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Organic Acid Test (OAT): Nutrient Deficiencies & Methylation

Written by Biljana Novkovic, PhD | Last updated:
Puya Yazdi
Medically reviewed by
Puya Yazdi, MD | Written by Biljana Novkovic, PhD | Last updated:

Organic acid test (OAT) has gained popularity among many functional health experts in recent years. What can it tell you about nutrient deficiencies? And does the insight these tests provide justify the costs? Read the article and judge for yourself.

What is the Organic Acid Test?

Organic Acid Test, popularly known as OAT, measures the levels of organic compounds in urine that are produced in the body as a part of many vital biochemical pathways. It’s used to check for RARE inborn genetic defects of metabolism, most often in newborns.

A defect in a particular pathway can result in either accumulation or lowered levels of its byproducts. Thus, measuring the levels of these markers can help to identify which metabolic process is blocked or compromised.

However, OAT has been increasingly available as a pricey, direct-to-consumer test recommended by many alternative practitioners. In this article, we will break down the science behind testing for particular nutrient deficiencies that OAT tests for, weighing in on whether they make sense.

B vitamins and Other Nutritional markers

1) Methylmalonic acid (Vitamin B12 Marker)

Methylmalonic acid (MMA) is a legitimate functional indicator of vitamin B12 deficiency. That’s because vitamin B12 is required for MMA to be converted to succinyl-CoA. When B12 is low, MMA levels in the blood and urine increase [1].

Methylmalonic acid levels increase in the early stages of vitamin B12 deficiency, when total vitamin B12 levels may still be in the normal range. Therefore, measuring MMA can tell you if you have a mild vitamin B12 deficiency [2].

Elevated MMA levels can be caused by:

  • Vitamin B12 deficiency [2]
  • Small bowel bacterial overgrowth (SIBO) in short bowel syndrome [3]
  • Common harmless genetic mutations [4]
  • Genetic disorders (methylmalonic acidemia) [5]
  • Aging [4, 6]

Levels can be low in kidney disease, even when vitamin B12 deficiency is present [7].

If you have high MMA levels, work with your doctor to find out what’s causing them – your doctor will likely order a vitamin B12 test for confirmation. Many older people have high MMA irrespective of vitamin B12 levels [4, 6].

Elevated urine MMA can tell you and your doctor if your vitamin B12 is low. Your doctor may run additional tests to confirm vitamin B12 deficiency, because MMA can also increase due to other causes.

2) Pyridoxic acid (Vitamin B6 Marker)

Pyridoxic acid is the product of vitamin B6 breakdown. Vitamin B6 is needed for more than 160 different metabolic reactions within the body. It works with B6-dependent enzymes, which are important for amino acid production and breakdown and the production of neurotransmitters, such as serotonin, noradrenalin, and GABA [8, 9, 10].

While blood vitamin B6 levels reflect tissue saturation, urinary pyridoxic acid responds almost immediately to change in dietary intake [11].

Approximately 40 – 60% of dietary vitamin B6 is excreted as pyridoxic acid [11, 12, 13].

Studies suggest that pyridoxic acid can increase due to:

  • Increased intake of B6 or supplementation with this vitamin [14]
  • Bed rest [15]
  • Ginkgo seed poisoning (increases pyridoxic acid but decreases vitamin B6) [16]

Low levels have been found in:

Urine pyridoxic acid should not be used as a marker of vitamin B6 status, because of potential confounders, such as dietary fluctuation or kidney dysfunction [11].

That’s why if your urine pyridoxic acid is low, your doctor will likely want to confirm it by ordering a more reliable blood test.

Elevated urine pyridoxic acid can tell you and your doctor if you’ve recently had foods rich in vitamin B6 or B6 supplements. But it can’t tell you if you’re deficient in this vitamin. Blood tests, which are more reliable, are used for that.

3) Pantothenic Acid (Vitamin B5)

Pantothenic acid (vitamin B5) is a water-soluble vitamin. It is required for the process of producing energy from food. It’s also required for making cholesterol, sex and stress hormones, hemoglobin, and neurotransmitters (acetylcholine and melatonin) [19].

Vitamin B5 deficiency is extremely rare, because this vitamin is present in nearly all foods [20].

High levels may be due to recent supplementation and are generally of no concern [21, 22].

Low levels can indicate nutritional deficiency [21, 22]. Discuss low levels with your doctor.

