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Habitual coffee intake shapes the microbiome, modifies physiology and cognition

(www.nature.com)

After habitually consuming caffeine (not in coffee form) daily, usually multiple times a day, for more than a decade, a horrible mental health incident happened to me that forced me to stop it for a while. Afterwards I didn't resume the habit, and so I no longer have a tolerance.

This has let me evaluate what caffeine does with fresh eyes, so to say, because I can now consume it occasionally while having many non-caffeinated days to compare to. It's a profoundly psychoactive substance and does a lot of things to cognition. I guess I have decided I don't enjoy how it feels, having previously been dependent on it.

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Quitting caffeine after decades of use was a bit of a mixed bag for me in the short term, but positive in the long term.

Going caffeine-free made it much easier to lose weight as I have far less cravings for high carbs and sugar now, presumably this is related to the impulsivity impact talked about in the paper.

Going caffeine-free also made me very depressed for a while with severe anhedonia, this lasted way longer (like 3-4 months) than one would generally expect for caffeine withdrawal symptoms.

I had seemingly become so used to the increased dopamine signaling while buzzed on caffeine that my brain was a mess for a rather extended period of time as it got used to not having it.

Overall I view quitting as a positive for me, but I'd warn anyone thinking about doing it to do it carefully and closely monitor their mental health. AFAIK the impacts of quitting can be quite different for different people, so my experience may differ than that of others, but I had no idea how much of a (temporary) mental health crash quitting caffeine could cause until I experienced it.

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I experienced a similar anhedonia when quitting caffeine. I don't think the caffeine itself was the problem, I think it was just helping a lot more than I knew with the inertia of circling the pit without tottering in.

Turns out I needed stimulants from time to time, just not that one.

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What stimulants have you landed on? And do you feel they're better for you?

I'm pondering getting a coffee machine at home. 400 EUR is not a sizable investment and one I'd have forgotten about it 3 months but I'm getting cold feet when it gets to committing.

Americano coffee definitely picks me up and is a full net positive for me. But that's only if I drink 2-3 times a week. Not sure how it's going to be if I start getting it every day.

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I'm almost exactly 1 year coffee-free (not caffeine free, but significantly less because tea is much less addictive for me).

Also positive in the long-term for me. Fewer digestive issues, less spiky dopamine sensitive or impulsiveness and performance during the day, better memory. I wish it weren't so.

But damn was the 3-6 months of anhedonia awful. I still feel pangs of it.

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> Going caffeine-free made it much easier to lose weight as I have far less cravings

That's surprising to me. In my case one of the reasons I discontinued it (emotional effects aside) was mild but consistent weight loss. The stimulant part of the effect seems to suppress my appetite quite effectively although at least part of that is likely indirect due to sustained task focus leading me to skip meals.

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You may have naturally low dopamine production or release (or low ATP or GTP). Everyone will react differently because genetics so you are right, everyone needs to be mindful of their reaction.

You might want to look at this pathway, and the enzymes, and the cofactors for these enzymes:

https://www.researchgate.net/profile/Pingyuan-Gong/publicati...

Tyrosine 3-monooxygenase (TH) needs Iron

Aromatic-L-amino-acid decarboxylase (DDC) needs B6

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I've had the same experience. Caffeine is super addicting, the ritual & habits surrounding it is a potent pull. For myself, it makes me erratic, impulsive, more reactive and agitated. One cup a day puts me on edge, makes me sweat more, makes me more intolerant, makes everything feel too slow. It such a sneaky drug and it can really get under your skin without you realizing how much it changes you.
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I don't have the same experience, and I drink one cup of coffee (270 ml) almost every day. No agitation, no impulsiveness. I can drink coffee in late evening (let's say 8 pm) and sleep well. I guess I'm trying to say that we should not project our own experience on others, everyone is different.
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You have no baseline to compare to.
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My prior would rather be that people have wildly varying sensitivity to caffeine genetically. Some get panic attacks, some don't feel much.
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This happened to me with Pepsi cola.

