Coffee and decaf: what effects do they have on the microbiota?

It is now well established that coffee can influence cognitive function, affecting attention, alertness, memory, and the body’s response to stress. Yet the underlying mechanisms remain largely unclear. Are they mediated by the microbiota? And perhaps more intriguingly, is caffeine really the key compound behind coffee’s effects on the brain—or is there more to the story?

Understanding the links between coffee, the gut, and cognition

This is a legitimate question. Several nutritional studies have shown that coffee, through its bioactive compounds (chlorogenic acids, melanoidins, and other polyphenols), can significantly modulate the composition of the gut microbiota. Moreover, the gut microbiota and the brain are in constant communication through the microbiota-gut-brain axis. Beyond caffeine, this axis may help explain some of coffee’s effects on health.

To test this hypothesis, researchers in Ireland recruited 62 healthy adults who had not recently taken probiotics, prebiotics, or antibiotics. Half were habitual coffee drinkers, consuming three to five cups a day, while the other half did not drink coffee. The coffee drinkers first abstained from coffee for two weeks before resuming their usual habit for three weeks. During this period, they consumed either regular or decaffeinated coffee, while keeping their usual diet unchanged. The aim was to disentangle the effects of caffeine from those of coffee’s other compounds.

Throughout the study, the researchers collected stool, urine, and blood samples and assessed participants’ cognitive and behavioral performance at several time points, while also monitoring their dietary intake.

Positive effects on mood and cognition

Published in Nature Communications,¹ the study found that habitual coffee drinkers exhibited notable differences in their gut microbiota. In particular, they showed a higher abundance of Firmicutes CAG:94, a bacterial strain that has been associated with positive emotional states in women.

Following a period of coffee abstinence and subsequent reintroduction, both caffeinated and decaffeinated coffee were found to affect seven specific bacterial strains in the gut microbiota, without altering overall microbial diversity. 

The effects on the brain were equally intriguing. Reintroducing coffee—regardless of its caffeine content—was associated with several beneficial outcomes, including reductions in:

• perceived stress,
• experienced depressive symptoms,
• impulsivity, defined as the tendency to act quickly without considering the potential consequences.

However, only caffeinated coffee was associated with reduced anxiety, improved cognitive performance, and greater resilience to stress.

Perhaps more surprisingly, the consumption of decaffeinated coffee—but not caffeinated coffee—was associated with improved episodic memory, increased physical activity, and better sleep quality. 

The microbiota: a likely mediator between coffee and the brain

Analysis of stool samples from coffee drinkers revealed that, before the abstinence period and compared with non-drinkers, they had lower levels of indole-3-propionic acid–a metabolite involved in nervous system function–, and GABA, a neurotransmitter that plays an important role in anxiety and cognitive function.

The researchers also found that levels of five coffee-related metabolites (theophylline, hippuric acid, 1,7-dimethylxanthine, and two others) were strongly associated not only with cognitive and behavioral outcomes, but also with numerous species of gut bacteria.

According to the researchers, these fecal metabolite profiles primarily reflect the metabolism of coffee’s various polyphenols, regardless of whether the coffee is caffeinated or decaffeinated. Decaf is therefore clearly more than just 'placebo coffee'.