Coffee, Gut Flora, and the Benefits of Chlorogenic Acid

Coffee, Gut Flora, and the Benefits of Chlorogenic Acid

I have more than once tried to be a green tea guy, but the lure of coffee was too strong. As a result I am always on the lookout for studies that support my choice of morning beverage (habit). Thus, there are plenty of pro-coffee studies to be found in the archives of my newsletters and blogs. In this newsletter, we look at a new coffee study, one that leads down an interesting path.

Coffee and Gut Health

Recently, while searching for subjects for these newsletters, I found an article examining how coffee might impact the gut microbiome. According to Zhaoping Li, M.D., Ph.D. (professor of medicine, and chief of the Division of Clinical Nutrition at the University of California, Los Angeles), “Black coffee is beneficial to gut health, as long as you don’t overdo it.

The fact that black coffee seems to be the most beneficial comes as no surprise, since we all know that consuming too much in the way of sugar and low-value fats has a negative impact on general health. Therefore, one would assume that regularly consuming coffee loaded with cream and sugar (not even getting into the coffee monstrosities that Starbucks and their ilk offer) detracts from the benefits that coffee may provide. So, it is no surprise that nutritional experts suggest “it’s better to focus on coffees that are low in sugar or have no sugar at all to support gut health” (Keri Gans, R.D., author of The Small Change Diet).


Now, the Blood Type Diet supports the black coffee thesis, but only for blood types A and AB, since these two blood types are most prone to low stomach acid levels. Black coffee, which raises stomach acid levels, can be of benefit for these blood types when consuming animal protein, which requires high acid levels. However, the addition of cream and sweeteners to coffee impedes its ability to increase stomach acid, and so negates this value of coffee. Such coffee, which really constitutes a form of dessert, should be taken away from proper meals.  Now that we have that clear, let’s muddy things up again.

Coffee Study

Our aforementioned coffee study, “examining the association between caffeine consumption and the composition and structure of the colonic-gut microbiota”, was published in the American Journal of Gastroenterology (Oct, 2019).  In this study, researchers “analyzed gut microbiome samples taken during routine colonoscopies and found that people who drank two or more cups of coffee daily throughout the previous year had better gut microbiome profiles than those who had less or no coffee”.

“Higher caffeine consumption was associated with increased richness and evenness of the mucosa-associated gut microbiota, and higher relative abundance of anti-inflammatory bacteria, such as Faecalibacterium and Roseburia and lower levels of potentially harmful Erysipela Clostridium.”   (Source)

Now, “the observed association was seen regardless of age and dietary quality.” This is where things get a little “muddy”. Not only is “dietary quality” not an issue (which I take to mean referring to the rest of the diet of the subjects), but there was no attempt to distinguish between those who drank black coffee, and those who used cream and sugar.  Just for the record, I am one who likes my coffee with some sweetener and whitener, so this is kind of good news for me, and like-minded individuals. (I use “Silk” soy-based creamer, and raw honey, to at least keep those elements within a relatively healthy range.)

So, why did it not matter whether or not the coffee was black or a “double-double”?  The answer appears to be that the element found in coffee which supports the microbiome, works regardless of how we “fix” our coffee. And, it also appears that the active element is, contrary to the above study, not caffeine.

Integrative gastroenterologist Marvin Singh, M.D. says, “the chlorogenic acids in coffee have also been suggested to increase the diversity in the gut microbiome. It is felt that this may be one of the mechanisms by which it can impact metabolism and provide health benefits”.

Chlorogenic Acid Study

One group of researchers indirectly answered this question about coffee with or without cream and sugar, and determined that the broad benefits of chlorogenic acid seem to include neutralizing the negative aspects of adding these detrimental elements to our daily beverage.

Since previous studies have established that “chlorogenic acid intake has been associated with decreased risk of cardiovascular disease and type 2 diabetes”, these researchers “hypothesized that chlorogenic acid would improve cardiovascular, liver, and metabolic responses in a rat model of metabolic syndrome induced by a high-carbohydrate, high-fat diet”.

Let’s see how those rats fared.

Male rats were divided into 4 groups. Group one was fed with a corn starch diet for 16 weeks; group two was fed a corn starch diet for 16 weeks, with chlorogenic acid added to their food for the last 8 weeks; group three followed a high-carbohydrate, high-fat diet for 16 weeks; group four was fed a high-carbohydrate, high-fat diet for 16 weeks, with chlorogenic acid added to their food for the last 8 weeks.

And the conclusion was: “In high-carbohydrate, high-fat diet-fed rats, chlorogenic acid reduced visceral fat (fat stored deep inside the belly, wrapped around the organs, including the liver and intestines)...and abdominal circumference…reversed the elevated systolic blood pressure…decreased inflammation and fat deposition in the liver along with reduced plasma liver enzyme activities of obese ratsThus, chronic dietary chlorogenic acid attenuated diet-induced inflammation as well as cardiovascular, liver, and metabolic changes, suggesting that chlorogenic acid has potential for further clinical evaluation.”   (Source)

Oh, and confirming the previous study on coffee and the microbiome, this study also found that “chlorogenic acid increased diversity of gut microbiota”.

So, it appears that adding sugar and fat to our coffee will not negate the benefits of chlorogenic acid because it is so damn powerful that it can prevent the damaging aspects of these compounds from having an impact on the body. (Still though, how much chlorogenic acid does one need to counteract a Chocolate Cookie Crumble Frappuccino?)

Other Sources of Chlorogenic Acid

But Ken, you say, I don’t like coffee, it makes me agitated and keeps me up at night. How can I still reap the plentiful benefits of chlorogenic acid?  Good news: this powerful compound is one of the main polyphenols found in the human diet, and it is widely distributed through many foods other than just coffee.  For example, these foods and herbs are all relatively high in chlorogenic acid: apples, artichoke, betel, burdock, carrots, eggplants, eucommia, grapes, honeysuckle, kiwi fruit, pears, plums, potatoes, tea, tomatoes, and wormwood.

Other Benefits of Chlorogenic Acid

Chlorogenic acid has been extensively researched, and in the link to source at the end of this section, you will find solid scientific studies linked to each claim I reiterate here.

“Chlorogenic acid has antioxidant, anti-inflammatory, anticancer, antilipidemic, antidiabetic, antihypertensive, and anti-neurodegenerative activities. Moreover, most research regarding the health benefits of chlorogenic acid has been done on disorders related to metabolic syndrome, which is defined as a group of interconnected physiological, biochemical, clinical, and metabolic factors that increase the risk of cardiovascular diseases, type 2 diabetes mellitus, and all-cause mortality.”

Furthermore, chlorogenic acid has shown antimicrobial activity against a wide range of organisms, including amoebas, bacteria, molds, yeasts, and even viruses.   (Source)


We can now clearly see a mechanism which explains why coffee has so many proven health benefits: chlorogenic acid. But, as always, for optimal health benefits from any food, try to choose organic, in order to avoid health-competing pesticides. (If you are on the road, A&W now has organic, fair trade coffee.)

And, in the case of coffee, it is important that it be fresh in order to gain the most from its valuable antioxidant compounds, which degrade an hour or so after brewing (apparent from that funky taste coffee has when it has been sitting around for too long). So, when you are not at home, making fresh coffee, choose an Americano or Espresso, which are made from fresh-ground beans.

Also remember that pre-ground coffee allows the oil to oxidize, creating free radicals and negating some of the antioxidant value inherent in coffee beans, so ideally you should grind your own beans for the optimal, healthy (not to mention flavorful) coffee experience.

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