Metabolism is the essential bodily process of creating energy from food. Food consists of nutrients that the chemicals of the digestive system break down into sugars and acids for fuel.

Metabolic disorders disrupt these natural chemical reactions. For example, some metabolic disorders affect the breakdown of amino acids, while others affect that of carbohydrates or fats.

Therefore, a person with a metabolic disorder may have too much or too little of certain substances. This imbalance can cause specific substances to build up in the bodily fluids, leading to bad breath, or halitosis.

This article looks at the metabolic disorders that cause bad breath and the potential management options.

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In up to 90% of people with persistent bad breath, the cause is oral in origin and involves poor dental hygiene, leading to gum disease.

When someone does not clean their teeth properly, bacteria break down any food particles in the mouth and produce sulfurous compounds that smell unpleasant.

Additionally, the bacteria create a sticky film of bacteria called plaque. The plaque can spread and grow beneath the gumline. The toxins that the bacteria produce irritate the gums, cause inflammation, and break down and destroy the gum tissues, contributing to bad breath.

Other causes of bad breath include:

  • respiratory diseases
  • upper respiratory tract infections
  • cystic fibrosis
  • leukemia
  • gastric ulcers
  • hiatal hernia
  • menstruation
  • certain medications
  • smoking
  • alcohol
  • metabolic disorders

Some metabolic disorders can cause bad breath, including:

  • trimethylaminuria (TMA)
  • diabetes
  • chronic kidney disease (CKD)
  • liver disease
  • phenylketonuria (PKU)
  • hypermethioninemia

These disorders may cause bad breath because of various issues with the intestines, blood, or liver. People with halitosis often have elevated salivary urea and uric acid concentrations compared with those without the issue.


Doctors also call TMA fish odor syndrome because it causes the body to release a smell of rotting fish in the urine, sweat, breath, and reproductive fluids.

People with TMA cannot break down the compound trimethylamine from certain foods. In people without the disorder, the body oxidizes trimethylamine into an odorless metabolite called trimethylamine N-oxide. When trimethylamine builds up, it causes an odor.

TMA runs in families and happens because someone has a fault with the FM03 gene.


People with this genetic metabolic disorder have mutations in the MAT1A, GNMT, or AHCY genes.

Some people may experience no symptoms, whereas others may have neurological issues, liver problems, and breath, sweat, or urine that smells like boiling cabbage.

The smell occurs because the body cannot break down a particular amino acid called methionine in the blood. As a result, the methionine builds up and causes the smell.

It may also happen because the person has liver disease or has eaten large amounts of protein.


If a person is unable to control their diabetes effectively, high glucose levels can cause harmful bacteria to grow. In combination with food, they produce a sticky film called plaque, which can lead to gum disease and bad breath.

Additionally, because people with diabetes have issues with insulin, cells may not receive the glucose they require for energy. When this happens, the body begins to burn fat instead, producing compounds called ketones. These may build up in the blood and urine and cause bad breath. One of these ketones is acetone, and it may cause breath that smells similar to nail polish.

If a person with diabetes notices the smell, they should seek medical advice, as it could indicate diabetic ketoacidosis, a potentially life threatening condition.


People with kidney failure may develop bad breath. As the kidneys begin to fail, they cannot efficiently excrete the metabolite urea in the urine, and it builds up in the blood and saliva. The body then converts the urea into ammonia, causing a bitter taste in the mouth and bad breath.

About 1 in 3 people on dialysis report that their breath has a urine-like odor.

Liver disease

One of the symptoms of liver disease is the presence of volatile organic compounds in the breath. If a person’s breath has a strong, musty smell, it is a sign that their liver is not filtering out toxic substances, indicating liver disease.

Doctors call this distinct smell fetor hepaticus or “breath of the dead” because of its association with severe and potentially fatal liver disease.


PKU is a genetic condition that causes the body to be unable to break down the amino acid phenylalanine. It is more likely to appear in white, Native American, and Alaska Native people than Black, Ashkenazi Jewish, and Japanese people.

The condition affects about 1 in 10,000–15,000 babies born in the United States each year. Doctors screen babies for PKU shortly after birth.

Learn more about PKU.

No universal option exists for the treatment and management of bad breath. Although good oral hygiene may help temporarily, it does not solve the underlying problem. Therefore, the first step should be to treat the condition causing the bad breath if possible.

If metabolites cause bad breath, people may manage their symptoms by taking the following steps:

  • reducing the intake of foods that contribute to the odor
  • avoiding delaying bowel movements to minimize the duration of digestive metabolism and the absorption of metabolites
  • treating constipation, if applicable
  • using probiotic and prebiotic treatments to attempt to change the bacterial composition of the gut to one that produces fewer metabolites
  • increasing water intake to help excrete the metabolites in the urine

The exact approach depends on which metabolites are causing the problem. However, basic dental hygiene is the basis of bad breath management in all cases.

A person should speak with a doctor if they notice that their breath has a strong or unpleasant smell that does not go away.

The doctor can rule out common causes, such as gum disease, a urinary tract infection, or bacterial vaginosis.

If they cannot identify the cause, they may refer the person to a specialist who can perform tests and make a diagnosis.

If a person with diabetes notices changes in their breath, they should speak with their healthcare team urgently, as this can indicate diabetic ketoacidosis, a serious condition.

A range of metabolic disorders can cause bad breath. These include diabetes, chronic kidney disease, and liver disease. Certain genetic disorders, including TMA and hypermethioninemia, may also cause bad breath.

These conditions may cause metabolites to build up in the saliva, leading to bad breath.

Treatment approaches center around good oral hygiene practices and, if possible, addressing the underlying problem. People can also avoid certain foods, drink more water, and use probiotic and prebiotic treatments to rebalance their gut bacteria.

Anyone with a chronic bad breath problem that does not go away with standard hygiene practices should consult a doctor.

A person with diabetes should speak with a doctor immediately if they notice their breath developing an acetone-like scent. This odor can indicate a serious complication of diabetes called diabetic ketoacidosis.