Coffee and Digestion - The Complete Guide
Article by Stefan Burns - Updated July 2022. Join the Wild Free Organic email newsletter!
Besides water, coffee is one of the most consumed beverages worldwide next to tea. As a bitter drink containing various phytonutrients, coffee has an effect on digestion that can be quite variable, and depending on the gut heath of an individual, quite noticeable. Coffee exerts antioxidant and anti-inflammatory effects on the digestion system while also increasing gut motility and thinning gut mucosa.
Coffee is one of the most well-known foods to effect digestion, most commonly known to cause heartburn or to need to use the restroom soon after consumption in sensitive individuals. There are a few reasons why coffee has these heartburn and/or laxative effects, and in this article we’ll explain why this so frequently occurs for many people. This article will also discuss coffee’s overall effect on digestion and gut motility, the phytonutrients it contains, how coffee can change the microbiome for the better, coffee’s effect on the gut-brain axis, and specific ways to drink coffee so it improves gut health rather than make it worse.
Digestion and the Large Intestine (colon)
Roasted coffee contains thousands of bioactive compounds that together exert numerous biologic effects on the body. Coffee affects the nervous system, brain, cardiovascular system, and the digestive system. Before any discussion on the effects coffee has on digestion can be had, the basics of digestion must be understood.
A Simple Summary on Digestion
Digestion starts before anything is actually eaten, as before eating food just the sight, smell, or thought of it releases digestive enzymes in the mouth. These digestive enzymes assist with the breakdown of food that is chewed in the mouth, and they also prime the stomach to release more stomach acid. Chewing food physically breaks it down into smaller pieces, then it’s swallowed and moves down the esophagus before dropping into the stomach where strong acids break the food down even more at a chemical level. Once the stomach has done its job the slurry that the food has become moves into the small intestine, more digestive enzymes and bile are released, and muscular contractions further break down food into absorbable proteins, fats, and carbohydrates that pass through the lining of the gut and into the bloodstream.
If all is normal, what’s leftover after this are harder to break down food particles, namely soluble and insoluble fibers. It’s in the colon that the microbiome can then break down the final food remnants and produce beneficial compounds, such as short chain fatty acids from fiber. These fatty acids are absorbed by the colon and provide base-load energy to the body. The longer the microbiome of the large intestine has to work on the food there, the more beneficial nutrients can be metabolized by the microbiome to then be absorbed into the body, and this overall increases the stability of human metabolism.
It’s the introduction of new food/energy that stimulates the bowels to release the stool that it has been holding onto, as the body senses it needs to make room for a new influx of nutrients. It’s a balancing act between what new nutrients can be taken in (eating new food) and what nutrients can be synthesized and absorbed from the stool in the large intestine already mostly digested of its fats, carbohydrates, and proteins.
Gut Health Problems and Incomplete Digestion of Food
A lot of gut health problems stem from the incomplete digestion of food. Certain biologically valuable nutrients and chemicals are only produced by the microbiome in the colon, for example short chain fatty acids, metabolites of polyphenols, and neurotransmitters. If the microbiome consistently isn’t given enough time to breakdown the final remnants of food in the colon, then nutrient and neurotransmitter deficiencies can occur over time.
An easy way to directly experience the ability of the microbiome to very efficiently break down and upcycle food is to fast for 48 hours. If the final meal before a fast is of high-quality and consists of whole foods, like a grain bowl (rice, beans, vegetables, healthy fats like avocado), then once that final meal reaches the colon the microbiome will have plenty to begin breaking down as whole grains and vegetables contains an abundance of material not extractable by the small intestine. If the normal defecation stool volume from that meal is a “1” with a normal eating schedule, then during a 48 hour fast what’s likely to occur is that defecation isn’t induced for the entire two days until a refeed meal is eaten, and then when defecation of that pre-fast meal does occur, the final stool volume may only be 1/2 to 1/4 of normal, or even less.
When there is a physiological need to extract more nutrients from less input, and the microbiome is given time to do this, food is more efficiently absorbed than normal. I’ve personally experienced during many a 2 day fast that my pre-fast meal was nearly completely absorbed. In 2 days the microbiome was able to completely break down and upcycle what I ate before the start of the fast such that I simply absorbed nearly everything. It wasn’t until a normal eating schedule was resumed that “normal” bowel movements returned. What this indicates is that “normal” bowel movements are more wasteful bowel movement as compared to the maximum level of extraction possible under conditions of nutrient scarcity.