But then I found out I can drink coffee just fine, even 5 cups per day.

Now I'm thinking it was the artificial sweetener.

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After habitually consuming coffee daily in large quantities for two decades, I had mental health incident, during which I drank twice the amount of coffee and it felt like water. After that incident I still drink previous amount of coffee, but feel much better, much more rested, on an upward trajectory and like I have finally managed to escape the swamp I dragged myself into over many years.

After reevaluating your comment and my experience I declare that coffee is not always a cause of mental health incidents, sometimes it might help people.

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Agree, I drink it a lot and then stop drinking it at least once a year for a few weeks, and for sure it's a different mode of mind, but can't really qualify it besides that I remember my thinking being softer, calmer and perhaps even "more correct" without coffee.

(But I never had any mental-health incidents, and I drink a lot of it, more than all people that I personally know.)

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For many years I go to the same vacation spot (kayaking in the most beautiful nature place I have seen) and go cold-turkey. I didn't notice any side effects of lack of coffee besides slower muddier thinking. After I go back and start drinking coffee, feel back to normal.

I also had a very big life altering mental health incident very recently, drank A LOT of coffee during and I feel it helped, now I am much more calm, "more correct" despite drinking coffee like before.

Based on this I posit that coffee is used by humans to offset unwanted mentality changes, not a cause of unwanted mentality changes.

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Consider yourself lucky...You are one of these mythical creatures who don't get migraines from caffeine withdrawal. My wife is the same.

When I quit I get splitting headaches that are way more severe than a typical tension headache. Completely debilitating without medication. Get them for a week or so (also get the muddier thinking but I could live with that).

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Coffee is a plant demon that created the western civilization as we know it today...
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I like this worldview. Prior to coffee, Europe was in the grip of the beer dwarves. Coffee demons took over and invented nationalism, capitalism and Keynesian economics.
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Obligatory recommendation for: Uncommon Grounds: The History of Coffee and How it Transformed our World by Mark Pendergrast

Fantastic book. I first encountered it...in a coffee shop :) Read a chapter and immediately bought the book for myself.

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At least the coffee demons aren't quite as bad as the amphetamine demons that produced Nazi Germany.
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Notably, the article is looking at coffee, both caffeinated and decaffeinated. There is a lot more to coffee than just caffeine...
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The overwhelming majority of the enjoyable coffee experiences are caffeinated. While there is good decaf out there it's not the norm, specially in smaller markets.
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I think they meant that coffee contains a lot of other compounds than just caffeine, which something like energy drinks or teas will not include. So you can't necessarily extend conclusions from a study on consumption of coffee to effects that other drinks that happen to include caffeine might have.

Edit: this is especially relevant here, as the study found similar effects in decaffeinated coffee drinkers. So the effects they observed, if real, are not related to caffeine.

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Yes, same here. I have schizoaffective disorder and realizing that caffeine affected my mental health so drastically was the beginning of my recovery journey 30 years ago. I can use caffeine now as a drug when I need it. Same with alcohol.
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I do believe a lot of it boils down to tolerance. I for example feel basically 0 effects, and drink it just because I like the taste (of a good one with milk, or exceptionally some good espresso / ristretto after big dinner).

I recently traveled and didn't have coffee for more than a week. No change I could feel, no craving, nothing. But one of my ex-gf was quite sensitive on many things, had frequent headaches, low blood pressure and coffee was helping with those visibly. So YMMV.

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How do you know that caffeine was the cause?
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This of course cannot be generalized, but withdrawal is quite noticeable for personal well-being in a positive way.
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Funded by the Institute for Scientific Information on Coffee (ISIC) — an industry body — which is a notable conflict of interest the authors disclose but don't extensively discuss
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It does not sound like an outcome that big coffee paid for it to be so:

Behaviourally, coffee drinkers exhibited greater impulsivity and emotional reactivity, whereas non-coffee drinkers demonstrated better memory performance.

