Skatole and indole, two compounds produced by gut bacteria as they break down the amino acid tryptophan, are the primary chemicals behind the mothball-like smell some people notice in their stool. A landmark gas chromatography study of human feces found that these two benzopyrrole volatiles produce what researchers described as a “naphthalene-like mothball odor,” both in their pure crystalline form and when extracted from actual stool samples.1PubMed. Gas-chromatographic and mass-spectrometric analysis of the odor of human feces So if your poop smells like mothballs, the chemistry is not mysterious at all: your nose is picking up on one or both of these compounds at elevated concentrations. What varies, and what matters, is why those concentrations rise and fall.
The Actual Chemicals Responsible
Naphthalene is the compound that gives traditional mothballs their distinctive sharp, slightly sweet smell. Skatole and indole are structurally related aromatic molecules, and when concentrated, they share that same pungent, waxy quality. This is not a coincidence or a trick of perception. The molecules belong to overlapping chemical families and activate similar odor receptors in your nose. Skatole in particular has been well characterized as having a fecal-naphthalene crossover odor at moderate to high concentrations.
What makes the connection especially interesting is that indole, at very low concentrations, actually smells floral. It is found naturally in jasmine and narcissus blossoms and is widely used in the fragrance industry to add a rich, floral note to perfumes and even food products like dairy and tea.2PubMed Central. Production of indole by Corynebacterium glutamicum microbial cell factories for flavor and fragrance applications Only when the concentration climbs does indole flip from pleasant to foul, and at the levels found in stool, it lands firmly in mothball territory. Skatole does not have this dual personality; it smells unpleasant at virtually any concentration people encounter.
How Your Gut Bacteria Make These Compounds
Both skatole and indole are produced when bacteria in your large intestine metabolize tryptophan, an essential amino acid found in protein-rich foods. Tryptophan arrives in the colon either because it was not fully absorbed in the small intestine or because it was part of undigested protein. Once there, specific bacterial species break it down through a process that yields indole and its derivatives.3PubMed Central. New Insights Into Gut-Bacteria-Derived Indole and Its Derivatives in Intestinal and Liver Diseases Skatole is then produced from indole through further bacterial metabolism.
This means the mothball smell is not random. It reflects what is happening inside your gut microbiome at a given time. The total amount of tryptophan reaching your colon, the specific bacterial communities living there, and how quickly material moves through your system all influence how much skatole and indole end up in the final product. When conditions favor higher production of these compounds, the mothball note becomes stronger and more recognizable.
Why the Smell Might Be Stronger on Some Days
If you have noticed the mothball quality is not constant, that tracks with the science. Several factors push skatole and indole production higher or lower:
- High-protein meals: More dietary protein means more tryptophan reaching the colon. A steak dinner, a large serving of eggs, or a heavy day of protein shakes can increase the raw material available for bacterial fermentation, amplifying the mothball odor the next day.
- Low fiber intake: Fiber gives gut bacteria an alternative food source. When plenty of fermentable carbohydrate is available, skatole-producing bacteria preferentially use the carbohydrate instead of tryptophan, which reduces skatole output. Fiber fermentation also produces short-chain fatty acids that lower the pH in the colon, and that lower pH shifts bacterial metabolism toward making indole rather than skatole.4Animal Nutrition. Mulberry leaf supplementation inhibits skatole deposition by regulating gut microbiota and upregulating liver cytochrome P450 1A1 expression in finishing pigs Since skatole smells worse than indole at comparable concentrations, less fiber can mean a more pungent result.
- Slow transit time: Constipation or slower bowel movements give bacteria more time to work on tryptophan. The longer stool sits in the colon, the more volatile compounds accumulate. This is one reason why the first bowel movement after a period of constipation can smell especially strong.
- Gut microbiome composition: Not all bacterial communities produce skatole and indole at the same rate. Shifts in which species dominate your gut, whether from travel, stress, illness, or diet changes, can alter the chemical profile of your stool and therefore its smell.
The fiber connection is worth highlighting because it suggests a practical intervention. Research in animal models has demonstrated that increasing dietary fiber and plant-derived polysaccharides substantially reduces skatole accumulation by shifting how gut bacteria handle tryptophan.4Animal Nutrition. Mulberry leaf supplementation inhibits skatole deposition by regulating gut microbiota and upregulating liver cytochrome P450 1A1 expression in finishing pigs While these studies used pigs rather than humans, the underlying microbial pathways are well conserved. Adding more vegetables, whole grains, and legumes to your diet is a reasonable first step if the mothball smell bothers you.
When the Smell Could Signal a Health Problem
A passing mothball smell in your stool is usually just a reflection of what you ate and how your gut bacteria handled it. But a sudden, persistent change in stool odor, especially if it comes with other symptoms like diarrhea, cramping, or changes in stool consistency, can sometimes point to something that deserves medical attention.
Certain infections change the volatile chemical profile of stool in measurable ways. Clostridioides difficile infection, for example, produces elevated levels of indole and a compound called p-cresol (4-methylphenol), both of which have been identified as potential volatile biomarkers for the infection.5PubMed Central. Faecal volatile biomarkers of Clostridium difficile infection People with C. diff often describe their stool as having an unusually distinctive, chemical-like smell, and the presence of elevated indole is part of why. That said, C. diff typically comes with watery diarrhea and fever, not just an odd smell, so the smell alone is not diagnostic.
More broadly, researchers have found that the volatile organic compounds in stool shift in detectable patterns during various gastrointestinal disorders. The idea behind volatile metabolomics is that the odorous changes people notice during illness are not imaginary but correspond to real shifts in the metabolic activity happening in the gut.5PubMed Central. Faecal volatile biomarkers of Clostridium difficile infection Conditions like inflammatory bowel disease, malabsorption syndromes, and bacterial overgrowth in the small intestine can all alter which volatile compounds dominate stool odor.
