Alcohol and the Gut Microbiome: The Science behind the Day After Drinking Diarrhea!
- Melody Bartlett
- Jun 4
- 6 min read
If you've ever woken up after a night of drinking and found yourself running to the bathroom, you're not alone. Many people experience irregular bowel movements, often loose stools or diarrhea, after consuming alcohol. But why does this happen? The answer lies in the fascinating world of your gut microbiome and how alcohol throws it off balance.
Let's review
Your gut is home to trillions of bacteria, viruses, and fungi collectively known as the gut microbiome. Most of these microbes are beneficial: they help digest food, produce vitamins, support your immune system, and keep harmful organisms in check. When this community is balanced, your digestion runs smoothly and your body feels good.
How Alcohol Changes the Microbiome
Alcohol acts almost like a wrecking ball for your gut's delicate ecosystem. Even after just one night of moderate to heavy drinking, alcohol can start to change the composition of your gut bacteria within 30 minutes! It does this first by killing off good bacteria. Alcohol can kill beneficial bacteria, allowing potentially harmful bacteria to flourish. It does this by changing the availability of nutrients that gut microbes rely on. Ethanol is a poor energy source for most beneficial bacteria. Shifts in nutrient sources can disadvantage these populations while favoring other, more harmful, bacteria. With fewer good bacteria, harmful or pro-inflammatory bacteria can take over, leading to a state called dysbiosis; an imbalance in the gut microbiome. A topic my clients have hears all about. Alcohol, especially in excess, can lead to an overgrowth of bacteria in the small intestine, a condition known as SIBO (Small Intestinal Bacterial Overgrowth).
Alcohol and Gut Inflammation
Alcohol is inherently irritating to the gut lining. It increases inflammation in the digestive tract, making the gut wall more "leaky" or permeable. Normally, the gut lining acts as a barrier, allowing nutrients into the bloodstream while keeping toxins and undigested food out. Alcohol promotes leaky gut by damaging the intestinal lining and disrupting tight junctions between cells. Tight junctions are a type of cell to cell relationship that is very protective in keeping contents on one side of the environment. And believe you me, you want this in the digestive tract! When you consume alcohol it increases the release of zonulin, a protein that hold these tight junctions when regulated normally. So think of zonulin as a protein thats a "regulator" and its job is to keep the tight junctions...tight. Alcohol increases the release of zonulin, higher zonulin loosens the tight junctions between intestinal cells, leading to increased gut permeability or "leaky gut." This allows toxins and bacteria to pass more easily from the gut into the bloodstream. Im gonna provide a picture of this dynamic below so you can better understand.

usbiotek. Fecal Zonulin: What Does It Tell Us? usbiotek website. https://www.usbiotek.com/blog/fecal-zonulin-what-does-it-tell-us. Published August 10, 2022.
How does this lead to the "Day after drinking Poops!"
All these changes translate into the bathroom issues you might experience after drinking and heres how. Alcohol can inhibit the production of digestive enzymes, making it harder for your body to break down and absorb nutrients from food. This leaves more undigested food in your gut, which bacteria ferment, producing gas, bloating, and loose stools. The inflammation and increased permeability caused by alcohol can make your colon secrete more water, leading to diarrhea. Also, drinking alcohol changes the metabolism of the microbes which shifts what bacteria are more abundant and active. This shift in gut bacteria means more potentially harmful byproducts (like endotoxins) are produced. These can irritate the gut and "speed up transit time", resulting in urgent, loose bowel movements. All of these mentioned impacts disrupt digestion and absorption in the digestive system.
Does It Happen to Everyone?
Not everyone experiences these symptoms to the same degree. Your individual gut microbiome, genetics, and overall gut health play a role in how you respond to alcohol. Some people may tolerate a drink or two without issue, while others are more sensitive. This also has to do with liver genetics and your ability to process alcohol, the metabolites that are produced by the liver, and the impact of those metabolites on the gut microbiome.
Liver health and the Gut Microbiome
Alcohol metabolism in the liver produces metabolites such as acetaldehyde and acetate, which enter the gut and disrupt the balance of the gut microbiome by reducing beneficial bacteria and promoting harmful species. In addition to these direct effects, alcohol significantly alters bile acid metabolism. Bile acids are steroid acids synthesized from cholesterol in the liver and secreted into bile, where they play essential roles in digesting and absorbing dietary fats and fat-soluble vitamins. After being released into the intestine, bile acids help emulsify fats, making them easier for digestive enzymes to break down and absorb. Primary bile acids are made in the liver, while secondary bile acids are produced when gut bacteria modify primary bile acids in the colon. Bile acid metabolism is important for gut bacteria because bile acids directly shape the composition and function of the gut microbiota through their antimicrobial properties (balance within the ecosystem), regulating host immune responses, maintaining intestinal barrier integrity, and protecting against inflammation and overgrowth of harmful bacteria. Alcohol also impacts the production of short-chain fatty acids (SCFAs) by altering microbial populations that ferment dietary fibers, leading to reduced SCFA levels, which are important for gut barrier function and immune regulation. Together, these metabolic disturbances contribute to gut barrier dysfunction, systemic inflammation, and progression of liver disease.

Calleja-Conde J, Echeverry-Alzate V, Bühler K-M, Durán-González P, Morales-García JÁ, Segovia-Rodríguez L, Rodríguez de Fonseca F, Giné E, López-Moreno JA. The Immune System through the Lens of Alcohol Intake and Gut Microbiota. International Journal of Molecular Sciences. 2021; 22(14):7485. https://doi.org/10.3390/ijms22147485
In Summary
Alcohol disrupts your gut microbiome by killing off good bacteria, promoting harmful bacteria, and making your gut lining more permeable. This leads to inflammation, poor digestion, and irregular bowel movements, often experienced as diarrhea or loose stools, after a night of drinking. The more you drink, the more pronounced these effects become, but even a single night out can throw your gut off balance. If you want more information about the state of your biome and more insight into how your ecosystem needs targeted help, book some time with me, Melody, at Brain and Body Rehabilitation! Id be honored to be part of your gut health journey!
References
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