The unusual odor of stool, often described as “burning,” reflects the chemical processes occurring in the digestive tract. This smell is not caused by burning material but by highly concentrated gaseous byproducts of metabolism and microbial action. The human nose detects these smells as volatile organic compounds (VOCs) released during the final stages of digestion. These VOCs are the gaseous end products of food breakdown by the trillions of bacteria residing in the large intestine. Any change in diet, nutrient absorption, or the balance of the gut’s microbial community can dramatically shift the profile and intensity of these compounds.
Dietary Triggers and Supplements
A sudden change in stool odor is most frequently linked to the consumption of certain foods or supplements, which alters the raw material available for gut bacteria. Foods high in sulfur are primary contributors to strong, chemical-like odors. When gut bacteria break down sulfur-containing amino acids, they produce gases like methyl mercaptan and hydrogen sulfide, which can be perceived as a pungent or rotten-egg smell.
Cruciferous vegetables (broccoli, cauliflower) and alliums (garlic, onions) are rich in these sulfur compounds. Similarly, a diet high in animal protein provides the amino acid tryptophan, which is fermented by colon bacteria into compounds like skatole and indole, contributing to an intense odor. Certain supplements, particularly high-dose protein powders, increase the nitrogenous material bacteria must process.
Iron supplements can also change the character of stool odor, often described as metallic. Unabsorbed iron passes into the colon, where it interacts with sulfur compounds, intensifying the foulness of the smell. Artificial sweeteners and sugar alcohols, which are poorly absorbed, reach the colon where they are rapidly fermented, leading to increased gas and a chemical-like smell. These dietary factors often result in a temporary odor change.
Malabsorption and Undigested Fats
When the body struggles to absorb nutrients properly, the resulting condition is known as malabsorption. This can cause a distinct, rancid odor often interpreted as chemical or burning, particularly in cases of fat malabsorption, medically termed steatorrhea. Steatorrhea occurs due to a deficiency in necessary digestive components, such as bile from the liver or fat-digesting enzymes (lipase) from the pancreas.
Without sufficient bile or enzymes, dietary fats pass undigested and reach the large intestine. Colon bacteria then ferment these large amounts of fat, leading to the production of volatile fatty acids and other byproducts that create an unusually foul, greasy smell. Stools affected by steatorrhea are typically bulky, pale, float in the toilet water, and leave an oily residue.
Conditions that damage the small intestine lining, such as Celiac disease or Crohn’s disease, can impair the ability to absorb fats, leading to this severe odor. Chronic inflammation of the pancreas (pancreatitis) or cystic fibrosis can also limit enzyme production, directly causing fat malabsorption and the associated pungent smell.
Shifts in Gut Bacteria and Infections
The community of microbes in the gut, known as the microbiome, plays the largest role in determining stool odor. A dramatic shift in the balance of these organisms, called dysbiosis, can lead to a highly unusual and chemical smell. Pathogenic infections, especially those causing severe gastrointestinal distress, are a prime example of this microbial shift.
One notable infection is Clostridioides difficile (C. difficile), a bacterium that can overgrow, often following a course of antibiotics that eliminates beneficial bacteria. C. difficile produces a specific profile of VOCs, including compounds like 4-methylphenol (p-cresol) and indole, which result in a distinct, foul odor. This unique metabolic signature from the pathogen creates the strong, non-typical smell.
Other infections, such as those caused by the parasite Giardia or various bacteria, disrupt normal fermentation pathways, leading to the rapid putrefaction of proteins and carbohydrates. The altered microbial activity generates an excess of foul-smelling gases that overwhelm the typical odor profile. Antibiotics can also temporarily cause a chemical smell by killing bacterial species, allowing odor-producing strains to gain an advantage.
When to Consult a Healthcare Provider
While a temporary change in stool odor is usually harmless and related to diet, a persistent or worsening “burning” or chemical smell warrants medical evaluation. The most important factor is the duration and presence of accompanying symptoms. Odor changes lasting longer than one week, especially if unrelated to a recent dietary change, should be discussed with a doctor.
There are specific red flags that indicate a need for prompt medical attention. These include:
- Visible blood in the stool.
- Unexplained weight loss.
- Persistent, severe abdominal pain or cramping.
- Fever or chronic diarrhea.
- Signs of nutritional deficiency, such as new fatigue or easy bruising.
Persistent, greasy, and pale stools that are difficult to flush may signal a serious malabsorption issue that requires diagnosis and treatment for an underlying condition like Celiac disease or chronic pancreatitis.