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Is Coffee Good or Bad For the Gut?

If you’re like most Americans it’s likely you had a cup of coffee this morning. An estimated 2.25 billion cups of coffee are consumed everyday worldwide, and in America, coffee is the number one source of antioxidants in most people’s diets. 

The scientific community has done an excellent job compiling data on the impact of coffee on sleep, how we metabolize caffeine differently based on genetics, and even the impact of consuming coffee on uric acid levels.

However, when it comes to coffee and digestive health, there is a surprising dearth of research.

What follows is a run down of some of the best studies on coffee and the microbiome, but at the end of the day, this is an area where personal experience is paramount. Watch your individual reaction to drinking coffee. Is a cup of black coffee before breakfast hard on your stomach?

If it is, switch to tea, or abstain from caffeine altogether to keep acid reflux symptoms in check. 

Does coffee cause GERD and acid reflux? 

Gastroesophageal reflux disease, or GERD, is a common problem faced by millions of Americans, in which stomach acid flows in the wrong direction back into the esophagus. GERD is essentially chronic acid reflux and it can be triggered by poor diet.

It would seem logical that coffee, with its high levels of acidity, could cause GERD, but does this assumption pan out in the research?

Not according to a 2013 meta-analyses of 15 studies, which didn’t find an association between drinking coffee and GERD.

Do keep in mind that just because this meta-analyses didn’t find the link between drinking coffee and GERD, it doesn’t mean that coffee might not be contributing to your symptoms. Some people do find that caffeine makes their heart burn worse and most physicians recommend that those suffering from IBS avoid coffee altogether

Coffee gets things moving

In other words, coffee makes you poop by stimulating the colon.

The coffee “gets things moving” phenomenon is something most of us have observed first hand and don’t necessarily need a study to confirm, however, believe it or not, it has been studied.

A very small study of 12 people from 1998, which appeared in the European Journal of Gastroenterology and Hepatology, found that regular coffee stimulated the colon on a level very similar to what eating a meal does. In the 12 subjects studied, the authors found that regular coffee stimulated the colon 23% more than decaf coffee.

While we are all inclined to believe this study due to first hand experience, the study size was way too small to draw large conclusions. Part of the equation here is that coffee is consumed in the morning, and we are much more likely to have a bowel movement in the morning than at other times during the day. Yes, even when we use the bathroom is dictated to a degree by our circadian rhythm, so perhaps the time of day we drink coffee has more to do with that trip to the bathroom than the coffee itself. 

Drinking coffee can increase healthy Bifidobacterium species

Part of what makes for a healthy gut is complex carbohydrates making their way to the colon where they ferment and feed “good guy microbes” that, in turn, protect our digestive tract. Bifidobacterium are a genus of bacteria with a number of species that do exactly that – they feed on glucose and turn it into short chain fatty acids (SCFA) that line the gut wall and which we can use for energy. 1

Studies in infants have demonstrated powerful anti-inflammatory activity by bifidobacteria species that protect the gut wall from damage. 

John has written previously about his experience with a strain of Bifidobacterium called B. Longum BB536 in a past blog post, and Jennifer, a microbiome researcher on our team, wrote an excellent piece on the difference between Bifidobacterium and another “good guy” species of microbe that lives in our gut called Lactobacillus

Bifidobacterium vs Lactobacillus

 BifidobacteriumLactobacillus
Gram-positiveYesYes
Acid-producingAcetate, LactateLactate
Energy produced from 1 mol of glucose2.5 ATP molecules, 1.5 mol of acetate, 1 mol of lactate (R)
2 mol of ATP, 2 mol of lactic acid (R)
Diarrhea from E. coli, Salmonella, Shigella, Rotavirus, GiardiaB. lactis L-3, B. longum, B. bifidum (R)L. acidophilus L-1, L. bulgaricus 6, L. plantarum 24-4B, L. fermentum 1, L. brevis 1 (R)
Susceptible to antibioticsYesYes
Prevention of UTINo dataL. casei GR-1, L. rhamnosus GR-1, L. fermentum RC-14 and CRL 1058 (R) (R) (R) (R)
AnaerobicStrictly anaerobic, cannot live in the presence of oxygenAble to live in the presence of oxygen
MotileNoYes, in some species
OccurrenceIsolated from feces, rumen of cattle, sewage, human vagina, dental caries, and honey bee intestineNearly ubiquitous, found in environments where carbohydrates are available such as food, respiratory, GI and genital tracts of humans and animals, and in sewage and plant material

