A new study is challenging long-held assumptions about coffee’s effects on digestive health, suggesting the popular beverage could offer benefits for both the gut and the brain.

The research, published in Nature Communications, examined 62 participants, half of whom were regular coffee drinkers, to explore how coffee consumption influences the gut microbiome and mental well-being. Using psychological assessments alongside dietary tracking and biological samples, researchers found that individuals who drank coffee, whether caffeinated or decaffeinated, reported lower levels of stress, depression and impulsivity.

The findings point to a growing scientific consensus: coffee is more than just a caffeine delivery system. According to the study’s authors, it acts as a complex dietary component that interacts with gut bacteria, metabolism and even emotional health.

Researchers also observed higher levels of beneficial bacteria among coffee drinkers, including strains linked to protection against harmful microbes and inflammation. Caffeinated coffee, in particular, was associated with reduced anxiety, improved attention and lower markers of inflammation.

Still, OSF HealthCare gastroenterologist Omar Khokhar, MD, cautions against drawing sweeping conclusions.

Kinds of coffee could make a difference

Dr. Khokhar points out it’s a small study that supports a hypothesis, but it’s not definitive proof that coffee will improve gut health or mood.

“There are so many different kinds of coffee. There’s Turkish coffee, there’s South American coffee, there’s Dunkin Donuts coffee, there’s Folger’s and Sanka for some of the people watching this on Facebook.” He points out, “It just comes down to each person and their own individual microbiome and how it responds to whatever particular type of coffee they’re ingesting.” 

Instead, Dr. Khokhar believes the study contributes to a broader shift in how scientists understand nutrition. Rather than labeling foods as strictly “good” or “bad,” researchers are increasingly focusing on individual responses, particularly how a person’s unique gut microbiome influences their reaction to what they consume.

Coffee itself is chemically complex, containing compounds such as polyphenols, which Dr. Khokhar says might act to feed beneficial gut bacteria.

“Now let’s suppose you’re at baseline and you have overall good gut hygiene and function; coffee could potentially be a good thing. It could be a prebiotic of sorts, that could potentially support your microbiome in that case.” 

This could help explain the observed microbiome changes in coffee drinkers.

However, those same compounds can have downsides. Coffee is known to relax the lower esophageal sphincter, potentially triggering heartburn, and Dr. Khokhar stresses coffee exacerbates symptoms in people with conditions such as irritable bowel syndrome.

The study did not differentiate between types of coffee, such as espresso versus brewed coffee, highlighting another limitation and an area for future research.

More research is needed

Dr. Khokhar says the study shows a link but not a direct cause and he thinks more controlled studies are needed to determine how specific varieties and preparation methods influence health outcomes.

“What I would like to see personally is if you controlled for what specific coffee a group of volunteers ingested and then either through blood or stool, looking at their exact gut microbiome diversification or pattern to see if that improved or how that changed from a robustness and a diversity point of view,” he says. “That would be more objective.” 

The research also raises intriguing questions about the gut-brain connection. Scientists now understand that the gut microbiome plays a role in producing neurotransmitters like serotonin, which can influence mood, sleep and behavior.

Whether coffee can enhance mood indirectly by improving gut health remains a hypothesis but an appealing one for millions of daily coffee drinkers.

For now, the takeaway is about embracing moderation and self-awareness. As Dr. Khokhar puts it bluntly, “If it makes you feel bad, don’t do it.” But he says if people can tolerate coffee well, in moderation, it might not be as harmful as once thought and could even be helpful, but more research is needed to prove that.

If you have questions about what's best for their health, talk to your primary care provider. 

Video clips with Dr. Omar Khokhar

B-roll-Coffee and gut microbiome

A study published in Nature found that “in the past two decades, the incidence of early-onset colorectal cancer, which affects individuals below 50 years of age, has doubled in many countries.”

Similarly, projections from Frontiers in Immunology warn that “with changes in western dietary habits worldwide, the incidence of CRC is expected to increase steadily, resulting in 2.2 million new cases by 2030.”

Emerging science suggests a key piece of the puzzle lies within our gut.

“We think of our microbiome as a separate, living organism within our body. It’s made of billions of bacteria, predominantly growing in our colon. There is a small number of bacteria that does exist in our small bowel, oral pharynx and nasal cavities. Just like we have bacteria on our skin everywhere,” says Daniel Martin, MD, a gastroenterologist with OSF HealthCare.

Colibactin and DNA Damage

Several harmful gut bacteria species, including strains of E. coli, Klebsiella pneumoniae and Citrobacter koseri, produce a toxin called colibactin. Research over the last two decades has linked this toxin to DNA damage that may lead to cancer.

“They have recognized that there’s a much greater incidence of exposure to this particular strain of E. Coli that makes the Colibactin toxin in patients under the age of 50 who are diagnosed with colorectal cancer,” Dr. Martin says. “There’s also a recognition that Colibactin itself has some DNA-damaging properties within the GI tract. This is likely a direct contributor to the development of early, pre-cancerous dysplastic (abnormal growth) changes that ultimately lead to colorectal cancer in those patients.”

