The organic acids test is a simple and safe test that can tell you if the microorganisms in your gut are making you sick by studying a urine sample. Read on the learn more about this amazingly useful test.

What is The Organic Acids Test?

Organic acids are a wide group of substances produced by our body during the processes of breathing, metabolizing food, and producing the different molecules it needs [R].

These substances are filtered by our kidneys and leave the body in the urine, where they have much higher concentrations than they do in our blood.

By studying the quantities of these molecules in our urine, we can identify if the levels of one or several organic acids are outside the normal values (that is, higher or lower than the average values for a set of healthy individuals).

The organic acids test can give us information on the state of our health and our nutrition, such as if there are any vitamin deficiencies or genetic defects. It can even detect poison [R].

What Changes the Levels of Organic Acids?

Our body produces and uses a great number of enzymes. Enzymes help make the chemical reactions in our body proceed at a faster rate. If an enzyme is not working properly or not working at all, the reaction it is in charge of (catalyzes) will happen very slowly and, similarly to a clogged pipe, the intermediate product will begin to build up. The OAT test measures the levels of these intermediate products.

  • An enzyme can be improperly produced, or even be completely absent, as a consequence of a genetic defect [R].
  • The age and diet of each person also influence the results, since the availability or lack of some nutrients can change the efficiency or production of the enzymes [R].
  • The presence of heavy metals, such as mercury, decreases the activity of some enzymes [R].
  • High levels of stress can decrease the function of enzymes involved in the production of neurotransmitters [R].
  • The uncontrolled growth of bacteria or yeast in the gut also changes our enzyme levels [R].

Yeast and Bacteria Change Organic Acid Levels

The gut microbiota is a combination of billions of bacteria, fungi, and viruses that naturally live in the gut. It develops with us throughout our life, and is influenced by our genetics, diet, and environment [R, R].

When the different species in our gut microbiota are no longer working together for mutual benefit, a condition called dysbiosis develops. This is when disease-causing microbes grow in large numbers over our “good” microbes [R].

Under healthy conditions, the substances produced by our microbiota help our gut to function properly. When this malfunctions, these substances can enter our blood as the intestinal barrier becomes more permeable. Our enzymes try to transform these substances but, as it might happen when using the wrong key in a lock — since the fit is wrong — the enzymes don’t work properly [R].

Dysbiosis can result in gut diseases like irritable bowel syndrome, celiac disease, and inflammatory bowel disease or in other conditions like obesity, metabolic disorder, heart disease, allergies, and asthma [R].

Organic Acids Testing: Yeast and Bacteria

The Organic Acids Test for yeast and bacteria measures the amount of certain organic acids from the first urine produced in the morning. These acids are produced by the microorganisms in our gut. The exact number and nature of the organic acids measured will depend on the laboratory performing the test.

The amount is reported as the concentration of the substance (as mmol or micrograms) in respect to a reference amount of creatinine (per mol or per milligram) found in the urine. The concentration of creatinine is used as a reference of how much water the person drank,  which can tell you if the sample is too diluted.

Normal Levels

The reference values for the organic acids included in this tests are [R, R, R]:

Acids related to yeast and fungus overgrowth:

  • Arabinose: ≤ 29 mmol/mol creatinine
  • D-Arabinitol: ≤ 73 µg/mg creatinine
  • Carboxycitric:    ≤ 29 mmol/mol creatinine
  • Citramalic: ≤ 3.6 mmol/mol creatinine
  • Furan carbonyl glycine: ≤ 1.9 mmol/mol creatinine
  • Furan-2,5-dicarboxylic: ≤ 16 mmol/mol creatinine
  • 5-Hydroxymethyl-2-furoic: ≤ 14 mmol/mol creatinine
  • 3-Oxoglutaric:    ≤ 0.33 mmol/mol creatinine
  • Tartaric: ≤ 4.5 mmol/mol creatinine
  • Tricarballylic: ≤ 0.44 mmol/mol creatinine (or ≤ 1.41 µg/mg creatinine)

