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Wednesday, December 14, 2011

How coffee may affect gut bacteria

There’s no shortage of folk wisdom about coffee and the gut. I was at a meeting once where someone put it memorably: “Coffee makes you poop, right?” Yet surprisingly, very few studies to date have examined how coffee impacts the workings of the digestive system. Caffeine gets a lot of attention, but not the whole drink – which, by the way, contains more than a thousand compounds.
Instant Coffee, by Habib.mhenni (Own work) [GFDL ( or CC-BY-SA-3.0-2.5-2.0-1.0 (], via Wikimedia Commons

A 2009 study set out to answer the question of how coffee affects the intestinal microflora. Now, if I were going to do this kind of study I would probably use ground coffee, which is the kind consumed by the vast majority of coffee-drinkers. But this study used instant coffee. Why might that be? 

The answer is found at the top of the paper, where it says the research was conducted by the Nestlé Research Center in Lausanne. Nestlé just happens to sell an instant coffee product like the one used in the study. So, okay, there may be a corporate interest here; if you study your own product, the results can't be generalized to other products. But let’s see what the study had to say.

The researchers put 16 subjects on a restricted diet (meant to cut out things like probiotics that could positively boost gut bacteria) for 3 weeks, then had them continue the restricted diet for 3 more weeks while they added 3 cups of instant coffee per day, made with hot tap water (mmm, delightful). Fecal samples were collected before and after the consumption of coffee. No control group was used.

After analyzing subjects’ fecal bacteria, researchers found that the coffee had no major impact on the dominant bacterial groups. Gut-friendly Bifidobacterium species, however, increased in 12 of the 16 subjects. Not all people increased their “Biff” numbers equally, though; those with the lowest initial levels showed the greatest increase over the study period.

The other four subjects, by the way, decreased their levels of Bifidobacterium species over the study period. So 25% of the subjects didn’t show the expected pattern. This was not discussed at length by the researchers, but I think it deserves mention. These could have been subjects with different genes, or with something else going on in their digestive systems.

So there we have it: instant coffee may or may not increase Bifidobacterium species in the gut. A little wishy-washy, maybe, but I have to say I have a fondness for studies like this which get subjects to consume an intact food or drink rather than an isolated compound – in this case, a cup of coffee rather than a sachet of caffeine, say. Because if the results are conclusive, they can be more directly applied to real life.

But I do understand that researching whole cups of coffee poses a kind of dilemma to the scientific mind: after reading this study, the next question is, “But what part of the coffee affected the Bifidobacterium species?” This study doesn’t provide the means to find out. Researchers rightly didn’t comment on which of the coffee’s active ingredients may have affected the gut bacteria, though they did say coffee is full of soluble fiber and phenolic compounds which are well used by the microbiota.

I’m certainly not going to become an instant coffee drinker now that I’m armed with this information – I know about a hundred other ways to increase my gut’s levels of good bacteria. (Fermented sauerkraut, anyone??). But if you happen to be a person who already drinks 3 cups of Nestlé instant coffee every day, hot and fresh from the tap, this study might give you a warm and fuzzy feeling that you’re doing alright by your gut.

Jaquet M, Rochat I, Moulin J, Cavin C, & Bibiloni R (2009). Impact of coffee consumption on the gut microbiota: a human volunteer study. International journal of food microbiology, 130 (2), 117-21 PMID: 19217682


  1. Coffee alters the flora of my mouth; hard to imagine that not extending south. I am a religious tongue scraper. And yet every day after a few packets of instant coffee I get this plaque buildup on my tongue as thick as a bandaid. I scrape immediately.

    I specifically searched for "coffe affect flora". NIce result.

    I drink lots of caffeinated instant coffee. The real stuff has side effects I can't handle. Packets are a lesser of evils... don't know why. They are fresher than even the first serving from a large container.

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  3. I had no idea about this, I don't drink coffee although I love it, I have Interstitial cystitis and i find it isn't helpful.
    I found your blog from Alive article you wrote about sweeteners and I actually emailed a question, I will enjoy folloing your blog very much.

  4. I meant to also add, YUK! Why would they do a test study with instant coffee made from hot tap water, are there people who actually drink it this way, if there are I obviously don't get out and about enough because its a first for me.It does nothing to increase my confidence in the study preparing it this way, studies should carried out on the general public of whom I feel I am one, I would never ever drink tap instant coffee prepared from tap water.I hope they paid the subjects well,

  5. This is promising news, especially to a coffee drinker/fermenter like me! Great article Kris!

  6. So first they put them on a diet that removed their gut bacteria, then they found coffee did not significantly alter their gut bacteria. Genius!