Low pantothenic acid (vitamin B5) levels may indicate a deficiency.

4) Glutaric Acid (Vitamin B2 Marker?)

Glutaric acid is produced as the breakdown product of some amino acids, including lysine and tryptophan [23].

Glutaric acid levels may increase in:

  • Celiac disease [24]
  • Genetic disorders called glutaric acidemias (very high glutaric acid levels) [25, 26, 27]

OAT proponents state that high glutaric acid levels may reflect vitamin B2 deficiency. However, we couldn’t find any research supporting this.

If your doctor suspects vitamin B2 (riboflavin) deficiency, they will likely order a blood or a urinary riboflavin test or erythrocyte glutathione reductase test [28].

Glutaric acid is also increased in a subset of children with autism (around 10%). Conversely, subjects with glutaric acidemia can have autistic features, e.g. lack of language and social skills, poor eye contact and stereotypical behavior [29].

Some studies suggest that people who have glutaric aciduria (multiple acyl-CoA dehydrogenase deficiency) or glutaric acidemia may benefit from:

  • Supplementation with B2, CoQ10 [30, 31]
  • Carnitine (to improve symptoms) [25, 32]
  • Restriction of dietary amino acids that can be converted into glutaric acids, such as lysine [33, 34]

Remember, that these disorders need to be diagnosed by qualified healthcare practitioners.

Glutaric acid test is mainly used to help diagnose rare inborn metabolic disorders.

5) Ascorbic acid (Vitamin C)

Ascorbic acid (Vitamin C) is a water-soluble vitamin and powerful antioxidant.

Vitamin C is essential for normal growth and development in the body. It is necessary for [35, 36]:

  • the formation, growth, and repair of bone, skin, and connective tissue
  • wound healing
  • maintaining healthy teeth and gums

Additionally, vitamin C is a powerful antioxidant and can regenerate other antioxidants, such as vitamin E [37, 38, 39].

Vitamin C also plays an important role in immune defense and improves the absorption of nonheme iron, the form of iron present in plant-based foods [40, 41].

Levels in urine reflect recent dietary intake rather than overall status in tissues [42].

If your urine levels are low and you are having signs and symptoms of vitamin C deficiency, your doctor will likely want to do a blood vitamin C test to check your levels. A urine test will reflect recent dietary intake, while a blood test reflects actual tissue levels.

Chronically high urine vitamin C levels, due to megadosing with vitamin C supplements, can increase the risk of oxalate kidney stones [43, 44].

Urinary vitamin C tests reflect recent dietary intake. They can’t be used to check for vitamin C deficiency.

6) 3-Hydroxy-3-Methylglutaric Acid (Coenzyme Q10 Marker?)

3-hydroxy-3-methylglutaric acid is a product of the abnormal breakdown of the amino acid leucine. It is also an intermediate compound in the production of cholesterol [45, 46, 47, 48, 49].

Elevated levels can therefore signal:

  • Issues in the leucine breakdown pathway [46]
  • Disrupted cholesterol-production (impaired function of HGM-CoA Reductase). Cholesterol is needed for making coenzyme Q10, sex hormones, bile acids, and vitamin D – so these may also be affected [50].

Elevated levels have been reported in diabetes and in people using statins [51, 50].

Very high levels are found in a rare inborn metabolic disorder called 3-hydroxy-3-methylglutaric aciduria, caused by defects in leucine metabolism [46, 47]. This disorder can be triggered by fasting or infection [46].

3-hydroxy-3-methylglutaric aciduria can be treated by a low-fat low-leucine diet [52]. Studies also suggest L-carnitine may help [47].

Ask your doctor to check your vitamin D, coenzyme Q10, and sex hormone levels if you suspect issues in cholesterol production. Coenzyme Q10 supplements may be beneficial if you have issues producing cholesterol, or if that pathway is purposefully blocked by statins [50].

Remember, always speak to your doctor before taking any supplements, because they may interfere with your health condition or your treatment/medications!

3-hydroxy-3-methylglutaric acid is used to screen for rare genetic disorders. It can also point to an issue in cholesterol production.

7) Methylcitric Acid (Biotin/Vitamin B7?)

Methylcitric acid is an intermediate compound of the energy metabolism.

