Dr. Michael Ruscio, DC is a clinician, Naturopathic Practitioner, clinical researcher, author, and adjunct professor at the University of Bridgeport. His work has been published in peer-reviewed medical journals and he speaks at conferences around the globe.
For many people, downing a cup of coffee is one of life’s pleasures — a morning ritual that helps our brains function better, boosts energy levels, and sets us up for the day.
However, it can be hard to work out if coffee has benefits or is harmful, as reports are so often wildly contradictory. One week, someone on the internet may say that it causes cancer, and the following week, that it prevents it.
We’ve taken a closer look at the available research on coffee, and found that for most people, the benefits of black coffee outweigh any downsides, with coffee intake being either neutral or somewhat beneficial to health. However, there are nuances to this that may be relevant to you, especially if you have a sensitive gut.
In this article, we’ll talk about the benefits of coffee drinking and caffeine consumption, including potential benefits to the liver, microbiome, and protection against heart disease and cognitive decline. We’ll also make sure to look at the science on both sides of the argument.
Before we investigate more, let’s first just take a quick look at what coffee actually is and what it contains.
What’s in a Coffee Bean?
The beans we brew to make a cup of coffee are the processed and roasted seeds from a fruit called a coffee cherry.
Two of the most brewed coffee beans around the world are Arabica and Robusta. Arabica produces a mild, aromatic coffee, while Robusta tends to be earthier with a more bitter edge.
Caffeine is a major ingredient in both these beans and the nervous system stimulant that we most associate with a cup of black coffee .
However, coffee beans also contain several other nutritionally beneficial components, including:
Potassium and magnesium (in small amounts, but still meaningful in the context of overall dietary intake for people who have more than a couple of eight ounce cups a day) 
Vitamin B2 (riboflavin), and vitamin B3 (niacin) 
Antioxidants of the polyphenol family, including chlorogenic acid, ferulic acid and caffeic acid 
Though the antioxidants in coffee don’t always get the same recognition as those in berries, green tea, or kale, they are nonetheless very beneficial.
For example, coffee’s antioxidants are thought to contribute to its protection against inflammation and chronic inflammatory diseases over time, while the antioxidant effect of chlorogenic acid in coffee may also play a role in generating new neurons (nerve cells) .
The Health Benefits of Black Coffee
There are numerous systematic reviews and meta-analyses relating to the benefits of black coffee, which means that we don’t have to try to parse through a lot of low quality studies in order to examine the evidence.
Systematic reviews and meta-analyses offer the highest level of evidence because they pool the result of multiple studies, creating enough statistical power to filter out rogue results and data anomalies.
It’s worth noting that most of the individual studies included within these larger scale reviews are population-based observational studies that can only highlight associations between coffee and health, not pinpoint cause and effect. And of course coffee is no panacea — it can only offer potential benefits as part of a healthy diet and lifestyle.
That said, according to these large scale reviews, the benefits of black coffee may include the following:
Coffee and All-Cause Mortality
Umbrella meta-analysis (meta-analysis of meta-analyses) and systematic review/meta-analysis
• 2-4 cups of coffee a day was associated with lower risk of death from any cause. • More specifically, the risk of dying from cardiovascular disease, various cancers, neurological, metabolic, and liver conditions were lower.
Systematic reviews/meta-analyses, and an umbrella meta-analysis
• Moderate coffee consumption has been associated with a lower heart disease risk. • 3-5 cups per day was the sweet spot, but a high consumption of more than six cups/day) was associated with neither a higher nor a lower risk for heart disease. • At least three cups of coffee per day was associated with a small (3%) reduction in the risk for high blood pressure. • However, one umbrella meta-analysis found inconclusive evidence that coffee was associated with higher cholesterol and blood pressure.
Combination of systematic reviews/ meta-analyses, and umbrella meta-analyses
• Coffee consumption was significantly associated with reduced liver cancer risk. • Heavy coffee drinkers were about half as likely to develop liver cirrhosis as coffee abstainers. • Risk of nonalcoholic fatty liver disease was 29% lower in coffee consumers than those who did not drink coffee. • NAFLD patients who drank coffee had a 30% lower risk of developing liver fibrosis.
Systematic review/meta-analysis and umbrella meta-analysis
• Risk of type 2 diabetes went down by 6% for each extra cup per day of coffee (similar for both caffeinated and decaffeinated coffee consumption). • Dose-response studies showed that the lowest risks for diabetes were associated with about 4-5 cups of coffee per day.
Systematic reviews/meta-analyses and an umbrella meta-analysis
• Coffee was protective against Alzheimer’s disease. • Lowest risk of Alzheimer’s was at 4–5 cups of coffee a day. • However one SR/MA found no significant association between coffee drinking and the risk of dementia or Alzheimer’s disease.
When it comes to whether the benefits of black coffee extend to your gut, the research isn’t quite so clear cut, with fewer gold standard meta-analyses and statistical reviews to call upon.