Diet, Antibiotics and the Microbiome

Western diets and overuse of antibiotics also play a role, research suggests.

“Also thinking about the infections we can have, both as infants and in adulthood. Over the last handful of decades, there’s the exposure of antibiotics, -- the antimicrobial medications we’re using to try and treat specific, acute illnesses,” Dr. Martin says. “But those can have a meaningful impact on our gut flora and microbiome in general.”

Processed foods, especially ultra-processed products with preservatives and dyes, may be particularly harmful. Dr. Martin recommends eating real food like beans, nuts, legumes, plants and lean meats.

“If you’re purchasing it in the middle of the grocery store, and it’s vacuum-packaged and sealed, looking nothing like its based product, it’s probably an ultra-processed food in every circumstance,” Dr. Martin says.

“When we are consuming a food product of some kind, if it’s going to go bad quickly, it likely has prebiotics and probiotics in it, and those are good for us. If you leave a banana out on the counter for two weeks, no one wants to eat it because it goes bad. If you leave a Twinkie out on the counter for two years, it hasn’t changed,” Dr. Martin adds.

Dr. Martin also warns about hidden culprits like sugary drinks, sports beverages and food dyes.

“Products like sports drinks, juices and sodas can be laden with sugars, whether real or added (which Dr. Martin refers to as ‘fake sugar’). Many of these products also contain food dyes and preservatives which are bad for our gut health.”

The Search for Balance

While probiotic and prebiotic supplements can support gut health, they are not a perfect science.

“Currently, prebiotic and probiotic supplements are created using the ‘95% confidence interval,’” Dr. Martin says. “This means that out of a sample of people, it was determined that 95% of them would benefit from a certain culture, probiotic or prebiotic being included in the product. Because as mentioned earlier, the 100% perfect pie chart of what everyone’s gut microbiome looks like is not currently known.”

For now, the advice remains straightforward: eat whole foods, avoid ultra-processed options and care for the trillions of bacteria that work inside of us every day.

Video Interview Clips

It’s no surprise that kids love sugary drinks. It’s also no shock that a group of health organizations including the American Academy of Pediatrics, the Academy of Nutrition and Dietetics and the American Heart Association, have released new recommendations encouraging healthier hydration options for children.

The bottom line, according to experts, is kids and teenagers should drink water and cow’s milk and stay clear of drinks that contain added sugar, artificial sweeteners and caffeine.

Mohammad Soud, MD, a pediatrician with OSF HealthCare, says while the recommendations aren’t new revelations, it’s an important message to drive home.

“Our markets are infiltrated with a lot of drinks that seem to be popular and harmless,” says Dr. Soud. “However, these drinks carry a lot of issues when it comes to kids’ health. They are overloaded with caffeine and other stimulants, and caffeine can have a lot of adverse effects on both the cardiovascular and nervous system.”

Dr. Soud says caffeine drinks can cause high blood pressure, heart palpitations, anxiety, depression and interrupted sleep – all of which can affect academic performance. Sugar can also severely impact children’s health, contributing to Type 2 diabetes and obesity.

“There is mounting evidence that these artificial sweeteners are linked to certain types of cancers, like breast cancer,” adds Dr. Soud. “Artificial sweeteners  can also alter the gut bacteria.”

Perhaps the biggest surprise from the new recommendations might be that cow’s milk is the choice over plant-based milk.

“We get lots of questions from parents about plant-based milk, almond milk, oat milk, soy milk and rice milk,” says Dr. Soud. “Those are missing a lot of nutrients compared to cow's milk.”

Cow’s milk contains high-quality protein, essential amino acids and plenty of vitamin D, calcium, phosphorus and iodine, which are important for bone growth and brain development in children. But soy milk has been approved by the American Academy of Pediatrics as an alternative to cow's milk for children who have dairy allergies.

Water should be the go-to drink every day, says Dr. Soud. How much water, however, depends on the age, activities they participate in and the climate they live in.

·         40 fl oz per day for 5—8-year-olds

·         61 fl oz per day for 9—13-year-olds

·         88 fl oz per day for 14—18-year-olds

But it’s unrealistic to think kids won’t reach for something unhealthy from time to time. Dr. Soud’s message to his patients and parents is simple –- stick with water and cow’s milk first. But on occasions like weekends or special events, it’s OK to opt for a smoothie, fruit punch or a sports drink. Being flexible, he says, is the key.

“I encourage parents to read labels with their kids,” says Dr. Soud. “Any drink that has high sugar, this is what I call a sometimes drink. This is not an everyday drink. I tell parents to be role models for their kids. So when they are drinking water over soda, often kids mimic that behavior.”

Dr. Soud says establishing good hydrating habits will serve children and teens well into adulthood.

“We all want our kids to grow up with healthy habits, and hydration is an important part of a balanced diet,” he says. “You’ve probably heard the saying that you are what you eat. That applies to what you drink too. The rule is sip smart, water first, milk next and skip the rest.”

Interview Clips