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

Tiffani Franada, DO, is a neurologist with OSF HealthCare who specializes in Multiple Sclerosis. Part of her passion is working with patients choosing brain-healthy diets and lifestyle, which prevents neurological diseases like Alzheimer’s, Parkinson’s and Multiple Sclerosis.

The MIND diet

"The MIND diet is a combination of the Mediterranean diet, which is healthy fats, olive oils, fish, fruits and vegetables. And the DASH diet, which is a low-sodium diet,” Dr. Franada says. “It's particularly helpful for patients who live with hypertension (high blood pressure). The two of those combined seem to be very effective at preventing the development of Alzheimer's."

Patients on the Mediterranean diet often have lower levels of inflammatory markers in their spinal fluid. Higher levels are suggestive of Alzheimer's. Patients also perform better on cognitive testing, Dr. Franada adds.

Fiber-rich foods

"In regard to carbs, whole grains are probably best, and they have really good fiber in them. As well as things like legumes and beans which have good fiber levels, which make you feel full for longer," Dr. Franada says. 

The National Cancer Institute (NCI) lists many high-fiber foods here. Lentils, vegetable soups, whole-wheat bread and pasta make the list. As well as fruits and vegetables like apples, apricots, broccoli and Brussels sprouts.

Berries and antioxidant production

"Blueberries are great, really berries of all kinds. They really help that antioxidant production," Dr. Franada says. "For vegetables, leafy greens are really helpful. They have a good amount of folic acid, which helps to reduce homocysteine (amino acid) in the brain. Homocysteine promotes inflammation and shrinkage in the brain, and we want to reduce that."

“Fats are not the enemy”

The word “fat” oftentimes has a negative connotation to it. Dr. Franada says there are healthy fats out there that offer benefits to brain health.

"Fats are not the enemy. Healthy fats are good for the brain. Your brain requires them, like fatty fish (salmon), which have good Omega-3s in them. If you don't eat fish, flax seed is a great alternative," Dr. Franada says. "Walnuts also have great, healthy fat in them. As well as olive oil, which has monounsaturated fatty acids which protects against inflammation in the brain." 

Lean meats, like chicken and turkey, can be good for brain health because there’s healthy amounts of protein and fiber in them, Dr. Franada says.

Don’t dismiss dark chocolate!

"Dark chocolate is great. Dark chocolate has good amounts of antioxidants. Of course, all things in moderation. But a dark chocolate square once a night, not a bad thing," Dr. Franada says. "Also, caffeine! Believe it or not, a cup of caffeine, like coffee or tea, can help with focus, attention and is helpful for the brain."

Dr. Franada recommends having your caffeinated drink of choice early in the morning, right when you wake up, instead of later in the day. Having it later in the day can give you a lot of energy, which leads to you not sleeping well at night. Sleep is also extremely important for brain health.

Foods to avoid

Ultra-processed foods have been trending lately, with health experts giving them more attention than usual because of their negative effects on people’s health. High sodium, added sugars and excessive amounts of bad fat headline are the reasons why we should avoid them, with these elements being linked to diabetes, obesity and cancer.

Obesity is typically part of a metabolic syndrome, where a person has elevated blood sugars, blood pressure and cholesterol. This puts patients at risk for stroke, sleep apnea, Alzheimer's and many other health issues. Those risk factors can put someone at risk for neurological disease. 

"Heavily processed foods are not great for the brain or the heart. Excess sugars, like added sugars, should be avoided as well. If you're going to have sugar, have something with natural sugar in it," Dr. Franada says. "Berries are much preferred to things with added sugars. Also, white bread and processed carbs should be avoided, too."

Effect on white brain matter

"There's some real-world data showing that the Mediterranean diet can prevent white matter changes on the brain, which are little white spots that develop on patients’ brains as they get older. It's also seen in patients with vascular risk factors," Dr. Franada says. "If you follow the Mediterranean diet pretty strictly, you can prevent getting those white spots. They also found people who adhere to that diet have better structural integrity. The left and right sides of the brain talk better to one another."

What about cheat days?

If you exercise five or six days a week and give yourself a “cheat day” where you splurge a bit, evaluate how the food feels in your body. Instead of packing on the calories and going bananas, Dr. Franada recommends reeling it in a bit and focusing on moderation.

"You'll probably start to recognize it doesn't feel so great," Dr. Franada says. "Maybe it's a chocolate dessert at night, or something smaller that you can do to still stay with your healthy diet, just in smaller quantities." 

Dr. Franada cautions against super rigid diets that make you "fall off the wagon" after a few weeks. "You have to find something that's sustainable for you," Dr. Franada adds. 

Video Interview Clips

"It can present in a variety of ways like vision loss, double vision, weakness, or numbness on one side or both sides of the body,” says Tiffani Franada, DO, a neurologist with the OSF HealthCare Illinois Neurological Institute (INI) who specializes in the autoimmune disease.

