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Coffee Is Good for You—Unless It’s Not!

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Numerous studies have linked drinking coffee with positive health effects like reduced risk of obesity, diabetes, and heart disease. However, recent research suggests that the effects of coffee on health aren’t the same for everyone, and may depend on genetics and other factors.

slow caffeine metabolism
Many feel that coffee is an important part to the start of their day. istock.com/kyoshino

I love coffee—and I’m not alone.

Americans drink 400 million cups a day (yes, you read that correctly) and we spend $30 billion on it every year.

The good news is that there’s a lot of research that links drinking coffee with health benefits, including lower risk of cancer, Parkinson’s disease, obesity, diabetes, metabolic syndrome, and heart disease. I covered that research in detail in a recent podcast.

Here’s the bad news: while coffee is undoubtedly beneficial for some people, it may be harmful for others.

I talked about some of the factors, including sleep, stress, and intolerance to proteins in coffee beans, that determine individual response to coffee in another podcast a while back.

But there’s another important factor to consider: genotype.

Coffee is the primary source of caffeine for Americans. Caffeine is metabolized by an enzyme in the liver that is encoded for by the CYP1A2 gene. Unfortunately, about 50 percent of the population has a variant in the CYP1A2 gene that leads to slow processing of caffeine.

For these “slow metabolizers,” drinking coffee:

  • Is associated with a higher risk of heart disease (1)
  • Is associated with a higher risk of hypertension (2)
  • Is associated with impaired fasting glucose (3)
  • May not have the protective effects against some cancers that it appears to for “fast metabolizers” (45)

That said, in some cases coffee appears to be beneficial even for slow metabolizers. For example, caffeine is neuroprotective and reduces the risk of Parkinson’s disease in both slow and fast metabolizers. (6) Other studies have even shown that fast—not slow—metabolizers of caffeine may be at higher risk of bone loss. (7)

Is coffee good for you? That depends.

Adding to the confusion, many of the large, observational studies I reviewed in my podcasts found that the overall effect of coffee intake in the populations studied was positive. If 50 percent of people are at higher risk of disease from drinking coffee because of their genotype, then why isn’t this showing up in these epidemiological studies?

What are we to make of these conflicting data?

The most obvious conclusion is that it’s impossible to make a general statement about the health impacts of coffee. The answer to the question, “Is coffee good for me?” is: “It depends.”

This shouldn’t come as a surprise. If you’ve been following my work for any length of time, or you’ve read my book, you’ve probably heard me say, “There’s no one-size-fits-all approach when it comes to diet.”

The most recent research on nutrition, including these studies on coffee and caffeine, confirm that this is true. While we share a lot in common as human beings, we also have important differences: genes, gene expression, metabolic activity, gut microbiome, lifestyle, activity level, and numerous other factors will differ from person to person, and all of these will impact how we respond to a particular food (or beverage, like coffee).

For example:

  • There is wide variation in post-meal blood sugar among people eating identical meals, and diets that are personalized on the basis of dietary habits, physical activity, and gut microbiota are more successful than “standardized” diets. (8)
  • Response to low-carb and low-fat diets in overweight people varies considerably and may depend on their insulin sensitivity and other factors that are not yet fully understood. (9)
  • Caffeine consumed in the afternoon or evening significantly disrupts sleep in some people, but not in others. (10)

These studies represent the future of nutrition research. In fact, I’m quite sure that in a relatively short period of time we’ll consider the current notion that there’s a single, optimal diet for everyone as an outdated and ignorant idea.

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Another conclusion that we might infer from the conflicting data on coffee is that even within a particular genotype the effects are variable. In other words, some slow metabolizers might be adversely affected by caffeine where others aren’t, and the opposite might be true for fast metabolizers. This also makes sense because there are a huge number of factors above and beyond the CYP1A2 genotype that would influence how coffee and caffeine affect an individual, from their baseline diet to their stress levels and sleep to their gut microbiota. It’s also true that being a fast or slow metabolizer of caffeine isn’t binary (i.e., two possible speeds: fast or slow), but more of a spectrum (ranging from very slow to very fast).