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> It does not sound like an outcome that big coffee paid for it to be so:

Who said anything about big coffee? These guys might be a secret, anti-coffee organisation. /s

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it's the barley cartel.
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Ah yes, yet another in the long line of results which confirm our suspicion of water being wet to have been right all along. In this case it's something that anyone who has spent a significant amount of time around routine coffee drinkers and regularly consumed it themselves already took for granted.
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Do they though? Any data on that? Also, the highly caffeinated people might also be sleep deprived, which impacts memory and emotional regulation
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The data is in the linked paper. It's a direct quote from the abstract.
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deleted
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Please delete this comment. It’s embarrassing
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Maybe he forgot?
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Every damn time, for chocolate, coffee, and red wine "studies."
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I switched from caffeine (coffee) to theacrine (pills) and I like it so much more. I feel alert and focused without added anxiety. It doesn’t seem to affect my sleep at all. I really didn’t like how hard it was to quit coffee.

I don’t like that it’s a pill. I tried making my own theacrine drinks, but theacrine is so bitter that I never found one that I liked. I am still haunted by the chicory + theacrine drink I made…

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thirty-one participants were moderate coffee-drinkers (CD, i.e., people that usually consume between 3 to 5 cups of coffee per day).

3-5 is moderate? To me, 3 is already high.

Also, sample size is pretty low and they're all Irish.

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I agree. I'm deep into specialty coffee and I love making and drinking coffee a lot, but three cups is already higher than what I drink on a normal day. Also, most of the time when I go above this threshold, I drink decaf.
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Are the Irish unique when it comes to metabolizing coffee?
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I drink a small cup in the morning (like 250 ml) and 1-2 Moka pot espressos (like one shot). This typically happens between 7-10am. No more coffee after that most of the time. I like to keep it in the morning routine with breakfast. Green tea and water in my afternoons.

Personally, I don't feel any kind of "drug like" effects from this routine. I wonder about the strength of coffee people are drinking and the effects of drinking throughout the day rather than just the morning.

Anecdotally, during grad school I drank more per serving and throughout the day, and I certainly felt quite different than my current routine.

Like most things, I think people need to find some moderation/balance.

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This study is Irish, so I think they likely use 170ml cups? That means a normal mug of ~500ml is 3 cups.

Perhaps they even use US coffee cup size, which is 118ml?

Honestly, using an unit of measurement that varies from 118ml to 250ml in a scientific paper brings the whole paper into question.

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The reactions to your comment got me curious enough to check. The mug I use for coffee and tea holds almost exactly 400 mL when comfortably full and I used to drink 2 of those per day (across 12 hours or so). Based on that, personally I'd consider ~800 mL of black coffee to be on the high end of moderate consumption.
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> a normal mug of ~500ml

woa where is half a liter of coffee a "normal" portion?

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Okay, you'll definitely have to explain the NORMAL mug of HALF A LITER!
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Does it matter what size the cup is? Usually you get the same amount of coffee water + additional water/milk/whatever.
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I’m Irish.

A NORMAL mug of 500ml??? this is insanity to me

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I do 6-10 espresso cups per day, so 3-5 does sound very moderate.
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It depends on how much caffeine is in your cup. Rather than measuring the size of a cup, I would go by the amount of coffee, as in the weight of the beans, used to brew it. The actual amount of caffeine is not as easy to measure, and even for the same kind of beans, there is natural variation.

For a traditional Italian espresso, about 7g of coffee beans are extracted. For a third-wave double espresso, it's usually 18g or more.

In my opinion, 10x7g is a lot. 2x12g is more than enough for me.

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caffeine extraction is largely a function of time in contact with water. Espresso is quite quick brew, so has less caffeine than other brewing methods (yes, there are plenty of other factors)
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There is no realistic scenario where, no matter your extractions or bean selections, 6-10 shots of espresso a day is not an enormous amount of caffeine
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A grande americano at Starbucks is a 16 oz drink with three shots of espresso. Have one in the morning and one in the afternoon and you are at six shots of espresso. That doesn't seem all that enormous to me.
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75mg per shot = 450mg caffeine

That's a bit over the recommended limit of 400mg a day the Mayo Clinic, FDA, etc. recommend. Not sure it it qualifies as 'enormous' or not.