Most people haven’t experienced long periods of nutrient scarcity like during a 48+ hour fast so what I described may seem outlandish, but all that’s required to prove this effect and ability for yourself is to go on a 48-72 hour fast. The quality of the last meal is very important to observe this effect, eat only whole unprocessed foods for final pre-fast meal. As shown by this phenomenon, fasting is one of the best ways to improve the functioning of the gut and to come to a better understanding of how the digestive system truly works.
As coffee alters the rate of digestion among other effects, it was important to present the information above as context for coffee’s specific impacts on digestion, which we’ll now dive into.
Together the digestive system and microbiome are the foundation of health from which everything else is dependent on.
The Holistic Gut Health Guide contains all the information you need to identify and understand the gastrointestinal and microbiome problems you may have while also providing you the most effective natural methods you can use to heal your gut. No gut health problems are unsolvable, give yourself every possible advantage along your gut health journey by reading an implementing the advice shared in the Holistic Gut Health Guide.
Some of the information in the Holistic Gut Health Guide isn’t common knowledge but when implemented it is highly effective in healing the gut and shifting the microbiome towards symbiosis. Give yourself every possible advantage along your gut health journey by reading an implementing the advice shared in the Holistic Gut Health Guide.
Coffee and Gut Motility
One of the most obvious effects that coffee has on gut health for many people is how it speeds up gut motility. Gut motility is the speed of movement of food through the digestion system, and one of the hallmark signs of poor gut health is highly variable gut motility. If some meals sometimes takes days to transit through the digestive system leading to constipation, while other meals seem to transit through the entire gastrointestinal system in under a day or even just hours, and this variability in gut motility is common, then that’s a clear indication that the gut is not in a state of ideal health. This state of variable gut motility is often referred to as irritable bowel syndrome (IBS).
How does Coffee make you Poop so Fast?
Coffee exerts a diuretic effect on gut motility through its stimulation of the hormone gastrin. Gastrin stimulates the secretion of gastric acid (HCl) in the stomach, aiding the breakdown and digestion of food. For about 90 minutes after drinking coffee the stomach environment is made more acidic because greater amounts of gastric acid are released. The release of gastric acid signals to the body that more food is incoming and therefore an increase in gut motility is observed, specially in the large intestine (colon). Melanoidins found in roasted coffee also increase gut motility through direct activation of the smooth muscles of the digestive system.
Caffeinated and decaf coffee significantly increase motor activity of the colon, activating greater propagated and simultaneous contractions. Eating a meal causes an increase in colonic motor activity as well (gotta make room), and caffeinated coffee is comparable in effect to consuming a meal. Caffeinated coffee is about 25% stronger in this effect than decaf coffee.
At least one-third of the population is susceptible to being stimulated to defecate soon after drinking regular or decaf coffee, with the effect more frequently observed in women then men. Within five minutes of drinking coffee rectosigmoid colon activity increases significantly and lasts for 30 minutes of more. The rectum is the final section of the colon a few inches long that attaches to the anus, and the sigmoid colon is the 1.5 foot long (40 cm) section of the colon just before the rectum. Coffee stimulates muscular contractions in these sections of the colon in a large percentage of the population, and this can cause rapid defecation for sensitive people, especially those who have IBS.
The colon stimulating effect of coffee is generally beneficial for people who regularly experience constipation, whereas people who suffer from already rapid gut transit times should stay away from drinking coffee.
Coffee and Frequent Bowel Movements
If coffee is consumed multiple times per day, as is commonly done by a large percentage of the population, then it’s ability to trigger waves of increased colon motor activity can result in bowel movements becoming more frequent, even to the point where it is problematic.
This is significant for reasons made clear by the earlier section on digestion and also in the microbiome section below. If food that recently made it to the large intestine is being released preemptively, then the body is missing out on a lot of beneficial compounds and metabolites only the microbiome can produce. Without a consistent stream of short chain fatty acids from the colon, metabolism suffers and energy volatility is more likely to be experienced. One of the functions of the large intestine is also to draw water out of the remaining food/waste, and frequent bowel movements can make dehydration a very real problem, or at least make dehydration more likely to occur.
