Coffee Changes the Gut Microbiome and May Affect Stress and Memory – but the Effect Is More Complicated Than It Seems

Regular coffee consumption is linked to noticeable changes in the gut microbiome, metabolism, mood and some cognitive measures. That is the conclusion of researchers at APC Microbiome Ireland at University College Cork, who studied how regular and decaffeinated coffee affect the gut–brain axis.

The experiment was small – it involved 62 healthy people aged 30 to 50 living in Ireland. Half drank 3–5 cups of coffee a day on a regular basis, while the second group drank no coffee.

The researchers analyzed stool and urine samples, the composition of the microbiome and metabolites, and also ran tests for memory, attention, mood, stress and other measures.

After giving up coffee, the microbiome began to change

Regular coffee drinkers were found to have a different composition of gut microbiota. In particular, certain species of Cryptobacterium and Eggerthella were more common in them, and the concentrations of several metabolites, including indole-3-propionic acid, indole-3-carboxaldehyde and the neurotransmitter GABA, differed from those of people who did not drink coffee.

Then 31 regular consumers gave up coffee completely for 14 days. During that time, the researchers found changes in the microbiome and metabolic profile, and some of the coffee-related differences weakened.

After that, the participants were randomly divided: 16 people received caffeinated coffee again for three weeks, and another 15 received decaffeinated coffee.

Bringing back both versions of the drink again caused changes in the microbiome. Some of them were seen regardless of whether caffeine was present, which points to a possible role for other substances contained in coffee, including polyphenols.

Regular and decaffeinated coffee acted differently

After coffee was reintroduced, both groups reported lower perceived stress, fewer symptoms of depression and less impulsivity.

However, differences emerged between the two versions of the drink.

In those who received caffeinated coffee, the researchers recorded lower anxiety and psychological distress, as well as improvements in some measures of attention and alertness.

In the decaffeinated coffee group, results improved on certain tests of learning and memory. The authors see this as one indication that coffee’s effects cannot be explained by caffeine alone.

But the results were far from clear-cut. In the initial comparison, regular coffee drinkers showed higher impulsivity and emotional reactivity, while participants who did not drink coffee had an advantage on some measures of memory.

After two weeks without coffee, habitual consumers also showed reduced impulsivity and improved attention measures.

The authors specifically caution that some of the improvements on cognitive tests may have been due to a practice effect from repeating the tasks, although some changes after coffee was reintroduced persisted even when this factor was taken into account.

The study does not prove that coffee “improves the brain”

The main limitation of the work is its small sample. The study involved only 62 people, and the initial groups were not formed randomly: some participants already drank coffee regularly, while others did not drink it at all.

So the differences between them may have been linked not only to the drink itself, but also to other features of lifestyle or physiology.

In addition, the work identified links between coffee, the microbiome, metabolites and cognitive measures, but did not prove that changes in gut bacteria directly cause changes in mood or memory.

The study was also funded by the Institute for Scientific Information on Coffee (ISIC) – an organization tied to the coffee industry. The funding and potential conflicts of interest are disclosed in the paper itself, which was peer-reviewed at Nature Communications.

University College Cork believes the results primarily help to better understand how the drink works. Coffee is a mixture of thousands of compounds, so caffeine and the other components may affect gut microorganisms, metabolism and the nervous system in different ways.

So the work does not offer a simple conclusion about whether coffee is good or bad for the brain. It shows that regular and decaffeinated coffee can change the microbiome and physiological measures in different ways, and the proposed link between those changes and mood and cognitive function still needs to be tested in larger studies.