Antibiotics deserve special mention. Broad-spectrum antibiotics can dramatically reshape the gut microbiome in a short period, killing off some bacterial populations while allowing others to flourish. One case study documented how oral antibiotic therapy shifted the dominant bacterial species in the gut and significantly changed the composition of volatile metabolites the patient produced.6PubMed Central. Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year If your stool started smelling like mothballs during or after a course of antibiotics, the likely explanation is that the antibiotic disrupted the balance of bacterial communities responsible for tryptophan metabolism, temporarily favoring species that produce more skatole or indole.
How Complex Your Stool’s Chemistry Really Is
Skatole and indole get the attention because of their strong odors, but they are just two compounds in an enormous chemical soup. Advanced analytical techniques have identified around 270 volatile organic compounds in human stool, a number that expanded existing knowledge of the fecal volatilome by roughly 20%.7PubMed Central. Advancing fecal volatilome profiling by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry and image pattern recognition These include short-chain fatty acid esters, aldehydes, alcohols, terpenes, and various aromatic hydrocarbons, most of them produced by microbial fermentation in the gut.
This matters because what you perceive as a single “mothball smell” is actually your brain interpreting a complex mixture of dozens of volatile compounds. Skatole and indole may dominate when they are at high concentrations, but the overall odor character is always a blend. Two people eating the same diet might produce noticeably different stool odors because their gut bacteria are producing different ratios of these 270-plus compounds. This is also why stool odor varies so much from day to day even for the same person: a slight change in diet, hydration, or transit time can shift the relative concentrations enough for your nose to notice.
The Concentration Flip That Makes Indole Fascinating
Indole’s behavior at different concentrations is one of the more surprising facts in odor chemistry. At the trace levels found in flower petals, it smells like jasmine, and perfumers have used it for over a century to create rich floral notes. At the much higher concentrations found in feces, the same molecule smells like mothballs and decay. The fragrance industry considers indole a high-demand ingredient, and researchers have worked on producing it through microbial fermentation precisely because extracting it from plants yields so little.2PubMed Central. Production of indole by Corynebacterium glutamicum microbial cell factories for flavor and fragrance applications
This concentration-dependent flip is not unique to indole, but indole is one of the most dramatic examples. It is a good illustration of why “chemical” does not automatically mean “bad.” The molecules themselves are neutral; it is the dose and context that determine whether we experience them as pleasant or repulsive. Next time you smell jasmine, part of what you are smelling is the same compound your gut bacteria produce every day.
Why We React So Strongly to Fecal Odors
There is a reason you notice a mothball-like smell in your stool and feel compelled to ask about it. Humans are exquisitely sensitive to fecal odors, and the disgust reaction they provoke is not just a social construct. Research in evolutionary biology describes disgust as an adaptive behavioral immune system, present across many species, that drives organisms to avoid contact with materials that carry pathogens.8PubMed Central. Disgust as an adaptive system for disease avoidance behaviour Feces is a major vector for intestinal parasites and bacterial pathogens, so the aversion is well calibrated from an evolutionary standpoint.
The response goes deeper than just avoidance behavior. Experiments have shown that smelling disgusting odors actually triggers a measurable immune response in the mouth. Exposure to foul smells raises levels of TNF-alpha, an immune signaling molecule, in saliva. Researchers interpret this as serving two purposes at once: priming the body’s defenses against potential incoming pathogens, and increasing sensitivity to bitter tastes, which further discourages eating contaminated food.9PubMed Central. Disgusting odors trigger the oral immune system Your revulsion at a strong mothball-like stool odor is, in a real biological sense, your immune system going on alert.
This sensitivity also explains why changes in stool odor grab your attention so effectively. Your nose is tuned to notice deviations from what it expects. A familiar odor, even an unpleasant one, fades into the background. A new or different odor breaks through, which is exactly why a sudden mothball quality might register as alarming even though the underlying compounds have been present in your stool all along, just at different levels.
Practical Steps if the Smell Persists
For most people, an occasional mothball-like note is just their gut bacteria doing their job with whatever tryptophan was available. If it bothers you and you want to reduce it, increasing your fiber intake is the most evidence-supported dietary strategy. Fiber gives your colonic bacteria an alternative energy source, reducing the extent to which they break down tryptophan into skatole. Fruits, vegetables, whole grains, and legumes all count.
Cutting back on concentrated protein sources, especially late in the day when transit time overnight may be longer, can also help. Staying well hydrated and physically active tends to keep transit time reasonable, which means less time for bacterial fermentation to accumulate volatile compounds.
If the mothball smell is new, strong, and accompanied by diarrhea, abdominal pain, blood or mucus in stool, fever, or unexplained weight loss, see a doctor. Those combinations point toward infection, inflammatory bowel disease, or malabsorption, all of which can shift stool volatiles. If the smell appeared during or shortly after antibiotic use, the most likely explanation is a temporary microbiome disruption that often resolves on its own over weeks, though persistent symptoms after antibiotics, especially watery diarrhea, warrant testing for C. difficile.
Probiotic supplements and fermented foods are sometimes suggested for normalizing gut bacteria after disruption. The evidence for their effect on stool odor specifically is thin, but they are generally safe and may help restore microbial diversity more quickly after antibiotic courses. What you should not do is use air fresheners or dietary supplements marketed as “internal deodorizers” as a substitute for investigating a genuinely new and persistent change in your stool. The smell is information. If it changed meaningfully, the question to answer is why.