In 1992 it was published in the British Medical Journal that nearly one quarter of the general population has smooth muscle dysfunction and other symptoms consistent with irritable bowel syndrome. Considering that the majority of the world’s population on average has become less healthy in the 30 years since that study, it’s likely that IBS affects an even greater percentage of the population now than it did in 1992.
Coffee Digestive Issues
Before we get into all the ways coffee improves digestion let’s finish covering how coffee can cause digestive issues for people with sensitive gastrointestinal systems. How is it that coffee can cause digestion problems while also having the ability to improve gut health?
Certain herbs have a dual ability to improve a bodily system or to cause problems. A good example of an herb that does this is cannabis. Cannabis that contains an even ratio of cannabinoids like THC and CBD if used in moderate amounts occasionally is neuroprotective and stimulates neurogenesis, increasing connectivity within the brain while also boosting creativity overall. Cannabis that is too high in THC though, and if used in excessive amounts, can cause mental health problems like paranoia, insomnia, and anxiety, and long term use of cannabis in this way can shrink the gray matter of the brain and cause memory problems. The dose of certain herbs like cannabis or coffee is critical in how their consumption will affect the body, and what’s also important is the state that the body is in prior to use.
Coffee (and cannabis, among other herbs) has the characteristic of exacerbating certain health issues if a bodily system is already out of balance. Think of it as a wake up call, with coffee highlighting preexisting health issues by making their symptoms more obvious, and in this manner this effect is beneficial in diagnosing health problems. So if drinking coffee is causing digestive issues like heartburn, stomach pain, or diarrhea, then that’s a big sign that coffee consumption should be stopped until gut health is improved, because when the gut and microbiome are healthy, coffee has a net positive influence on the digestive system and gut microbiota as we’ll see later.
Coffee and Irritable Bowel Syndrome
Irritable bowel syndrome (IBS) is the most common gastrointestinal disorder, with up to 30% of the population or more having regular symptoms consistent with IBS. Most people with gut health issues never seek the help of the medical system, and as a result the prevalence of gut health issues is thought to be much larger than what’s reported in the literature. Irritable bowel syndrome is most prevalent in people in the 20-40 and over 60 age groups, and women in their 30’s-40’s in particular seem to have higher rates of IBS
The main symptoms of IBS are abdominal pain which is relieved by defecation, abdominal distension, more frequent and looser bowel movements progressing up to diarrhea, general digestive pain, and heartburn. Less common symptoms of IBS that are still experienced at a higher rate than in the normal population include rectal bleeding and the passage of mucus. Underlying these symptoms of IBS are smooth muscle abnormalities.
What is Smooth Muscle?
Smooth muscle is a type of non-striated muscle that is activated by the autonomic nervous system to apply pressure to various organs by contracting. Smooth muscle is a critical component of the digestive system, as it’s waves of smooth muscle contractions that cause food to move through the gut. Smooth muscle contractions are stimulated by nerve impulses, certain hormones (like gastrin), and other chemicals released by various organs. Smooth muscle contractions are much slower but sustained longer than skeletal muscle contractions. The amount of intracellular free Ca2+ is a key regulator of smooth muscle tone and contractility.
Why does Coffee make my Stomach Hurt?
Coffee lowers lower esophageal sphincter pressure while simultaneously stimulating the production of gastric acid via gastrin. For sensitive individuals with thin stomach mucosa linings and/or preexisting stomach ulcers, increases in stomach acid can cause stomach pain, and with the sphincter valve separating the stomach from the esophagus becoming more relaxed, the chance of acid reflux also increases.
If drinking coffee is causing stomach pain then the consumption of coffee should be ceased and steps should be taken to heal the stomach back to normal function. Coffee has not been shown to modify gastric wall compliance, wall tension, or sensory function.
Why does Coffee give me Diarrhea?
Alongside its effects on the stomach, coffee also increases contractile pressures in the rectosigmoid area of the colon, which can cause an increased and sometimes very rapid need to defecate. Both the possible symptoms of heartburn and diarrhea from drinking coffee point to coffee’s ability to affect smooth muscle function, and both of these symptoms are also common to IBS irrespective of coffee consumption. Basically if smooth muscle function is dysfunctional overall, then the smooth muscle stimuli that coffee causes can be too powerful and further exacerbate symptoms of IBS.