Nevertheless, there’s some encouraging research suggesting that regular coffee drinking can improve the health and diversity of the gut microbiome. This evidence comes largely from animal and laboratory studies though, so needs to be taken as preliminary and may not necessarily apply to humans [16, 17, 18].
On the other hand, if you have a more sensitive gut, it pays to take care and listen to your body.
For example if you have heartburn or GERD, caution is warranted — while one Japanese study suggested no link between these conditions and regular coffee consumption , other research suggests that coffee can promote reflux in people prone to the condition [20, 21].
People with diarrhea-predominant IBS might also run into problems with caffeine, given the compound is a known gut stimulant. While this is a bonus in some situations — for example coffee consumed after surgery can help people recover gastrointestinal function more quickly than those who don’t  — it’s not so great with people who have over-active bowels. In one study, regular (caffeinated) coffee stimulated colonic motility similarly to a meal, but was 23% stronger than decaf coffee and 60% stronger than water .
If you have overt gut issues, and find that drinking coffee makes your symptoms worse, you might want to cut back or avoid it, at least while you’re working on improving your gut health.
However, I like to reassure my patients with gut issues that giving up coffee doesn’t necessarily have to be a permanent thing. People can understandably lose the confidence to try favorite foods and beverages again after months or years of chronic symptoms and reactivity, but once your gut has regained heath with an appropriate healing regimen, there’s no reason you shouldn’t go back to enjoying the benefits of black coffee as part of your daily routine.
Other Coffee Sensitivities
Independent from gut health, too much caffeine from coffee (or tea, cola or chocolate) can be an issue for some people. More specifically:
Pregnant women should stick to less than than 200 mg of caffeine (the caffeine content of around two cups of black coffee) daily, as there is weak evidence that consuming more may be associated with low birth weight, preterm birth, and miscarriage [4, 5].
People with type 2 diabetes may react differently to caffeine — in one study, diabetics who consumed caffeine equivalent to 4–5 cups of coffee daily had higher average day time glucose concentrations and exaggerated glucose responses after eating . However this was only a small study and the effects may be very individual — if you are diabetic, it’s helpful to monitor your own blood sugar responses to caffeine.
Individuals with a known sensitivity to caffeine can become jittery or anxious if they consume too much of it. This predisposition is often genetic [25, 26].
Gluten in Coffee
A few articles have suggested that a cup of black coffee isn’t your friend if you have gluten sensitivity. Fortunately, you can largely relax about this — researchers who examined this issue (in animals and the lab, not in humans) found that the vast majority of coffee samples didn’t have any cross-reactivity with gluten, though a couple of highly-processed instant coffee products did [27, 28].
According to the researchers, what is likely happening here is that the heavy processing some instant coffees undergo can change the proteins they contain, such that the body starts to perceive them as a threat. In turn, this can create the same inflammatory reactions as gluten in those that are sensitive or allergic to it.
However, if you buy freshly ground coffee, or grind your own, you won’t encounter this potential issue. Having your coffee as unprocessed as possible also gets round the problem of gluten contamination during the manufacturing process, which has also been highlighted as a potential issue .
Mycotoxins in Coffee
Mycotoxins (toxins produced by mold) such as aflatoxins are another issue that some people worry about with coffee. Mycotoxins are of concern for human health as they have been linked with cancer, liver damage, and immune problems. But the overall evidence suggests that this isn’t an issue when it comes to coffee, as the trace amounts sometimes found in coffee don’t seem to rise to the level of being dangerous.
For example, one 2015 Spanish study analyzing the mycotoxins present in coffee found that 53% of all coffee samples (however processed) had traces of mycotoxins, which sounds concerning. But in no case were the levels high enough to present a risk of mycotoxin illness for consumers .
If you do want to play it really safe, you may want to only purchase coffee from a reputable source, and store it away in a cool, dry, dark place away from damp.
Coffee and Fasting
Fasting, particularly intermittent fasting, has become very popular and has potential benefits for metabolic health, though more research is needed [30, 31].
The great thing about coffee is that it can be consumed while you are fasting. Whether you are fasting or not, I generally recommend freshly ground black coffee without additives or sweeteners, though if this is unpalatable, a splash of plant or cow’s milk (if you have no dairy intolerance) is generally acceptable too.
Coffee with added fat — MCT oil is recommended — is another option for people who want to feel fuller while they are fasting and want to get the benefit of medium chain triglycerides. In some exploratory studies, replacing other fats (like corn oil and other cooking fats) with these fatty acids have been shown to benefit glucose metabolism and insulin resistance in animals and humans [32, 33, 34].
However if you have a tendency towards diarrhea, coffee with fat in may not be a good idea. As ever, listen to your body about the foods it can tolerate and those it can’t.
The Bottom Line
Coffee used to have a bad reputation, and some people still try to find arguments against it. But when you look at the highest quality scientific evidence, the pendulum swings in favor of the beverage and its potential health benefits. Choose fresh ground coffee from a reputable source (or grind your own beans) and it should be a safe, enjoyable drink.
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