Acids related to bacterial overgrowth:

  • Benzoate: ≤ 9.3 µg/mg creatinine
  • Hippuric: ≤ 613 mmol/mol creatinine (or ≤ 1070 µg/mg creatinine)
  • 4-Hydroxybenzoic: ≤ 1.3 mmol/mol creatinine (or ≤ 1.8 µg/mg creatinine)
  • 2-Hydroxyhippuric: ≤ 1.3 mmol/mol creatinine
  • 4-Hydroxyhippuric: 0.79-17 mmol/mol creatinine
  • 2-Hydroxyphenylacetic: 0.06-0.66 mmol/mol creatinine (or < 1.4 µg/mg creatinine)
  • Indican: ≤ 90 µg/mg creatinine
  • D-Lactate: ≤ 4.3 µg/mg creatinine
  • Phenylacetate: ≤ 0.18 µg/mg creatinine
  • Phenylpropionate: ≤ 0.06 µg/mg creatinine

Acids produced by “good” bacteria:

  • DHPPA: ≤ 0.38 mmol/mol creatinine

Acids related to Clostridium overgrowth:

  • 4-Cresol: ≤ 75 mmol/mol creatinine
  • 3,4-Dihydroxyphenylpropionate: ≤ 0.05 µg/mg creatinine
  • HPHPA: ≤ 208 mmol/mol creatinine
  • 4-Hydroxyphenylacetic: ≤ 19 mmol/mol creatinine (or ≤ 34 µg/mg creatinine)
  • 3-Indoleacetic: ≤ 11 mmol/mol creatinine (or 0.60-10.50 µg/mg creatinine)

Yeast and Bacterial Overgrowth Causes

1) Antibiotics

The use of oral antibiotics is a common cause of changes in the microbiota. The effect will depend on the dosage, how long the antibiotic was taken, and the type of antibiotic [R].

Changes in the microbiota can allow fungi or bacteria normally present in the gut to grow out of control, which often causes issues such as diarrhea. This is the case for different species of bacteria, such as Clostridium difficile, and of the yeast Candida albicans [R].

The imbalance can also allow microorganisms that cause diseases to reproduce and cause an infection [R].

2) Stress

Our body responds to stress by releasing hormones. Our microbiota responds to these hormones by releasing active compounds into the blood [R].

High levels of stress can diminish the amount of the beneficial bacteria, Lactobacillus and Bifidobacterium in our gut. It also lowers the natural protection of the gut, making it an easy target for infection-causing microorganisms like E. coli or Y. enterocolitica [R, R].

3) Diet

High-protein Diets

When we eat an excess amount of protein, some of it is not completely digested. The protein that has not been broken down by the enzymes in the stomach can reach the gut. There, the protein is used by the microbiota, which produces different substances than our body would. This is especially true of animal protein [R, R].

High Carbohydrate and Sugar Diets

A large amount of refined sugar in the diet causes fermentation to occur in the gut. It also changes the production of bile acids and their use by our gut bacteria, altering the gut environment and the microbiota balance [R].


Sulfate is found in food preservatives, dried fruits, dehydrated vegetables, packaged fruit juices, and most alcoholic beverages. The protein in cow’s milk, cheese, eggs, and meat also contain large amounts of sulfur that can be converted into sulfate in the body. Large amounts of sulfate change the gut environment, thus helping the growth of microorganisms that cause disease [R].

4) Lowered Immune System Response

In the gut, a very close interaction between our immune system and microorganisms takes place. Our microbiota helps develop our adaptive immune response (the type that produces antibodies), and they balance each other. When the immune response is weakened (we become immunosuppressed), the balance is broken,  allowing for the uncontrolled growth of some species [R, R].