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That’s not normal. It’s like saying “I drink 6-10 beers a day so 3-5 is very moderate”
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I’m super interested in this sort of study! However, it looks like n=62 here, which I think weakens the results —they’re probably just useful as suggestions of possible effects. Also, any food is expected to have similar effects on the microbiome. They didn’t test caffeine in isolation. In some ways that’s better (I don’t consume caffeine in isolation), but in some ways that’s less useful (it’s possible you get similar results from many random vegetables)
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In 1995, NASA did spiders experiment. Caffeine is a siginificant impulsivity trigger. :)

https://rarehistoricalphotos.com/nasa-spiders-drugs-experime...

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Warning: those photos in the dot-com website are negative images, not the original black-on-white. Lousy with animated ad banners, too.

https://ntrs.nasa.gov/api/citations/20100033433/downloads/20...

Don't ask me why some blogger posted the PDF in 2013, and also don't ask me how English Wikipedia editors determined that a Wordpress blog is a "Reliable Secondary Source". I did locate the original on NASA's own website. Public Domain (USGov).

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LSD has unconnected strands in the air. I guess this is expected.
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The LSD and sleeping pills were not in the original study I believe. That might be an artists representation of the image at the bottom of the original study, which I remember showed the results in a single row.
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Nice web, Mr. Crack spider.
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> They didn’t test caffeine in isolation

But they did test both caffeinated and uncaffeinated coffee, and found the same effects in both, indicating that the effect is caused by something in coffee other than the caffeine

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Doesn't decaf also contain caffeine, just a lot less of it?
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Typical extraction yield is 18-20%. For a 20g dose that's 4g of material consumed, or about 30 individual beans.

I wonder if you could find similar effects with 4g or broccoli sprouts, or garlic, or ginger, or cumin seed, shiitake mushroom, seaweed, soursop leaf, or...

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Was this thread invaded by AI? Casually reading the first comments, 3 different users mentioned they had a recent "mental health incident" related to caffeine??

Search this page for "mental health incident"

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That doesn't seem even remotely surprising to me. Much of the readership here likely consumes inadvisable quantities of caffeine nearly every day and one of the most common side effects is anxiety followed closely by a number of other emotional perturbations.
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It would have been interesting to see if there was any difference relating to CYP1A2 (Cytochrome P450 1A2), the fast metabolizers and the slow metabolizers.
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Caffeine is an extremely potent drug.

It’s actually kind of crazy to think that a large portion of a country’s population could be “high” on it basically all of the time. And there is a huge industry in place for delivering said drug to as many people as possible by having it available on almost every street corner.

And that most people take a fairly non-chalant attitude to giving this drug to kids through sweet drinks that are primarily marketed to them as well.

The scale of it is kinda mind boggling to me.

Mind the nonsensical rant, I haven’t had my coffee yet this morning…

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That's normalising clean-ness (i.e. the state of being free of all psychoactive chemicals) perhaps too much.

The original humans adapted to a wide range of diets across the world (one reason why we're such a successful species), but most groups seem to consume mild psychoactives a lot (it's hard not to, so many wild plants have some level of activity) and seek out more powerful ones occasionally and for specific situations.

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This week as I tried to lower my coffee usage or stop altogether, I had dropped from 3 cups a day to 1. That one suddenly started to make me feel noticeably high, like a bump of cocaine in the morning. I realised that I craved it in the same way and it clicked for me - coffee is literally just a drug I like to take by myself and read the newspaper. It's no different. It's the first thing I think of in the morning because I'm addicted. Currently trying to go cold turkey.
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I went from 60oz per day to 36oz. I went from perpetually stimulated to basically on stimulated during work hours. Even with a minor cutback, I’ve noticed the change in potency of an individual dose as well.

