Study Links Coffee to Gut Microbe and Brain Function Changes

A study published in Nature Communications has shed new light on how both caffeinated and decaffeinated coffee alter the human gut microbiota and influence psychological measures along the gut-brain axis. Researchers evaluated 62 adult participants to closely examine short-term biological, metabolic, and cognitive responses following regular coffee intake, temporary abstinence, and subsequent reintroduction.

The scientific team categorized the subjects into two distinct cohorts: 31 regular coffee drinkers who consumed three to five cups daily and 31 non-regular drinkers. Psychologists administered specialized memory and mood evaluations while analyzing detailed stool and urine samples after providing participants with either caffeinated or decaffeinated coffee in a blinded format.

The Gut-Brain Connection and Coffee

The microbiota-gut-brain axis is a communication network linking emotional and cognitive centers of the brain with peripheral intestinal functions. While previous investigations have associated moderate coffee consumption with reduced risks of type 2 diabetes, cardiovascular diseases, and neurodegenerative conditions, the underlying biological mechanisms remained poorly understood until now.

Data from the trial revealed that both beverage types correlated with reduced levels of perceived stress, depression, and impulsivity. However, distinct psychological differences emerged based on the presence of caffeine. Participants who received decaffeinated coffee demonstrated improved scores in learning and episodic memory assessments, whereas caffeinated coffee intake was linked to heightened attention, vigilance, and lower baseline anxiety alongside reduced inflammatory signals.

Key Behavioral and Cognitive Findings

• Regular Coffee Drinkers: Exhibited higher initial baseline scores on impulsivity and emotional reactivity scales compared to non-drinkers.
• Caffeine Abstinence: A mandatory two-week washout period resulted in reduced impulsivity scores and elevated fatigue or drowsiness, which subsided over time.
• Decaffeinated Coffee Reintroduction: Led to notable gains in memory performance, sleep quality, and physical activity metrics.
• Caffeinated Coffee Reintroduction: Successfully reduced general anxiety and psychological distress while increasing alertness.

Microbial Shifts and Faecal Metabolite Profiles

Using shotgun metagenomics and targeted metabolomics, researchers tracked shifts in faecal microbiome composition and metabolic byproducts. Habitual coffee drinkers displayed an increased relative abundance of specific bacterial strains, including Cryptobacterium curtum and Eggerthella species, alongside reduced levels of specific indoles and the neurotransmitter gamma-aminobutyric acid (GABA).

Additionally, untargeted faecal metabolomics identified significant spikes in coffee-associated compounds such as theophylline, 1,7-dimethylxanthine, and hippuric acid among coffee consumers. Overall microbial alpha-diversity did not dramatically shift between groups, suggesting that coffee selectively targets specific bacterial strains rather than broadly altering overall microbial richness.

Immune Function and Phenolic Acid Metabolism

The investigation also tracked inflammatory markers and immune responses. Regular coffee drinkers showed lower baseline plasma levels of the acute-phase protein C-reactive protein (CRP) and higher concentrations of the anti-inflammatory cytokine interleukin-10 (IL-10). Ex vivo whole-blood stimulation with lipopolysaccharides (LPS) confirmed that coffee consumers secreted significantly less interleukin-6 (IL-6), pointing toward an immunomodulatory effect likely driven by coffee’s rich phenolic acid content.

Urinary metabolomic profiles mirrored these dietary signatures, showing elevated excretion of phenolic metabolites-such as caffeoylquinic, cinnamic, and phenylpropanoic acids-following the consumption of both caffeinated and decaffeinated brews. This reinforces the concept that non-caffeine phytochemicals play a major physiological role in human health.

Frequently Asked Questions

Does decaffeinated coffee impact the gut microbiome just as much as regular coffee?

Yes. The study demonstrated that many microbial shifts and improvements in stress and gut-brain metrics occur independently of caffeine, meaning decaffeinated coffee exerts significant biological activity through its unique polyphenol and chemical composition.

How does coffee affect stress and cortisol levels?

Despite altering perceived stress and emotional reactivity, neither caffeinated nor decaffeinated coffee significantly altered salivary cortisol awakening responses or cortisol reactivity during physical and social stress tests, indicating that mood benefits occur without driving major HPA-axis stress hormone spikes.

What specific gut bacteria are influenced by coffee consumption?

Regular coffee consumption was associated with distinct changes in microbial populations, including increases in Cryptobacterium curtum and various Eggerthella and Firmicutes species, which fluctuate dynamically during periods of coffee intake and withdrawal.

Did coffee consumption negatively impact sleep or daily physical activity?

While caffeinated coffee improved attention, decaffeinated coffee drinkers specifically showed improvements in overall sleep quality (PSQI) and physical activity metrics, highlighting distinct functional benefits between the two beverage varieties.