https://www.mdpi.com/2072-6643/11/2/433
Equol is an estrogen receptor β agonist produced by the microbiome from isoflavones found in soy and red clover, but only some people have the bugs to produce it in substantial quantities. If you have any at all, you can encourage them by eating it regularly (just be sure to get organic, conventional soy is subject to some serious chemical abuses.)
Oh, so it's not just an overblown popsci culture war* meme after all, that's interesting. I actually don't care that much for soy anymore after being raised on it (weird for an Asian, I guess), but this is worth an Experiment For Science. Agreed that a lot of low-quality soy flooded the market back when Westerners were getting really into it, which was inevitable, but I think also counterproductive in that it gave a bad first impression. Keep running into acquaintances who are like "oh I'm soy-sensitive" and I can't help but think it's cause they only ever ate the cheap adulterated stuff. Now they're all off doing...nutmilks or whatever.
*politicized microbiome = Cultured War
Oh that's good. I'm putting that one in the pocket with "bowel movement".
also: probably still avoid the plastics.
https://stephenskolnick.substack.com/p/the-thousand-secret-ways-the-food-f96
I did read that post, and mostly came away thinking it'd probably be extra good for my health to be less poor. The grocer I work for is notorious for plasticizing *everything*, so the stuff's difficult to avoid. Could shop elsewhere, but passing up the hefty employee discount is...not impossible financially, yet a large burden.
At some point a lot of the OG crappy black plastic trays switched over to some kind of supposed plant-based alchemy thing (still wrapped in plastic, ofc), which per your columns I treat with equal distrust. Have to admit some envy for coworkers happily microwaving stuff in the tray without a care though, it sure looks convenient. Oh, to be naive again. (People think I'm weird for always eating out of personal glassware with my own utensils, and it's hard to explain why without sounding a little unhinged. It's not really because the communal sink is disgusting, that's just a plausible cover...)