Now that we’ve established that coffee and caffeine can be both beneficial and harmful, how do you know how it affects you? Here’s what I suggest:

  1. Listen to my podcast called Is Drinking Coffee Good for You? in which I discuss some of the non-genetic factors that determine individual response to coffee.
  2. If you haven’t already done this, titrate yourself off coffee (reduce your consumption slowly until you’re off it completely) and other sources of caffeine for at least 30 days. Then add it back in and see how you respond.
  3. Find out whether you’re a “slow” or “fast” metabolizer. You can get this kind of genetic data through companies like 23andme and SmartDNA. If you’ve done 23andme, log in, go to “My account,” select “Browse raw data,” and type “CYP1A2” into the “Jump to a gene” search box. Once on the search results page, find the rs762551 SNP. In the far right column, it will give your variant of that SNP. If you are AA, you’re a fast metabolizer. If you are AC or CC, you’re a slow metabolizer (with CC being slower than AC).

We live in exciting times. At some point in the future, we’ll be able to create much more precise nutritional recommendations based on our genotype and epigenetic factors, in addition to all of the other factors I’ve discussed in my book—such as health status, lifestyle, physical activity, and goals.

Right now, we’re only scratching the surface and still have a lot to learn. But we already know enough to stop asking questions like “Is coffee (or carbohydrate, fat, etc.) healthy” and start asking questions like “Is coffee (or carbohydrate, fat, etc.) healthy for me?”

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177 Comments

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  1. In the last six months my LDL has increased from 101 to 154. That is when I started drinking coffee. I have factor 5 and hypothyroidism as well. I find it odd that my LDL has increased since i started drinking coffee. I have normally 1 cup a day during the week and 2 cups a day on the weekends.

  2. I am A/C on 23&me a slow metabolizer. If I drink regular coffee it upsets my gut. Espresso is fine as it has less acid. I drink 3/4 decaf shot of espresso and get lots of energy for several hours. I have to be homeopathic about it and do this not every day. I guess given I’m a slow metabolizer that’s why a mostly decaf shot gives me such a boost. I’m about to try bulletproof again making it with mostly decaf and small amount of caff to see if the “crash” coming down part is easier. It’s hard to resist the energy boost. I didn’t drink coffee for 10 years before I found this formula that works for me

  3. Does anyone else get nighttime leg cramps from coffee and/or chocolate? I can generate cramps by consuming these things, especially if I take them in the evening, and can stop the cramps by going off them. The more nice, dark chocolate I eat, the worse the cramps. Just curious, as I have found little mention anywhere that others experience this cramping from chocolate or coffee. I have recently learned that I am a ‘slow metabolizer’ of caffeine.

    • I would guess your body is not getting enough magnesium. Most people get it through via their water supply. I’m retired but still enjoy putting in full days of very physical work that depletes my magnesium. I began to take Epson Salt baths and cramping would stop in 10-15 minutes. Now I take these baths regularly 1-3 times a week and cramping is a thing of the past.

      • Supplemental magnesium works amazingly well for restless legs also. Take some before bed, and after one or two nights, RLS will be a thing of the past.

    • After a serving or two of chocolate I get a crampy, “restless” leg thingy at night. I don’t drink coffee because of this and other sensitivities. Thanks for posting!

  4. I feel that I need coffee just to get up to the speed of non-caffeinated humanity. I drink about a cup after each meal, even dinner. It helps my digestion and seems to keep me from eating more. But I’m also careful, paying attention to how different roasts and brands affect me. I don’t like to feel too hyped up and always use cream (preferably) or half and half, and I always consume coffee with a meal that includes adequate protein and fat. A friend of mine, who knew someone in the coffee roasting business, once said that the darker the roast of the beans, the lower the caffeine. I have found this to be true and prefer darker roasts. It’s important to try different brands and then stick with the ones that make you feel good and not crazy. Feeling too nervous just doesn’t seem like a good thing for our bodies.

  5. For me, it seems that even different brands of coffee affect me differently. I could drink Folgers like water and never feel anything from it, but some of the Starbucks varieties are almost too strong and give me stomach problems. Its interesting to tinker and find what works.

    • Yes, Becky, I also get strong stomach reactions from some brands/blends. Consuming coffee with cream or half and half helps. I used to use 2% milk back in the old days of my low fat life, and I experienced far more problems, but still, I must continue to be careful and always have a meal first.

  6. Thank you very much for explaining the 23&me site. I took an introduction MOOC on DNA a while ago which helped me for a time, but I’ve forgotten what I learned and your article helped me get back there.