Having covered how coffee can trigger the same pathways already imbalanced in those who have IBS, we’ll now discuss the phytonutrients coffee contains and how these nutrients can benefit gut health and the microbiome.
Coffee Phytonutrients
Roasted coffee contains thousands of biologically relevant compounds, and many of them have beneficial antioxidant, anti-inflammatory, neuroprotective, and metabolism boosting health effects. Together these chemicals influence the functions of the digestive system, cardiovascular system, nervous system, and the gut-brain axis.
Coffee and Caffeine
The most well-known chemical found in coffee is caffeine. Caffeine is a central nervous system stimulant that is rapidly absorbed into the body by the stomach and small intestine. Caffeine increases fat oxidation, in general boosts metabolism, and has been shown to improve cognition, especially for the elderly. One cup of black coffee contains ~95 mg of caffeine, and the upper bound for caffeine that shows health benefits is ~300 mg per day. Consuming more than 300 mg of caffeine per day causes significant hormonal alterations and can cause health problems best avoided.
If you have a built-up caffeine tolerance that you want to reset, and/or also want guidance on how to best use and dose caffeine, then read our guide on the subject for more information.
Coffee Polyphenols
Coffee also contains abundant polyphenols, which possess strong antioxidant properties. The polyphenols in coffee are not greatly effected by the decaffeination process. Flavonoids, a subgroup of polyphenols that are abundant in coffee, significantly increase the expression of proteins at epithelial tight junctions, improving their strength and reducing intestinal permeability which is a good thing. Weak tight junctions are a key symptom of leaky gut, food intolerances, and food allergies.
The polyphenol chlorogenic acid (CGA) is a major component of coffee, and chlorogenic acids have a regulating effect on glucose and lipid metabolism, which is why they have anti-diabetic, anti-carcinogenic, anti-inflammatory, and anti-obesity effects. One-third of free chlorogenic acids are absorbed in the small intestine and the rest of the polyphenols reach the colon where they are broken down into simpler molecules by the microbiome. Polyphenols influence the microbiome directly (more on that below) while also requiring microbial activity for their alteration into other compounds that have beneficial health effects when absorbed by the body.
Coffee Melanoidins and N-Methylpyridium
The chemical composition of green coffee beans is noticeably altered by the roasting process, and two of the notable chemicals produced from the heat-driven Maillard reactions that occur are melanoidins and N-Methylpyridium.
Melanoidins are brown pigment chemicals that are created when sugars and amino acids combine under high heat. Melanoidins have several health promoting properties such as being antimicrobial, antihypertensive, anti-inflammatory, antitoxin, and antioxidant in nature. Melanoidins are mostly indigestible and therefore act as dietary fiber, being fermented in the gut by the microbiome. People who drink a lot of coffee along with eating other foods that have undergone Maillard reactions (like crusty bread) may receive up to 20% of their dietary fiber from melanoidins. Melanoidins have a pro-motility on the gut not only because of their fiber effect but also through direct activation of the smooth muscles of the digestive system. In addition to melanoidins, dietary fiber is present in coffee.
N-methylpyridium (NMP) is an interesting chemical found in coffee that exerts an opposite effect on the stomach than coffee in general, as it reduces gastric acid production by stomach cells. NMP is only generated by the roasting process, and as such darker-roasted coffee contains more NMP than lightly roasted coffees, up to twice as much. For people who want to enjoy coffee and its health benefits but want to reduce their chance of experiencing heartburn and increased gut motility, drinking a darker roasted coffee is recommended.
Coffee and Gut Microbiome
On average 75% of feces are water, with the remaining 25% being solid materials. Bacterial biomass make up 25-55% of the solids in feces (6-14% total). This bacterial biomass is composed of dead and also living bacteria, and therefore as you can see, every bowel movement changes the microbiome because it’s removing a portion of the total microorganism population out of the body.
