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What Color is Your Poop?


Did you know that you have two brains? Well, not literally.

However, the gut is now widely recognized as the “second brain” given that the Enteric Nervous System of the GI tract can act independently of the Central Nervous System. The gut-brain axis represents an intricate network with constant bi-directional signaling between the nerves in your gut, gut bacteria (microbiota), and the HPA-T (Hypothalamus-Pituitary- Adrenal-Thyroid) Axis, among other pathways. Studies have shown that manipulating existing bacteria, good and bad, within the intestines can influence mood and cognitive function. In the opposite direction, brain chemistry can also influence gastrointestinal health.

One important finding is that stress may induce a change in the gut’s bacterial community that could lead to inflammation and consequently result in gastrointestinal disorders such as irritable bowel syndrome (IBS), Crohn’s disease, or ulcerative colitis (Carpenter, 2012). Stool color may indicate the health of your second brain.

What Does Your Stool Color Mean?


Brown – it may not be the prettiest color – but it is the healthiest. When your stool color is brown, this means your liver and intestines are doing their job. Why is our poop brown? It all started with bilirubin. Bilirubin is the result of dead red blood cells being processed by the liver and excreted as bile, a yellowish-green substance used in fat digestion. Because of this bile, our feces actually start out yellowish-green, but as it travels through the intestines, bilirubin is metabolized by gut bacteria creating a colorless by-product. When this by-product reacts with oxygen, it turn the fecal matter brown, indicating a healthy waste excretion pathway.


Green stool color may be the result of poor metabolic activity in the intestines, or simply a hearty, leafy salad. When lots of green, leafy vegetables are ingested, the pigmentation of wastes may represent that meal. However, it can also be a sign of wastes moving through the digestive tract too quickly. When bilirubin is not properly metabolized by gut bacteria, the colorless metabolite is never produced, and thus, reactions with oxygen never turn the feces brown. If you find this color in your stool often, consider consulting your doctor about digestive issues.


Yellow stool color is likely accompanied by a greasy texture and a worse-than-normal smell. This could be a result of malabsorption caused by stress, celiac disease, or disorders of digestive organs scubas the pancreas, liver, or gallbladder. These organs are responsible for secretion of enzymes and substances that metabolize fat, so dysfunction of any of these systems may lead to excess fat being excreted. Less likely, but still a possibility, is the presence of giardia. Giardia is a parasitic disease that causes chronic diarrhea in its host. Talk to your doctor if you commonly experience yellow stool that seems greasy.

Serotonin in the Gut

While serotonin is more commonly recognized as a neurotransmitter in the brain that promotes good moods, in reality, most of our serotonin within the body is found in the gut.

In this Enteric Nervous System, serotonin increases lipid metabolism by increasing the concentration of circulating bile salts needed for proper digestion of fats and promotes peristalsis (Watanabe et al, 2010). How does this relate to the gut-brain axis? One study has revealed that certain gut microbes regulate the formation of serotonin by cells within the GI tract lining, which has a significant impact on modulating GI motility (Yano et al., 2015).

IBS: A Look at Serotonin and Cortisol in the Gut-Brain Axis

Now we know that GI serotonin is necessary for peristalsis, the movement of matter through the digestive tract, by triggering secretions of other GI hormones and neurotransmitters to stimulate peristaltic action. Too much serotonin may mean too much motility within the gut, leading to diarrhea. Sufferers of IBS, diarrhea-predominant, may have an increase of serotonin, leading to fast, uncomfortable bowel movements.

Another factor that may increase movement throughout the GI tract is cortisol. This hormone, among others, rises in response to stress, and increased stress response has been shown to increase gut permeability. This increase in permeability causes the release of pro-inflammatory proteins, resulting in IBS symptoms (Konturek et al., 2011, Padhy et al., 2015, Fukudo, 2007).

When food does not have time to properly digest, it can be expelled via feces of a yellow/green color. This color is the product of bile that was unable to be processed by gut microbiota, as good bacteria within the intestines is required for oxidative reactions that change feces from this green/yellowish color to the expected brown color. (SciShow, 2014). Therefore, it is also safe to say that maintaining appropriate levels of serotonin and good bacteria within the gut, as well as reducing the levels of stress, is essential for helping to reduce the diarrhea of IBS-D.

IBS-Constipation Dominant, on the other hand, is also associated with serotonin function, acting on different receptors that inhibit peristalsis. With constipation, stool is generally much darker brown, as it is continually concentrated as it remains within the colon. From these studies, we see that a proper balance of serotonin is an essential component of addressing IBS.


Carpenter, S. (2012). That gut feeling. Monitor on Psychology, 43 (8), 50.

Fukudo, S. (2007). Role of corticotropin-releasing hormone in irritable bowel syndrome and intestinal inflammation. Journal of Gastroenterology, 42 (17), 48-51.

Konturek PC, Brzozowski T, Konturek SJ. (2011). Stress and the gut: pathophysiology, clinical consquences, diagnostic approach and treatment options. Journal of Physiology and Pharmacology, 62 (6), 591-599.

McKay, S., PhD. (2012, December 7). Gut-Brain3 [Digital image]. Retrieved April 4, 2016, from

Padhy SK, Sahoo S, Mahajan S, and Sinha SK. (2015). Irritable bowel syndrome: Is it “irritable brain” or “irritable bowel”? J Neurosci Rural Pract, 6 (4), 568-577.

SciShow. (2014, Sep 10). Why is my poop green? [Video file]. Retrieved from

Watanabe H, Akasaka D, Ogasawara H, Sato K, Miyake M, Saito K, Takahashi Y, Kanaya T, Takakura I, Hondo T, Chao G, Rose MT, Ohwada S, Watanabe K, Yamaguchi T, Aso H. (2010). Peripheral serotonin enhances lipid metabolism by accelerating bile acid turnover. Endocrinology, 151 (10), 4776-86.

Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, Nagler CR, Ismagilov RF, Mazmanian SK, Hsiao EY. (2015). Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis. Cell, 163 (1), 258.


Clinical Contributor

Annabelle Bennett

Clinical Support Specialist at Sanesco International, Inc.

Annabelle Bennett is a Clinical Support Specialist at Sanesco. She is a recent Clemson University alumnus with a Bachelor of Science in Biological Sciences. She enjoys getting her dopamine boosts from coffee, the beach, and her two little dogs.

Ramona Richard, MS, NC

Ramona Richard, MS, NC

Ramona Richard graduated with honors from the University of California with a Bachelor’s Degree in psychology and graduated summa cum laude with a Master’s Degree in Health and Nutrition Education. She also holds a Standard Designated Teaching Credential from the State of California, is a California state-certified Nutrition Consultant and a member of the National Association of Nutrition Professionals.

Ramona has participated in nutrition education in both public and private venues, including high school and college presentations, radio and public speaking for the past 20 years. She is the owner of Radiance, a nutrition consulting company, the Director of Education for Sanesco International, and a medical technical writer.

Disclaimer: The information provided is only intended to be general educational information to the public. It does not constitute medical advice. If you have specific questions about any medical matter or if you are suffering from any medical condition, you should consult your doctor or other professional healthcare provider.

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