  7. From dbSNP, about 53% of persons of Euro ancestry are “fast” metabolizers on rs762551, which is used as a marker for both caffeine clearance and for phase 1 liver detox taken as a whole. 38% are “intermediate” and 9% are “slow” on metabolizing caffeine and on phase 1 liver detox generally.

    Compare genetics to actual function of phase 1 vs. phase 2 liver detox in present time with Doctor’s Data lab’s Hepatic Detox Profile, which can be gotten through health professionals or direct-to-consumer at directlabs.com: https://www.doctorsdata.com/resources/uploads/sample_reports/Sample%20Report%20Hepatic.PDF

    Genetically I’m a fast metabolizer on CYP1A2, rs762551, but very fast (99%ile) on phase 1 liver detox per the DD lab report. Fortunately my phase 2 is faster than average both genetically and functionally.

    Genetic and functional testing are complementary and, in my opinion, should be done together for best perspective.

    • HI Carol. Can you tell me how you’ve become so “gene literate”? I have my 23 and me raw data and some “translations” from Livewello and Nutrahacker. Would love to buy a book which could help me to understand.
      I am a slow metaboliser. Because I have been very ill, when I gave up caffeinated coffee, I totally crashed. Have spent 3 weeks in bed. Hard to believe that coffee is that powerful a drug!

      • The population/ethnic percentages in dbSNP for any given SNP, are linked in the 23andme raw data browse.

        I’ve been an avid student of genetics for 6 years now, autodidact, using pubmed, google (where you’re limited only by your imagination), genecards, entrez gene for gene aliases, snpedia, wikigenes, dbSNP and canonical biochemical pathways (I sometimes question these), and lots of observations. I came to biochemistry via genetics, at age 60. I like to cross-reference genetics with functional testing as a reality check. I think it’s dangerous to recommend based on genetics alone without relevant functional testing.

        Your own genetics are good place to start. Then begin to expose yourself to some of the topical SNP lists in LiveWello and comments in Promethease, for example. Survey the supplementary information in 23andme’s raw data browse feature for each gene and SNP.

        Most medical-related genetics reports and education should be considered historically preliminary and are nearly always inadequate, often misleading, with key information omitted, but these reports and education are the beginning of getting exposure to genes and SNPs. Don’t believe everything you hear and read. Rather, step back and reserve judgment until you’ve made enough of your own observations over time. Consumers are used to having everything handed to them on a silver platter, in a nice package all tied up with a bow. Don’t look for that with genetics, it’s a simplistic trap, but will appeal to most people.

        In my opinion, the subject of genetics is for natural systems thinkers, geeks who are also very patient over time, have learned how to be comfortable with ambiguity, devoid of habits like jumping to conclusions and emotionalism, who see information about a system as having intrinsic value with possible applications at some point or maybe never in their lifetime. In other words, surveying a system doesn’t necessarily have to be “actionable” to have value. The average consumer, doctors, and medical insurance companies want “actionable” items, else they see no value and so can’t justify the cost or time. There are more actionable items to be found in functional testing and personal experience. You can learn a lot about genetics from functional testing, finding where these mirror each other and where we find what we might expect to find, vs. where they don’t mirror each other and something else is contributing to a functional or experiential result.

  8. Have not done the gene thing but I’m well aware of drinking coffee after 10 a.m does a number on my sleep as does the consumption of white sugar or high fructose corn syrup products. My brother has the same problem. I can take or leave the coffee but it’s a social activity in the morning and I don’t like tea. As for the sugar once I get started on cookies, cake or sweets of any kind it takes a lot of discipline to knock it off again. I also feel rude when declining deserts when dining at friends. They should look at fast and slow metabolizing of sugars the way they did for coffee. We can do without both.

  9. I am CC, so slow metabolizer. So it comes as no surprise that even a cup with only an inch of coffee in it will get me jacked up. I have given up coffee except for decaf and even that has an effect. If I do indulge, even with decaf I awake with big bags under my eyes. Have not been able to figure out why, but maybe its due to the proteins you mention that some people have trouble with? Its like taking an aging pill, not pretty!

  10. Caffeine has absolutely NO effect on me. I drink tea usually, because I like it and its health benefits, and coffee occasionally, but I also don’t have any negative effects of suddenly going a few days without it. I’d love to know what it feels like to experience the “pep” and sharpness coffee gives people! And I’ve yet to meet anyone else like me. I must be a super-fast metabolizer? I did a little research myself and came to the conclusion that I must be high in an enzyme called CYP1A2 isozyme, which can be raised by eating lots of certain vegetables (which I do) but then why wouldn’t I meet a ton of other people with the same thing? I know loads of vegetarians, for example. What gives?