Coffee through its ability to trigger increased smooth muscle activity for the colon can cause defecation, and through this mechanism coffee influences the development of the microbiome. Microorganisms divide and reproduce on very fast timespans on the timespan of 20 minutes to 24 hours, with bad pathogenic bacteria typically dividing faster than good symbiotic bacteria. The longer stool stays in the colon, the longer the microbiome has to divide and evolve, which changes the overall population characteristics and diversity of the microbiome. If a healthy meal is eaten rich in vegetables and fiber, then symbiotic microorganisms will increase in population numbers, whereas if a junk food meal is eaten containing lots of highly processed foods and chemicals, then pathogenic microorganisms will better be able to survive and expand in population.
Coffee’s ability to trigger defecation can then be considered good or bad for the microbiome depending on the context. If the content of the stool in the large intestine is of a poor quality, then triggering defecation is a good thing as it’ll reduce the growth of pathogenic bacteria and remove toxins from the body. If the stool is composed of what’s left of a healthy meal from whole unprocessed foods, then triggering defecation early won’t be advantageous as valuable nutrients will be lost and symbiotic microorganisms will have less time to diversify and expand their populations.
Here’s the thing though, in my personal experience it’s the current contents of the digestive system that determine coffee’s defecating activating effect. When I eat healthy meals full of whole unprocessed foods, such as a rice and bean bowl with vegetables and avocado on top, coffee doesn’t trigger any significant increase in motor activity in the colon. If I eat a lower quality meal though, then I can definitely feel that coffee creates a stronger urge to use the restroom. At the beginning of the article I discussed how coffee can improve gut health because it highlights existing gut health issues like IBS by making the symptoms worse, and diet quality is a factor as to why that is the way it is. If you’re struggling with eating a good diet, resetting your dietary beliefs is an important step towards eating healthier.
If low quality junk food is in the digestive track, then it behooves the body to push it out quickly and hope for a higher quality meal to follow. Of course if junk food continues to be eaten then nutrient deficiencies develop and other health issues can compound, but having a longer transit time for these foods wouldn’t necessarily be better than a short transit time due to the presence of toxins in the food.
“There’s no way to win by eating poor quality food”
The benefits of coffee on the microbiome are further amplified by the abundant polyphenols that coffee contains. Coffee decreases populations of pathogenic bacteria such as Escherichia coli, Enterococcus spp., Clostridium spp., and Bacteroides spp., while increasing populations of beneficial microorganisms like Lactobacillus spp. and Bifidobacterium spp., and this is thought to be primarily an effect of polyphenols, as polyphenols from things like herbs have shown similar effects.
Polyphenols both influence microbiome populations, and are also metabolized into different beneficial chemicals by the microbiome. By containing abundant polyphenols, dietary fiber, and melanoidins coffee exerts a strong influence over the microbiome and shifts microbial populations towards greater symbiotic function and away from pathogenic overgrowth. Drinking herbal teas are another way to shift the microbiome towards greater symbiosis, as an herbal tea blend like a 1:1:1 chamomile, peppermint, and dandelion tea contains abundant flavonoids and each of those herbs is already well-known for improving gut health.
Coffee and the Gut-Brain Axis
Coffee as a natural source of many chemicals like caffeine and polyphenols exerts an influence on the gut-brain axis, from changing emotional status to altering neurogenesis and neurodegeneration. Caffeine is the main psychoactive compound found in coffee, easily crossing the blood-brain barrier and stimulating the sympathetic nervous system in addition to the overall central nervous system. Caffeine increases extracellular dopamine concentrations and causes a greater expression of dopaminergic receptors and transports, leading to an overall cognitive improvement, especially amongst the elderly.
Additionally caffeine reduces the activity of the Gamma-aminobutyric (GABA) system and modulates GABA receptors. GABA is an inhibitory neurotransmitter that acts on the central nervous system, lessening the ability for nerve cells to create, transmit, and receive signals to other nerve cells. Through this inhibitory effect GABA can produce a sense of calm as it reduces the activity of the nervous system, but as with anything too much GABA isn’t beneficial. Chronic caffeine intake is related to a long-term reduction in GABA, and that is also not good, as GABA plays a role in controlling stress, anxiety, and feelings of fear.