My next goal is to cut back to one fully caffeinated drink in the moring and then doing decaf the rest of the day.

The ritualistic habit is the hardest thing to break for me. Also the social aspect of “let’s go for coffee” with friends, family, spouse etc…

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What's cool is this effect exists even in decaf coffee, as someone who primarily drinks decaf black, for flavor and for a good night's rest as I'm sensitive to caffeine.
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What kind of decaf coffee do you drink? There are differences between the cheap chemical Methylene way to create decaf coffee and the expensive co2 way to get rid of the caffeine.

https://cleanlabelproject.org/wp-content/uploads/CLP-Decaf-C...

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Is that methylene way even legal? It basically uses petroleum fuel in the process right? I assume it was outlawed a long time ago but that might be extreme naievete for US regulatory capability...
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https://www.thedecafproject.com/ (Dec 2024) let you order matching swiss water, CO₂, and Ethyl Acetate (sugar cane byproduct) decaffeinated coffee from the same batches of beans. The EPA banned methylene chloride earlier in that year, but because of toxicity to workers, not because of risk from the resulting coffee itself (and it looks like the FDA didn't ban it.) So I guess you couldn't make decaf with it in the US but you could probably still import and sell it?
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I don't buy the methylene processed ones, generally it's Swiss water processed or like you said the CO2 processed ones.
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I am not a coffee drinker, but I met with a friend at a cafe who said he was going to get a cup of insect poison, referring to coffee :)
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At least subjectively, coffee seems to help my memory. But maybe that's why I started drinking coffee?

I would probably drop coffee it was proven to have negative effects on memory.

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> But maybe that's why I started drinking coffee?

you don't remember why, do you?

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> The coffee provided was consumed with a quantity of hot water, milk, sugar chosen by the participant.

Could it be the sugar?

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I have not much followed the science of gut microbiome and psychology. Is this really going where this article is pointing? That we can tease out causation in foods and habits via gut microbiome towards behavior and psychology? Pretty rad.
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There's a decent amount of research going into the hormones that our GI biome produce and how it affects us. Our body has a few different biomes and they all seem to play somewhat important roles.
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Yeah there's nontrivial evidence that among other things, the complex community living inside you manipulates your brain.
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My psychiatrists agree that “hallucination” (in lay terms: “hearing voices” or “seeing things”) only refers to things that aren’t real.
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Coffee modifies physiology and cognition? You're telling me this for the first time.
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The paper is about previously unknown ways coffee affects the body.
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I was so surprised at this headline that I nearly leapt out of my chair!
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But it says it’s the same for decaf. That is more interesting
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Been treating coffee as caffeine with aroma. Any important points about coffee itself?
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Humans known since 45 minutes after first drink
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Would be real interesting to see a similar study on tea.
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I must be weird, but coffee (or caffeine) doesn’t really “wake me up” in the mornings and I could drink it in the night and still sleep well. Because of that I don’t drink coffee; I prefer tea
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I find that the effects can be pretty subtle, and if I'm already tired there's usually no coming back. What I think has worked best for me is to re-up on caffeine a few hours before I think I'll be tired, or around when a previous dose is wearing off. Also, if trying to stay awake, food and entertainment are also quite important. If I hit a point where I'm hungry, cold, and tired, and going to the kitchen to eat sounds like a chore, it's usually too late for me. When the bed's closer, it's hard to resist.

I've also noticed that I have a sort of natural energy in the morning. I think of it as being similar to how a seed has enough energy in itself to sprout and then get sunlight. It's probably so I can make myself eat and whatnot. I don't really need caffeine to "wake up" as much as I need it to stay awake later in the day, and even if I do have a coffee with breakfast, I'll often get tired before the normal day is over.

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I think this description is often associated with ADHD memes.

Falling asleep after a can of energy drink.

