How Your Wake-Up Juice Affects Your Gut

When the American colonists met in Griffin’s Wharf in 1773 to dump tea into the Boston Harbor, they suspected that the repercussions of their actions would include liberty, and enraging King George III.

They had no idea it would infect the future United States of America with the coffee mania still felt today. 

At the time of writing, there are 24,000 coffee shops in America.

That number is expected to increase to 50,000 in the coming years.

Not to mention that approximately 150 million Americans drink coffee every day

And while we know a lot about how coffee affects blood pressure, heart rate, and even what it does to the teeth, we don’t often talk about what coffee does to the microbiome in the gut.

Since Americans, on average, consume 1.6 cups of coffee per day, coffee is likely having a more significant effect on the bacterial populations in our guts than most people realize.

Let’s take a look at common gut reactions to drinking coffee…

Coffee, Caffeine, and Bacterial Diversity

Most people have experienced have their morning bowel movements after their morning coffee. 

This does happen for a reason – and it’s not caffeine-related. According to a recent 2019 study, decaffeinated coffee got the bowels moving in the same way that caffeinated coffee does.

The same study confirmed that coffee increased the ability of the small intestines and colon to contract, thus serving as a laxative. It also found that after three days of exposure to coffee, the bacterial count in rat intestines lowered – although more research is required to determine whether the good bacteria or bad bacteria suffered the loss.


Additional studies have delved a little deeper. 

In fact, one study completed in 2019 identified specifically which bacteria were impacted by caffeinated coffee. And what they found was heavy-coffee drinkers had higher populations of Faecalibacterium and Roseburia, two beneficial strains of bacteria.

They also had lower populations of Erysipelatoclostridium, a potentially harmful bacteria. This particular strain has been linked to diet-induced obesity. 

Overall, the study concluded that those with stronger caffeinated coffee habits experienced a rise in anti-inflammatory bacteria, a decrease in negative bacteria, and an overall richness of variety.

This is partly because of the antioxidants and polyphenols found in coffee, which are also found in plant-based foods and typically support a healthy microbiome. 

But as with any science, there are exceptions. And while coffee may provide lots of benefits for those with a regularly functioning gut… it can have disastrous effects on a sensitive one.

When Coffee Can Actually Hurt Your Gut

If you have a preexisting gut condition, like leaky gut syndrome or colitis, drinking coffee can actually exacerbate those symptoms.

You see, coffee is an acidic substance. You’ve probably heard about the benefits of alkalizing your body…

Basically, decreasing your acid intake and focusing on substances that are more basic can produce positive health effects.

Ingesting acidic substances when you have a sensitive stomach can further erode the intestinal lining and cause major irritation and even more complicated issues if the lining becomes perforated.

Tangentially, coffee can worsen insomnia in those who experience it regularly. This can cause the gut’s microbiome to suffer because of how crucial deep and restful sleep is to a diverse and flourishing bacterial population. 

Since no gut is created alike, the decision to drink coffee must be a personal one. (There are alternatives out there, after all.)

If you don’t typically have gut issues or don’t suffer from a known condition, like gastritis or leaky gut, coffee can help increase the population of healthy bacteria in the digestive tract and strengthen the contractions of the small intestine and colon, allowing for healthy and regular evacuation of the bowels.

If you do have gut problems, however, coffee will likely irritate those issues by eating away at the lining of the intestines and preventing restorative sleep.

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Dr. Pedram Shojai

NY Times Best Selling author and film maker. Taoist Abbot and Qigong master. Husband and dad. I’m here to help you find your way and be healthy and happy. I don’t want to be your guru…just someone who’ll help point the way. If you’re looking for a real person who’s done the work, I’m your guy. I can light the path and walk along it with you but can’t walk for you.