Decaf Surprise: Coffee Reshapes Gut Microbes and Mood

A University College Cork study found both regular and decaf coffee shifted gut bacteria and were linked to lower stress, depression and impulsivity.

Scientists at APC Microbiome Ireland, University College Cork, studied 31 regular coffee drinkers who consumed 3–5 cups a day — the amount the European Food Safety Authority defines as safe and moderate — alongside 31 non-drinkers. The drinkers first gave up coffee for two weeks, during which researchers repeatedly collected stool and urine samples and psychological assessments, tracking metabolites produced by gut microbes. When coffee was reintroduced, participants did not know whether they received caffeinated or decaf. According to ScienceDaily, both groups later reported lower perceived stress, depression and impulsivity scores, with measurable shifts in gut bacteria and metabolite profiles. The study was published in Nature Communications.

The most striking result challenges the assumption that caffeine drives coffee's cognitive effects. ScienceDaily reports that improved learning and memory were observed only among participants drinking decaffeinated coffee, suggesting compounds such as polyphenols — plant-derived substances that can interact with gut microbes — may contribute to cognition. Caffeinated coffee, meanwhile, was associated with reduced anxiety, better vigilance and attention, and links to reduced inflammation. The Economic Times notes this does not make decaf a brain-enhancing drink, since the study examined short-term reactions in a controlled setting, and it also flags that the research was sponsored by the Institute for Scientific Information on Coffee, an organisation backed by coffee companies — useful context when weighing the findings.

Researchers detected changes in several groups of gut bacteria. ScienceDaily reports that *Eggertella* sp. and *Cryptobacterium curtum* were more abundant among coffee drinkers — the former thought to contribute to acid secretion in the stomach and intestines, the latter possibly involved in bile acid production, processes that could discourage harmful bacteria. Higher levels of Firmicutes, previously associated with positive emotions in females, were also observed. According to The Economic Times, the gut and brain communicate bidirectionally through immune reactions, hormones, neural circuits and microbial metabolites, which may explain why coffee's thousands of non-caffeine compounds can influence mood and attention.

The study involved only 62 participants over a relatively short period, so it does not prove coffee causes mood, memory or gut changes, nor that it prevents depression or disease — a limitation both ScienceDaily and The Economic Times emphasise. Still, the findings offer clues about the biological pathways behind earlier coffee associations. "Coffee is more than just caffeine — it's a complex dietary factor that interacts with our gut microbes, our metabolism, and even our emotional well-being," said corresponding author Professor John Cryan of University College Cork. He suggested coffee could potentially be harnessed as an intervention within a healthy balanced diet. Larger and longer studies are needed to test whether some of coffee's effects arise from interactions between its many compounds and the microbes in the gut.