What drinking coffee every morning does to your gut health

The impact of coffee on our gut flora appears to be twofold. Photo / 123rf

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 better than others?

That morning cup of coffee doesn’t just wake you up for the day, it also gives a boost to billions of friendly microbes residing in your digestive system. Because, according to a growing body of research, there is evidence that your espresso may positively influence your microbiome – gut bacteria – leading to better overall health and even a longer life.

“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 are increasingly being seen to benefit our metabolic health, weight management and mental health,” she says. “Coffee contains several compounds that act as a prebiotic, which means that they nourish 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 investigated the association between caffeine, coffee consumption and the colonic microbiome. Results showed the richness of the microbiome to be higher with regular coffee drinkers, who had increased numbers of the helpful Alistipes and Faecalibacterium types (thought to have preventive effects against liver fibrosis and cardiovascular illness), and lower levels of the harmful Erysipelatoclostridium, which causes gut problems. This follows an earlier study where coffee consumption was found to be associated with an increase in bifidobacterium, microbes thought to help with the digestion of fibre and prevent infections.

Coffee also contains plant compounds called polyphenols, a category of compounds naturally found in plant foods, such as fruit, vegetables, herbs, spices, tea, dark chocolate, and wine. “Polyphenols act as an anti-inflammatory antioxidant,” says Shubrook. “They can help reduce the risk of cancer by neutralising harmful free radicals, the chemicals that damage cells.”

The specific polyphenol in coffee is known as chlorogenic acid. According to a 2020 study published in Experimental and Clinical Sciences, patients who consumed coffee rich in chlorogenic acid lowered their risk of Type 2 diabetes and non-alcoholic fatty liver disease – they also lost weight. Scientists concluded this was probably related to an increase in intestinal bifidobacteria (one of the “good” ones).

Established studies have also shown caffeine is good for your gut, stimulating the colon and leading to regular bowel movements. One 1990 study showed 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 tend to be unanimous 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 Kopczynska, a microbiologist at the Polish Institute of Biochemistry and Biophysics in Warsaw who has developed a “healthy coffee” tool for the company Omni Calculator. “Adding tonnes 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.”

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 Kopczynska. “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.”

Shubrook says her go-to is Exhale Coffee, which is a dark Arabica grown with the highest level of antioxidants. “It’s the perfect black coffee, not at all messed with.”

The length of time the beans have been stored will also influence their polyphenol levels, with a reduction seen in coffee beans stored for 12 months or longer.

What about instant coffee?

Though studies show that instant coffee may contain even more polyphenols and minerals than ground coffee, it also contains 100% more of a chemical called acrylamide – coffee substitutes can even have 300% more. “Acrylamide forms in coffee during the roasting process, and if people are exposed to it in higher amounts, they could raise their risk of nerve damage and cancer,” says Kopczynska.

There is no cause for alarm, however. “Coffee consumption, both instant and ground coffee, is not linked to cancer development,” Kopczynska says. “However, the European Food Safety Authority recommends reducing the amount of acrylamide in our diet. This is why we also recommend classic ground coffee above instant and substitutes.”

How many cups should I drink a day?

A recent study of the centenarians living in the European “long life” Blue Zones of Sardinia and Ikaria, Greece, revealed that almost all of them drank two to three cups of black coffee a day. “Presuming a cup of coffee is 8oz/ 220ml, two to three cups is the sweet spot, with five the upper limit,” says Kopczynska.

Before grinding your beans or stamping your loyalty card, it’s worth bearing in mind the caffeine content of your drink. “Although coffee is beneficial, not everyone can metabolise it as efficiently,” says Shubrook. Kopczynska agrees. “The maximum recommended amount of caffeine is 400mg a day. Anything above 600mg has been linked to insomnia and high blood pressure.”

According to Kopczynska, a home-brewed cup of coffee contains between 70mg and 140mg of caffeine, depending on the bean and brewing method. Meanwhile, the average high street coffee has 180mg of caffeine. Others can be higher: a medium Costa cappuccino in Britain has 325mg – almost your entire recommended daily allowance in one cup.

You may also be surprised to hear that most espressos are lower in caffeine than other types of coffee: the caffeine found in 30ml espressos from three major British coffee chains ranges from 33mg to 75mg. (But a cup of espresso is also a far smaller amount of liquid than a latte or a cappuccino.)

How should I prepare my coffee?

How you fix your beans preserves different compounds, those which are beneficial, and the ones which are less good for you. Brewed coffee contains cafestol and kahweol, chemicals known as diterpenes. “Cafestol and kahweol are known for their anti-inflammatory, anti-diabetic, anti-cancer, and polyphenol-preserving properties,” says Kopczynska. “These are 30 times higher in unfiltered coffee.”

On the other hand, she says, unfiltered coffee contains oils that have been shown to raise cholesterol levels. “Filtered coffee not only contains fewer coffee oils but also contains less caffeine compared to unfiltered coffee brewing methods.”

If you can get around the fiddliness of using an Aeropress, a 2023 study published in the journal Foods revealed this method to be the best for preserving polyphenols. “In our study, the lowest total polyphenol content was found in the coffee from the French press (133.9g gallic acid/litre) and the highest was observed in the Aeropress brew (191.29g gallic acid/litre),” wrote the authors. “Of all the highest antioxidant potential and polyphenol content was observed in the brew made in the Aeropress.”

Can I make my coffee healthier?

Adding natural spices – as opposed to sugars or syrups – can bring extra health benefits. “Cardamom is an anti-inflammatory and regulates blood sugar levels,” says Kopczynska. “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.”