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tea also has caffeine, although in smaller quantities. Maybe you mean that you don't care so you go by taste, just specifying because there's a common misconception about tea not having caffeine.
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Some tea has caffeine, most has don't.
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all tea has caffeine unless it's decaf. some things that aren't tea are called tea casually, but they aren't tea, for instance peppermint "tea" is not tea. by the same logic that one would call peppermint a tea, one would have to call coffee a tea. and beef broth.
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That depends on culture. All camelia s. teas have it (green etc) but almost none of common herbal teas in Europe have it (chamomile, menta, sage etc.) They are not called casually teas.
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> They are not called casually teas.

are you saying chamomile isn't called tea but it's one of the teas without caffeine? if so that's very confused.

camelia sinensis is tea. when i said that other things are casually called tea, i mean that what chamomile tea, for example, ought to be called is a tisane or an herbal infusion. casually, people might call it a tea; some people are so casual about it that they think it actually is tea. but it isn't.

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Whatever the case, a cup of coffee is basically what kickstarts my day.
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Yes, well, nevertheless. Sip
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I only use caffeine or caffeinated beverages such as coffee at the most three times a week. And that's a heavy week for me.
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good thing I have claude to summarize this and quickly realized that sample size was small and nothing much new unless you are a microbiome researcher
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If the effect size is big small sample sizes does not matter as much as otherwise.

You really have to look at the power analysis and the sample size together.

Saying this as a general truth. I am not sure about the power of the method in this papper, i only read the abstract.

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> ... reintroduction triggered acute microbiome changes independent of caffeine.

This sounds interesting. I've never really considered the constituents of coffee other than caffeine and what unique effects they may bring.

I wonder if I would experience behavioral effects if I replaced my coffee intake with caffeinated non-coffee drinks or pills?

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Studies seem to indicate that coffee is at least as healthy, if not healthier than tea, and I have not heard this about caffeine specifically (aka the same effects coming from pills or energy drinks).

One fun fact: we still haven’t figured out why coffee makes us poop. We’ve studied every chemical in there and can’t seem to find a link, but the association is uh… well-known.

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>why coffee makes us poop.

That seems to vary wildly between individuals. It doesn't have that effect on me.

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The only good thing that keeps me from collapsing into a state of limbo is coffee and now, even that's bad (seems more like a mixed bag, but still)? Sigh.
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There have been positive and negative reports for a long long time. If coffee was going to kill us, I’d certainly have died in school!
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Don't fret. You're allowed to enjoy things that aren't part of the scientific reductionist longevity influencer lifestyle fad :)
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Nitpick: What you’re referring to is not scientific.
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Maybe I have some neurological issue or something but whenever I quit coffee I find it extremely difficult to maintain any kind of motivation to sit in an open plan office and code. Coffee makes me a worker bee, I can understand why employers give it away for free.

So, the coffee stays for now.

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Yeah, exactly. I can totally relate to this. I have actually monitored my productivity on an excel sheet and the days with coffee win by a large margin. I am not sure if it's withdrawal symptoms on the days without, though.
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Coffee in general is unreasonably healthy as a beverage. The overwhelming majority of science agrees it’s a quality health drink.
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Non-industry funded science?
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Relax. Tomorrow there will be a paper/article saying coffee is great for you.
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Did you know:

    By replacing your morning coffee with herbal tea, you can remove up to 87% of the little joy you still have left in your life.  /s
Keep the coffee buddy.
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Haha, that was a funny quote!
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"These findings reveal previously unrecognised effects of coffee on the microbiota–gut–brain axis, suggesting that microbiome profiles could potentially predict coffee consumption patterns", or, perhaps, just ask the patient?
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Could you elaborate on how to interpret your comment without it leading to anti-intellectualism?
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It was a joke
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You are missing the point.

If you can predict someone's coffee intake based on testing of their microbiome then you've proven that coffee intake has predictable effects on the microbiome.

The important part isn't predicting coffee use, it's just the proof that there's you can predict and perhaps control in the opposite direction leading to more research.

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