Written by James McIntosh — Fact checked by Kevin Cyr, MD
Coffee doesn’t just impact your energy levels first thing in the morning; it also influences the makeup of the gut microbiota, which in turn could influence mood and stress levels.
This is according to new research from APC Microbiome Ireland, a research center based at University College Cork, in Ireland. The study is published in Nature Communications.
“Coffee is more than just caffeine,” said study author John Cryan, PhD, Principal Investigator at APC Microbiome Ireland, in a press release. “It’s a complex dietary factor that interacts with our gut microbes, our metabolism, and even our emotional well-being.”
The term gut microbiota refers to all the different micro-organisms such as bacteria that live inside the digestive tract. They are a vital part of the gut microbiome, which refers not only to the microbes but also the environment they live in.
Research has already established that there is a two-way relationship between the gut and the brain, known as the gut-brain axis. This means that changes in the brain can lead to changes in the gut, and vice versa.
Gut microbiota play a key role within this relationship.
“Public interest in gut health has risen hugely,” said Cryan. “The relationship between digestive and mental health is also increasingly being better understood, but the mechanisms behind coffee’s effects on this gut-brain axis have remained unclear.”
Other research has suggested that gut microbes react to coffee, as well as associating different levels of coffee consumption with certain health outcomes. These include reduced risks of some chronic diseases, lower rates of all-cause mortality, and a lower risk of depression.
Researchers have not investigated the effects of coffee drinking and withdrawal over time on drinkers as well as their gut microbiota in depth up until now.
How did the study assess the effects of coffee intake?
The study began with a comparison of one group of 31 non-coffee drinkers with 31 coffee drinkers. Coffee drinkers were people who regularly consumed between 3 and 5 cups of coffee a day.
With each participant, the researchers assessed several parameters with a range of tests, questionnaires, self reports, and stool and urine samples. These included:
- cognitive function
- stress levels
- physical health
- mood
- immune function
- diet
- gut microbiome composition.
After these baseline tests, the non-coffee drinker group played no further part in the study.
The coffee-drinking group then stopped drinking coffee for 14 days, while also abstaining from other sources of caffeine, such as sodas and dark chocolate.
After this time, they reintroduced coffee to their diets. However, half of them (15 people) reintroduced decaffeinated coffee while the other half (16 people) reintroduced caffeinated coffee.
The participants then drank whichever type of coffee the researchers had blindly assigned to them for 21 days. Their instructions were to drink four sachets of instant coffee each day.
The researchers carried out further assessments on this group of participants throughout their period of abstinence from coffee and then again during the 3-week intervention phase.
How coffee reshapes the gut
The researchers found that when participants returned to drinking coffee after the 14-day abstinence period, both caffeinated and decaffeinated coffee were associated with improvements in mood.
The participants’ questionnaires revealed lower levels of stress, depression, and impulsivity after returning to either type of coffee.
Caffeinated coffee alone was associated with reduced anxiety and improved vigilance, attention, and blood pressure. In contrast, decaffeinated coffee was associated with improvements in learning, memory, physical activity, and sleep.
Interestingly, the researchers did not note any differences between the coffee drinkers and the non-coffee drinkers at the start of the study and after the abstinence period when it came to many of these factors. This included blood pressure, stress, anxiety, depression, sleep quality, and physical activity.
Alongside the changes in mood and cognition, the researchers also observed several changes in the guts of the participants.
During the 2-week abstinence period, they noted changes in levels of certain metabolites, which are small molecules that are produced during the process of metabolism.
These levels largely returned after the participants started drinking coffee again, although levels of metabolites closely associated with caffeine did not rise for those drinking decaffeinated coffee.
Overall, the researchers identified nine key metabolites that were closely associated with coffee drinking. These included theophylline, caffeine, and selected phenolic acids, and were “strongly linked to microbial species and cognitive measures.”
There were also clear differences between the gut microbiomes of coffee drinkers compared with nondrinkers. There were higher levels of specific species of bacteria associated with positive health effects in the guts of the coffee drinkers.
These included:
- Cryptobacterium curtum, which is associated with oral health
- Eggertella sp. CAG:209, which is associated with bile acid synthesis
- Firmicutes CAG:94, which is associated with positive emotions in females.
“Our findings suggest that coffee, whether caffeinated or decaffeinated, can influence health in distinct but complementary ways,” said Cryan in the press release.
Only caffeinated coffee linked to lower anxiety
“Our findings reveal the microbiome and neurological responses to coffee, as well as their potential long-term benefits for a healthier microbiome,” said Cryan in the press release. “Coffee may modify what microbes do collectively, and what metabolites they use.”
Medical News Today asked Cryan if it was possible that the coffee drinkers had less stress and depression after drinking coffee again, due to the psychological impact of being able to return to a habitual behavior rather than this being driven by the coffee itself.
Cryan told us that the return to a habitual behavior can itself have psychological benefits, including reduced stress and improved mood, but that they designed the study to address this.
“We included both caffeinated and decaffeinated coffee, and both groups showed improvements in stress and depression. This suggests that non-caffeine factors, including psychological or behavioral effects, may play a role,” he said.
“However, only caffeinated coffee reduced anxiety and psychological distress, indicating that caffeine-specific biological effects are also involved,“ he added.
“Taken together, the findings suggest that the observed benefits are likely due to a combination of factors, biological effects of coffee compounds — including caffeine and (poly)phenols — microbiome-mediated mechanisms, and psychological effects linked to routine and expectation.” – John Cryan, PhD
While these early results are of interest, it is important to note that the study was a relatively small one, with only data from 62 participants. The researchers also did not analyze differences due to ethnicity due to the majority of the participants being Caucasian.
The study also only investigated the effects of instant coffee. MNT asked Cryan whether different coffee types or preparation methods might provide different results.
“Different coffee types and preparation methods can significantly influence the chemical composition of the final drink,” he said. “The brew method affects levels of caffeine, (poly)phenols, and other bioactive compounds such as diterpenes and chlorogenic acids.
“In our study, we focused on controlled interventions using standardized caffeinated and decaffeinated coffee to isolate biological effects. However, instant coffee may differ from freshly brewed coffee in its polyphenol profile and processing-related compounds, which could influence how it interacts with the gut microbiome and metabolism,” Cryan explained.
“While we would expect broadly similar directional effects across coffee types, the magnitude and specific microbial or metabolic responses may vary depending on preparation method,” he continued. “This is an important area for future research, particularly in the context of personalized nutrition and microbiome responses.”
For now though, this study provides additional insight into the mysteries of the gut microbiome and the role that one of the world’s favorite drinks may have to play in health.
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