High levels can be due to:

  • Vitamin B7 (biotin) deficiency, sometimes caused by eating raw eggs [53, 54]
  • Vitamin B12 (cobalamin) deficiency [55, 56, 57]
  • Genetic disorders [58, 59]

In a study of 281 subjects aged 65 and older, those with elevated methylcitric acid had worse cognitive function [60].

Although it’s used as a marker of biotin (vitamin B7) in OAT, levels of methylcitric acid can increase in both biotin and vitamin B12 deficiency.

If your methylcitric levels are abnormal, your doctor will likely test both your biotin and B12 blood levels.

Methylcitric acid can signal vitamin B7 (biotin) or vitamin B12 (cobalamin) deficiency. It’s also elevated in rare genetic disorders.

Methylation Markers

8) Uracil/Thymine (Folate)

Uracil is a pyrimidine naturally found in the body as a component of RNA. By methylation, uracil gets converted to thymine – one of the building blocks of DNA [61].

High values of uracil suggest folic acid deficiency, because folate is needed to convert uracil to thymine by methylation [62].

Both uracil and thymine are high in a rare genetic disease, dihydropyrimidine dehydrogenase deficiency. This disease has been linked to seizures and autism [63+, 64].

If your urinary uracil is high, your doctor may want to test your blood folate levels.

Remember, folate is a proxy of your fresh fruit and vegetable intake – make sure there’s plenty of them in your diet!

Elevated uracil without an elevation in thymine may point to folate deficiency. Elevated levels of both may indicate a rare genetic disorder.

Mineral Metabolites

9) Phosphoric Acid

Phosphorus (phosphate, phosphoric acid) is the second most abundant mineral in the human body. It’s crucial for muscle and nerve function, cell and DNA structure, and blood acid-base (pH) balance [65, 66, 67].

In order to keep the blood phosphate levels more or less constant, urine phosphate levels increase or decrease depending on the circumstances. In healthy adults, urinary phosphate levels usually reflect the dietary phosphate intake [68].

This means that your urine phosphate levels can tell how healthy your current diet is — i.e. urine phosphate levels can be used as a proxy for the amount of junk food and processed food in your diet (these types of food are rich in phosphate) [67, 69, 70, 71].

The following can increase urine phosphate levels:

The following can decrease urine phosphate levels:

  • Low-phosphate diet (including conditions of malabsorption, diarrhea, and starvation) [71]
  • Phosphate binders, meds used to decrease the absorption of phosphate in the gut [86]
  • Low parathyroid hormone levels (hypoparathyroidism) [72, 87]
  • Vitamin D toxicity [88]
  • Chronic kidney disease [72]
  • High blood pH (respiratory alkalosis) [89]
  • Some hereditary disorders [72]

Causes shown above are commonly associated with high and low phosphate levels. Work with your doctor or another health care professional to get an accurate diagnosis. Your doctor will interpret your results, taking into account your medical history, symptoms, and other test results.

How Likely are Certain Nutrient Deficiencies?

Many vitamin deficiencies are rare/unlikely and happen only in people who are severely malnourished or have specific medical issues known to cause nutrient deficiencies, such as gut disorders that impair nutrient absorption. Doctors will usually test people who are either at risk or who show signs or symptoms of a particular deficiency.

In developed countries, doctors will most often test vitamin B12, vitamin D, and folate. Other vitamin deficiencies are less likely.

Read more about common vitamin and mineral deficiencies here.


Some of the nutritional markers tested as a part of OAT may point to valid nutrient deficiencies, mainly: methylmalonic acid, pantothenic acid, methylcitric acid, and uracil/thymine. However, in all of these cases, blood tests are more reliable and your doctor is likely to order them for confirmation.

Further Reading

To find out which parts of the OAT test can be useful, and which are nonsense, we delve into the science and look into each of the marker types in isolation:

Learn more about OAT with the CEO of SelfDecode Joe Cohen and Dr. Tommy Wood: 

About the Author

Biljana Novkovic

Biljana Novkovic

Biljana received her PhD from Hokkaido University.
Before joining SelfHacked, she was a research scientist with extensive field and laboratory experience. She spent 4 years reviewing the scientific literature on supplements, lab tests and other areas of health sciences. She is passionate about releasing the most accurate science and health information available on topics, and she's meticulous when writing and reviewing articles to make sure the science is sound. She believes that SelfHacked has the best science that is also layperson-friendly on the web.


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