For our purposes here, suffice to say that Bifidobacterium are a type of bacteria we want to have populating our gut, and as it turns out, drinking coffee may play a small role in helping us achieve this aim. A small study of only 16 participants from 2009, which appeared in the International Journal of Food Microbiology, found that participants who drank instant coffee for 3 weeks saw an increase in beneficial Bifidobacterium species.

Coffee might help you absorb more antioxidants from food

One of the challenges of some beneficial antioxidants, like curcumin and glutathione, is that they are notoriously low in bioavailability.

Coffee contains an alkaloid called theobromine which as been shown in rat studies to increase the absorption of some polyphenols. 2 While studies like this are interesting, we can’t put much stock in them due to the fact that the data thus far has only been compiled in rats. Having said that, coffee itself is a great source of polyphenols, so there is a health benefit from that perspective. 

Heavy coffee use might be detrimental to the microbiome 

In this interesting study from 2020, which appeared in the peer reviewed Journal Nutrients, researchers evaluated the microbiomes and biomarkers of 147 subjects based on coffee consumption.

Subjects were placed into three groups: non coffee drinkers, moderate coffee drinkers, and high coffee consumers, which was defined as drinking more than 45 mL of coffee a day. As a side note, 45 mL of coffee (much less than one cup) is hardly heavy use, but that is the parameter researchers set in this study. 

In the heaviest coffee consuming group, fecal analysis found that levels of Bacteroides, which are pathogenic strains of bacteria associated with several disease states, including diarrhea, were higher. On the plus side for regular coffee drinkers, lipoperoxidation was lower. This 2020 study gives us a clue as to why some people may experience an upset stomach and diarrhea after consuming too much coffee. 

Coffee, cream and lactose intolerance 

According to the U.S. National Library of Medicine, about 65% of the population has a reduced ability to digest lactose, the sugar found in dairy products, after infancy.

As such, and because so many of us add cream to our coffee, one of the scenarios in which coffee can be bad for the gut is in the case of undiscovered lactose intolerance. If you are having issues with digestion after drinking coffee, it could be the cream and not the coffee. 

For more on lactose intolerance, see our post on the 5 genetic variants that affect nutrient absorption

A personalized approach to coffee is best

Consider the image below that highlights some of the genetic variants that change the way certain people metabolize coffee and caffeine. The state of the scientific research is trending towards a personalized approach to coffee.

While some research shows modest increases in beneficial microbes in coffee drinkers, you’re much better off just eating more fiber if microbial diversity in the gut is your goal.

And yes, studies haven’t found a link between heart burn and coffee consumption, but that doesn’t mean coffee isn’t a contributing factor to your digestive issues.

There simply isn’t enough research on what coffee does, or doesn’t do, to the microbiome to draw any sweeping conclusions.

When it comes to coffee, the best course is to get a handle on how it affects you, especially your sleep, which is itself a key contributor the health of the microbiome.

If you notice a benefit with coffee as a part of your morning routine, keep brewing it in the mornings. Conversely, if you find coffee is too acidic on your stomach and even causes diarrhea, stop drinking it.

For more on how our food choices can affect digestive health, see my post on low FODMAP diets.

How does coffee affect your digestion? We’d love to hear from you in the comments.

Kristin Kirkpatrick, MS, RD, LD

Kristin Kirkpatrick is a nationally recognized registered dietitian, best-selling author, TODAY Show contributor, and member of the Dr. Oz Medical Advisory Board. She joined Gene Food as Chief Nutrition Officer after serving as the lead dietitian at the Cleveland Clinic in Cleveland, Ohio for 15 years.

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