The gut-brain axis is also heavily influenced by the microbiome because it’s the microbiome that produces a large portion of the neurotransmitters the body uses, directly producing dopamine, GABA, and norepinephrine, and indirectly influencing the bodies natural production of serotonin in epithelial enterochromaffin cells (intestinal epithelial cells that play a governing role in intestinal motility and secretion). The gut microbiome also regulates stress hormones produced by the HPA-axis and sends direct signals to the brain via the vagus nerve. Through these interactions with the brain the microbiome has a strong ability to influence human behavior.
A Better Coffee
After learning everything that has been outlined in this coffee and digestion guide, there are a few key takeaways to remember:
If currently experiencing gut health problems like IBS (either knowingly or unknowingly) coffee consumption has the possibility of increasing the negative symptoms being experienced as it’s a mechanism to bring consciousness to the problem and attempt to shift the microbiome to a more favorable symbiotic state.
If gut health is good then coffee consumption can further improve gut health by modulating the microbiome towards greater symbiotic integration with the host by increasing populations of beneficial microorganisms such as lactobacillus and bifidobacteria, while also providing the body a rich source of health boosting polyphenols, fiber, and other unique compounds.
Coffee consumption within reasonable parameters (<3 cups a day) improves brain health, especially for the elderly.
The darker the roast the less likely coffee is to trigger the excessive production of gastric acids thanks to greater concentrations of N-methylpyridium, and darker roasted coffees also contain more melanoidins which have beneficial effects on the colon.
With all this taken into consideration, when eating a healthy diet and with a healthy gut, drinking a dark roast black coffee has little chance of causing gut health disturbances and overall has gut health and metabolism boosting benefits. The cardiovascular and cognitive systems also benefit from reasonable coffee consumption.
Coffee can be made even better though!
When certain herbs are added to coffee, it improves the metabolic effects of coffee while smoothing out the increase in sympathetic nervous system activity that coffee causes, which can lead to energy volatility in some individuals. And if the autonomic nervous system is already unbalanced between sympathetic and parasympathetic states, with the sympathetic nervous system being too dominant, then drinking coffee can make that imbalance worse.
Adding cacao, ceylon cinammon, chaga mushroom, cistanche, and a small amount of honey to a black coffee creates what I call a dark mocha, and having enjoyed a bunch of dark mochas in my time it’s my experience that they have a much greater beneficial nootropic effect than regular black coffee while also improving energy metabolism noticeably. While a dark mocha still has a stimulant effect, it’s much more even keel and balanced than a regular cup of black coffee (or a cup of coffee with sugar), and the metabolism boosting effect seems to last all day rather than just for a couple hours.
I encourage you to learn more about why adding these ingredients to coffee makes it even better as it’s a good introduction to herbalism and it should significantly improve your day to day if you drink coffee often.
If you read all the way here then it’s clear to me that you’re ready to do what it takes to finally restore your digestive system and gut microbiome back to healthy and optimal function.
I wrote the Holistic Gut Health Guide to help you accomplish exactly this! It contains all the information that you need to understand the gastrointestinal system, gut-brain axis, and microbiome in-depth, and the Holistic Gut Health Guide also educates you on the natural methods you can holistically use together like fasting and herbalism to transform your health from the inside out.
I’m so excited to be able to help you along your gut health and overall wellness journey with the Holistic Gut Health Guide! Please contact me with any questions you have and wishing you the best.
References:
Iriondo-DeHond A, Uranga JA, del Castillo MD, Abalo R. Effects of coffee and its components on the gastrointestinal tract and the brain–gut axis. Nutrients. 2020;13(1):88.
Jones R, Lydeard S. Irritable bowel syndrome in the general population. BMJ. 1992;304(6819):87-90.
Bitar KN. Function of gastrointestinal smooth muscle: from signaling to contractile proteins. The American Journal of Medicine. 2003;115(3):15-23.
Rubach, Malte, et al. Identification of a coffee compound that effectively inhibits mechanisms of stomach acid secretion in human gastric parietal cells. Abstracts of Papers of the American Chemical Society. Vol. 239. American Chemical Society, 2010.
Rose C, Parker A, Jefferson B, Cartmell E. The characterization of feces and urine: a review of the literature to inform advanced treatment technology. Critical Reviews in Environmental Science and Technology. 2015;45(17):1827-1879.
Strandwitz P. Neurotransmitter modulation by the gut microbiota. Brain Research. 2018;1693:128-133.
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