"Typically (multiple sclerosis) presents in young patients between 20 and 50 years of age. It's more common in women than men," Dr. Franada says. These events are called attacks or relapses, and they last a few weeks and then they get better. Patients can go awhile without anything, and then they can get other attacks down the line."

The OSF HealthCare Illinois Neurological Institute has launched a clinical trial for patients with nonrelapsing secondary progressive MS (nrSPMS). Dr. Franada and her team are looking for further preventive treatments. The trial, sponsored by Sanofi, uses an antibody called frexalimab, to see if it delays the progression in those enrolled.

"It's a disease state with no current treatment options available,” Dr. Franada adds. "We are actively enrolling right now. The age range is between 18-60 years of age for patients with secondary progressive MS that's not active. This is different than the relapsing remitting phase, which is the most common. This comes after that phase.”

While some patients currently in the OSF INI clinic are candidates for the clinical trial, Dr. Franada and her team are looking to include patients outside the clinic as well.

People interested in the clinical trial can call OSF INI at (309) 624-4000 to learn more information.

Multiple Sclerosis treatment options

There are 20 disease-modifying therapies to prevent disease activity in MS, Dr. Franada says. “Some treatments are given by IV, some are given by mouth, and some are given as at-home injections. It just depends on what is right for that individual."

Dr. Franada says if someone has an MS attack, the team wants to know about it right away. Adding that treatment of MS is more effective when it’s started early.

"There are some acute treatments that can be given, typically in the hospital. But prevention is a mainstay of our treatment course for patients.”  

Prevention tips

"Getting good sleep at night (is important), about eight hours. Getting regular exercise, about 30 minutes 5 days per week. In fact, exercise helps increase levels of BDNF, which is one of the hormones in our body that helps with neurological repair, called remyelination," Dr. Franada says. "The problem in MS is stripping away the covering of the nerve, demyelination, so exercise helps the reparative process. We don't know what the best diet for MS is, but I usually encourage my patients to focus on a Mediterranean diet, which is heart healthy." 

Knowing family history is also important to assess your risk factor of getting the disease.

"The risk for developing MS is a combination of genetics and environment, it's not just one. If you have a family member who lives with an autoimmune disease, or MS, it does slightly increase your risk for developing the disease,” Dr. Franada says.

Hydration is paramount, as is stress reduction. “Exercise is a great way to manage stress.”

"Your brain sits in a pool of fluid, so we want to hydrate as much as possible," Dr. Franada says. 

If you know a family member has MS, there are things you can do to lessen your risk.

"That includes Vitamin D supplementation. If you're low in Vitamin D, it’s critical to supplement that to a normal level. Also, smoking cessation. If you're a smoker, we advise you to quit. But this is incredibly important for patients with MS, because smokers are more likely to develop the disease,” Dr. Franada says.

National recognition of the disease has gone up, Dr. Franada says, which drives more patients to the OSF Illinois Neurological Institute. 

While there is no cure for MS, there are treatment options available to help with day-to-day symptoms (fatigue, pain and cognitive issues).

For more information on OSF HealthCare Illinois Neurological Institute, visit the OSF HealthCare website.

Video Interview Clips

OSF HealthCare Little Company of Mary Medical Center in Evergreen Park now has CT (Computed Tomography) and MRI (Magnetic Resonance Imaging) perfusion capabilities, which are advanced imaging techniques that look at a patient’s blood flow to the brain.

Rapid AI helps neurovascular and vascular medical teams reduce time to treatment and improve patient outcomes. The artificial intelligence processes the images and gives clinical information to the clinician immediately, so the provider can more quickly decide the best course of treatment for the patient.

Tracy Jendruczek, the vice president of surgical and procedural services with OSF Little Company of Mary, says the addition of CT and MRI perfusions at the hospital is beneficial for the community.

“It’s available 24/7 for any patient that comes in through the emergency department,” Jendruczek says.

Who is eligible for CT Perfusion?

“Patients that might be at risk for stroke or are showing signs or symptoms of having a stroke, would be eligible for a CT perfusion of the brain. This looks at the blood flow to different areas of the brain,” Jendruczek says.

Who is eligible for MRI Perfusion?

“Patients that are eligible may be showing signs or symptoms of a tumor or have had a previously diagnosed tumor of the brain,” Jendruczek adds. “MRI perfusion, like CT, allows us to look at blood flow of the brain, but it’s specific for tumors. It’s looking at the severity and type of tumor.”

What’s the ultimate goal?

The ultimate goal of CT and MRI Perfusions is to expedite treatment for stroke patients.

“The perfusion capabilities will allow us to see the different areas of blood flow so we can quickly determine if a patient is eligible for further treatment. If we’re able to provide that treatment here at OSF Little Company of Mary, we will immediately start treating the patient,” Jendruczek says. “If not, we can more quickly transfer the patient to a place they can receive appropriate treatment.”

Video Interview Clips