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What Drinking Coffee Every Morning Does to Your Gut Health

Numerous studies have shown that a cup of coffee is good for the gut – but what’s the best way to prepare it, and are some methods better than others?

That morning cup of coffee doesn’t just wake you up; it also gives a boost to billions of friendly microbes in your digestive system. According to a growing body of research, your espresso may positively influence your microbiome—gut bacteria—leading to better overall health and even a longer life.

The Microbiome and Coffee

“The microbiome comprises legions of species of ‘good bacteria’ that work collectively and individually to improve our health,” says Nicola Shubrook, a registered nutritionist and functional medicine practitioner. “These microbes benefit our metabolic health, weight management, and mental health.” Coffee contains several compounds that act as prebiotics, nourishing the probiotic beneficial bacteria by providing them with nutrients necessary for growth and function.

The impact of coffee on our gut flora appears to be twofold. Firstly, caffeine itself acts as a stimulant, increasing the number of helpful bacteria in the gut. “The greater the diversity in your digestive system, the better,” says Shubrook.

A 2023 study published in the journal Nutrients found that regular coffee drinkers had increased numbers of beneficial bacteria like Alistipes and Faecalibacterium (which may help prevent liver fibrosis and cardiovascular illness) and lower levels of harmful bacteria like Erysipelatoclostridium, which can cause gut problems. An earlier study also linked coffee consumption to an increase in bifidobacterium, microbes that help digest fiber and prevent infections.

Drinking Coffee In A Morning

Polyphenols in Coffee

Coffee also contains polyphenols, a category of compounds naturally found in plant foods like fruits, vegetables, herbs, spices, tea, dark chocolate, and wine. “Polyphenols act as anti-inflammatory antioxidants,” notes Shubrook. “They can help reduce the risk of cancer by neutralizing harmful free radicals, chemicals that damage cells.”

The specific polyphenol in coffee is chlorogenic acid. A 2020 study published in Experimental and Clinical Sciences found that patients who consumed coffee rich in chlorogenic acid lowered their risk of Type 2 diabetes and non-alcoholic fatty liver disease and also lost weight. Scientists concluded this was probably related to an increase in intestinal bifidobacteria.

Regular Bowel Movements

Established studies have also shown that caffeine stimulates the colon, leading to regular bowel movements. A 1990 study revealed that people who drank coffee tended to need the loo 30 minutes after drinking a cup.

In so many ways, the gut appears to love a cup of joe. But is there a best way to prepare and serve your coffee?

Black or With Milk?

Experts generally agree that black coffee is better for you than a cappuccino, latte, or flat white. “Milk has been shown to impede the absorption of polyphenols,” says Julia Kopczyńska, a microbiologist at the Polish Institute of Biochemistry and Biophysics in Warsaw, who has developed a ‘healthy coffee’ tool for Omni Calculator. “Adding tons of cream or sugar turns your coffee into a dessert. Sugars will do more harm to your blood sugar levels than coffee can do good.”

Drinking Coffee In A Morning

Coffee cup with brain on foam. Refreshing concept.

Which Blend Should I Choose?

There are two main types of coffee bean: Arabica and Robusta. “Each has different qualities at particular roasting stages,” says Kopczyńska. “Though lighter roasts generally have a higher caffeine content, they preserve more antioxidants than darker roasts. Light-roasted Robusta beans have more antioxidants than the blonde roasts of Arabica coffee.”

Most UK chain coffee shops use medium-roasted Arabica beans, although Costa offers a blend of Arabica and Robusta. Black Sheep Coffee also sells Robusta. “My go-to is Exhale Coffee, which is a dark Arabica grown with the highest level of antioxidants,” says Shubrook. “It’s the perfect black coffee, not at all messed with.”

What About Instant Coffee?

Though studies show that instant coffee may contain more polyphenols and minerals than ground coffee, it also contains higher levels of a chemical called acrylamide. “Acrylamide forms during the roasting process, and higher amounts could raise the risk of nerve damage and cancer,” says Kopczyńska. However, she reassures that coffee consumption, whether instant or ground, is not linked to cancer development. Nonetheless, the European Food Safety Authority (EFSA) recommends reducing acrylamide in our diet. Thus, classic ground coffee is preferred over instant and substitutes.

How Many Cups Should I Drink a Day?

A study of centenarians in the European “long life” Blue Zones of Sardinia and Ikaria, Greece, revealed that almost all drank two to three cups of black coffee a day. “Two to three cups is the sweet spot, with five being the upper limit,” says Kopczyńska. However, the maximum recommended amount of caffeine is 400mg a day. Anything above 600mg has been linked to insomnia and high blood pressure.

A home-brewed cup of coffee contains between 70mg and 140mg of caffeine, depending on the bean and brewing method. The average high street coffee has 180mg of caffeine, while a medium Costa cappuccino has 325mg.

How Should I Prepare My Coffee?

How you brew your coffee preserves different compounds. Brewed coffee contains cafestol and kahweol, chemicals known for their anti-inflammatory, anti-diabetic, and anti-cancer properties. “These are 30 times higher in unfiltered coffee,” says Kopczyńska. However, unfiltered coffee also contains oils that can raise cholesterol levels.

If you can manage the intricacies of using an Aeropress, a 2023 study published in the journal Foods revealed this method to be the best for preserving polyphenols. The study found that the Aeropress brew had the highest antioxidant potential and polyphenol content.

Can I Make My Coffee Healthier?

Adding natural spices can bring extra health benefits. “Cardamom is an anti-inflammatory and regulates blood sugar levels,” advises Kopczyńska. “Ginger, a natural painkiller, improves digestive health and lowers cholesterol. If you’re using milk, turmeric added to a latte is known for its beneficial effects on metabolism and the immune system.”