5) Certain Medication

Drugs that alter the balance of the gut microbiota due to their effects, either directly or indirectly, are:

  • Antacids: Some medications that diminish the amount of acid in the stomach (proton pump inhibitors) such as omeprazole, lansoprazole, or pantoprazole, may cause SIBO (small intestine bacterial overgrowth) [R].
  • Antipsychotics: The use of atypical antipsychotics like risperidone, changes the gut microbiota in women but not men [R].
  • Metformin: diabetes medication, like metformin, that lower blood glucose levels can change the microbiota, possibly by affecting the bile acids available [R].
  • Opioids: The use of opioids can cause constipation and modify the gut environment [R].
  • Statins: certain drugs that help lower cholesterol levels can either cause constipation or act as laxatives [R, R].

Ways to Decrease Bacterial and Yeast Overgrowth

1) Antibiotics

Antibiotics Kill Clostridium Bacteria

Although antibiotics may cause a Clostridium difficile infection, they should be used to treat the infection. Complications from C. difficile infections are serious and may lead to loss of a part of the colon or death. Standard therapy for controlling C. difficile includes antibiotics like metronidazole, vancomycin, or fidaxomicin [R].

Rifaximin Improves Traveler’s Diarrhea

Rifaximin is a broad spectrum antibiotic that kills both gram-positive and gram-negative bacteria with very little effects on the microbiota [R].

2) Probiotics and Prebiotics Help with Diarrhea

Probiotics are living microorganisms that have a beneficial effect on our health. The most common are species of the Lactobacillus and Bifidobacterium families. Their effect on restoring the microbiota depends on the cause of the imbalance [R, R].

Prebiotics are substances that cannot be digested but stimulate the growth of specific bacteria in the gut. Oligofructose, a type of fiber, helped prevent diarrhea caused by C. difficile in a DB-RCT with 142 patients with a previous infection [R].

3) Fecal Microbiota Transplantation Stops Clostridium Overgrowth

In cases where the microbiota has been severely affected, gut bacteria from a healthy donor is transplanted into the patient’s gut, where they replace the unstable microbiota. This is usually effective to stop infections by C. difficile [R].

4) Whole Grains Help Good Bacteria

A diet rich in whole grains helps balance our gut microorganisms and increase the levels of Lactobacillus and Bifidobacterium [R, R].

5) Regular Exercise Balances Gut Microorganisms

Although excessive exercise can generate physical stress and damage the microbiota, regular exercise helps keep a varied and stable microbiota. Small but significant changes in the microbiota happen when a person begins working out [R, R].

6) Tributyrin Helps with Diarrhea Due to Antibiotic Use

Tributyrin is decomposed in the gut into butyrate, a short-chain fatty acid. A tributyrin supplement helped improve diarrhea caused by antibiotics in mice [R].

Genetics of Microbial Gut Imbalance


Nod2 is a protein that recognizes bacterial molecules and stimulates an immune reaction. Three polymorphisms in the NOD2/CARD15 gene affect Nod2 function [R, R]:


IL-23R is a subunit for the receptor of the inflammatory IL-23 that participates in the immune response in the gut mucosa. Several polymorphisms in the IL-23R gene are associated with autoimmune and inflammatory conditions, like inflammatory bowel disease or Crohn’s disease, in Caucasians [R]:


ATG16L is a protein that has an important role in the process that helps the body get rid and recycle old components. It is found in the gut and helps maintain microbiota balance. A T300A SNP, rs2241880, causes a lack of production of this protein [R].


IRGM is an enzyme that is also involved in the process that helps the body eliminate and recycle old components. Mutations in the IRGM gene (rs10065172) lead to reduced production of this enzyme [R].

Effect of Food on Organic Acids Test

Apples, grapes, pears, cranberries, and their juices will interfere with the test since they contain benzoic acid. It is advised to avoid them for 24 hours before the test.

Limitations and Caveats

The reference concentrations for the different substances of the Organic Acids Test were taken as the mean values for a set of males or females 13 years or older. Values might vary within that age group, as well as for different geographical zones or ethnical groups.

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