A change in stool odor is a common occurrence reflecting the complex chemical processes of digestion. The gastrointestinal tract contains trillions of bacteria that break down food, and the byproducts of this microbial activity create the characteristic smell of human waste. While most odor changes are temporary, a specific “mothball” scent is unusual enough to warrant examining its chemical and biological origins.
Identifying the Chemical Culprit Behind the Odor
The specific, aromatic smell likened to mothballs or industrial chemicals is often caused by an increased concentration of volatile organic compounds (VOCs) in the stool. Although mothballs contain naphthalene, the similar scent in feces is primarily attributed to indole and skatole. These are benzopyrrole compounds produced by specific gut bacteria.
These compounds are metabolites created when bacteria break down the amino acid tryptophan, a component of dietary protein. Indole and skatole are normally present in small amounts, but when their concentration rises, their pungent nature becomes noticeable. Skatole (3-methylindole) is the stronger odorant and, at high levels, specifically produces the chemical or naphthalene-like aroma. The level of these VOCs directly reflects the type and amount of material available for fermentation in the colon.
Common Dietary and Lifestyle Triggers
The most frequent cause of a transient, mothball-like odor is a change in diet, which alters the substrate available for bacterial digestion. Tryptophan is an essential amino acid found in high concentrations in protein sources like meat, dairy, eggs, and certain seeds. If a large amount of protein is consumed, especially protein poorly digested in the small intestine, excess tryptophan passes into the colon.
The anaerobic bacteria in the large intestine metabolize this surplus tryptophan, leading to increased production of indole and skatole. This explains why a sudden shift to a high-protein diet, particularly one involving low-digestibility protein sources or supplements, can produce a noticeable change in odor. High concentrations of casein, a protein found in milk, have also been shown to increase indole production.
The amount of dietary fiber consumed is another significant factor. Fiber is a fermentable carbohydrate utilized by beneficial bacteria. Increasing fiber intake shifts the microbial balance, favoring pathways that produce less-odorous compounds and effectively diluting tryptophan-fermenting bacteria. Therefore, a low-fiber, high-protein diet creates the environment for elevated indole and skatole levels.
Certain lifestyle factors, such as the use of antibiotics, can also temporarily disrupt the gut microbiome. Antibiotics reduce the total population of bacteria, including those responsible for breaking down tryptophan, leading to an unpredictable change in the stool’s chemical profile and smell. When the diet returns to normal or the body adjusts, these temporary odor changes typically resolve quickly.
Underlying Digestive and Malabsorption Issues
If the unusual odor persists for more than a few days, the cause may relate to malabsorption, an inefficiency in the body’s ability to break down food. In a healthy digestive system, nearly all protein is absorbed in the small intestine, leaving little tryptophan for colon bacteria. When malabsorption occurs, large amounts of undigested protein, fat, and carbohydrates are delivered to the large intestine.
This undigested material acts as an excessive food source for colon bacteria, leading to a significant increase in the fermentation of tryptophan and a corresponding rise in indole and skatole. One common cause is Exocrine Pancreatic Insufficiency (EPI), where the pancreas does not produce enough digestive enzymes, including the proteases needed to break down protein. The resulting stool is often characterized as steatorrhea—greasy, pale, and floating—which has a foul, sometimes chemical or mothball-like smell.
Inflammatory Bowel Diseases (IBD), such as Crohn’s disease, and Celiac disease also frequently cause malabsorption. Inflammation and damage to the small intestine lining reduce the surface area available for nutrient uptake. This damage ensures that more undigested food components, including tryptophan-rich proteins, reach the large intestine for bacterial over-fermentation. Any condition causing poor digestion or rapid transit time can contribute to this mechanism, increasing the concentration of odor-causing compounds.
Warning Signs and When to Consult a Physician
While a change in stool odor is often benign, certain accompanying symptoms suggest the need for a medical evaluation. The most important indicator is persistence; if the mothball odor continues for several days or weeks without an obvious dietary cause, a consultation is warranted.
Attention should be paid to the appearance of the stool, particularly if it becomes pale, bulky, or greasy, which are classic signs of steatorrhea. Stools that are difficult to flush or leave an oily residue in the toilet bowl indicate significant fat malabsorption.
Other warning signs include systemic issues pointing to nutrient deficiency or chronic inflammation. These include unexplained weight loss, chronic diarrhea, persistent abdominal pain or cramping, and fever. The presence of blood or mucus in the stool should also prompt immediate medical attention. A physician can perform a simple stool test to measure enzyme activity or fat content, helping to identify or rule out underlying malabsorption issues.