  11. Hi Wonderful Chris Caffeine inhibits COMT Therefore the suggestion is If you have SLOW COMT Limit coffee intake to one per day or preferably avoid caffeine all together esp if being treated for any Mood Disorder.
    Its all so complex and inextricably linked.We are glad to have people like you and Ben Lynch helping us. Thank you so much.

  12. I have been wondering about this since getting my 23andme results back, great article! I’m A,C. I was a moderate caffeine addict for years–I would brew a 4 cup moka pot of espresso every day, using half for an Americano in the morning, and the rest for an iced latte in the afternoon. However, my coffee consumption dropped to almost zero about a year ago while going through a period of stress. I just didn’t want it, and when I tried drinking coffee later, it made me jittery. Sometimes I even have a paradoxical effect from caffeine–I’ll brew a cup for a pick-me-up, and instead I feel completely fogged and lethargic before I even finish it.

  13. I have never been able to tolerate caffeine. It affects me for the next 3 days (following consumption of even just a 1/2 cup of regular coffee – not even Starbucks super caffeinated coffee). The affects that I have include intense migraine headaches for 2-3 days unless I have more caffeine) and/or jitters for that amount of time as though I am on speed (or imagine that it what it is like anyways!) I have always avoided caffeine. I will check into the DNA – so fascinating. And all these years I have been seen as an outcast!

    • It sounds like you’re sensitive to caffeine and the following 2-3 days are withdrawal symptoms. You’re not alone.

  14. I must be a fairly slow metabolizer; pretty sure my ex is a fast m. though. He always has to eat the minute he gets out of bed. No idea if that is related to genetics but…if I try to eat, I’d probably throw up – have to be up for at least a couple of hours before eating. Of course, I feel quite addicted to one modest cup in the morning (first thing I do upon waking almost) – fresh-ground dark roasted coffee made in an Aeropress. Having said all this, coffee makes me anxious esp. if I am already experiencing anxiety…..and this differs with the season. In spring, I have had to go to half or all decaff otherwise i can get pretty disregulated. And that’s from only ONE cup of coffee in the morning, with cream. The anxiety can last for hours. Especially if there are a lot of things “undone” like just before Xmas.. My two cents.

  15. I guess I must be a fast metaboliser as I can drink coffee at any time of the day or evening. In fact it has the effect of putting me to sleep in the evening, so if I cannot sleep on occasion I get up and make a small cup of coffee. Having said that I do only drink half strength coffee as never having used a sweetener – cannot keep sweet coffee down – I do not like the bitterness full strength coffee has. People are surprised when I tell them this as almost all say the opposite.

  16. I’ve found coffee useful in some situations. I’m prone to low periods around mid afternoon, and in winter this includes deep coldness and shivering not easily resolved by room temperature or adding clothing. I’ve started using a cup of coffee (organic, very dark roast) most afternoons in cold weather, and this seems to help combat the lethargy and cold. It’s also occasionally helpful for migraines. Interestingly I suffer from anxiety and sleep disturbance, but coffee doesn’t seem to aggravate either (although I don’t drink coffee after about 4 pm to help prevent further sleep disturbance).

  17. For me it seems that coffee itself is the trigger, not caffeine. I.e, it doesn’t matter if I drink caffeinated or decaf, I have the same uncomfortable response. On the other hand, I can drink tea and even natural sodas with caffeine.

  18. I went without coffee for a few months, but I got so depressed I couldn’t function. Coffee is the only effective anti-depressant I know of, and I’ve tried all the pharmaceuticals. I’m sure I’m a slow metabolizer because I can’t drink it past noon and expect to sleep that night. Other than that, no obvious side effects, and it restores my energy and desire to get things done. My one cup in the morning, regardless of risks, is totally worth it to me.

    • I’m the same way, but I know not to make it a habit because of the deleterious affects of long term caffeine on my body.

  19. Great article. I am A/A (fast metabolizer), which I have always known this because for the most part I can tell no difference from drinking a single cup of coffee to drinking an entire pot of coffee. I’ve always thought that was odd.

    Additionally, I can stop drinking coffee cold turkey (I drink several cups a day) and I never get headaches or have any other discernible symptoms of withdrawal either.

    We have a lot to learn.