The organic acids test includes markers of yeast and bacterial overgrowth. How reliable are these markers? What causes yeast and bacterial overgrowth and what can be done about it? Read on to find out.
What is The Organic Acids 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 pricy, direct-to-consumer test recommended by many alternative practitioners. In this article, we will look into the tests that purportedly signal yeast and bacterial overgrowth. We’ll also go over the causes of yeast and bacterial overgrowth and ways to address them.
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 lives and is influenced by our genetics, diet, and environment [1, 2].
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 .
Dysbiosis can has been associated with gut diseases like irritable bowel syndrome, celiac disease, and inflammatory bowel disease and with other conditions like obesity, metabolic disorder, heart disease, allergies, and asthma .
Read more about the gut microbiome and the roles it plays here.
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 can be 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 for how much water the person drank, which can tell you if the sample is too diluted.
Keep in mind that the reference values given in these tests are often not backed by scientific studies and need to be taken with a grain of salt.
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 Fungal Markers
There is a certain amount of scientific support backing the use of these markers [7, 8, 9]. However, in general, much larger and well-designed studies are needed to confirm that these markers are indeed suited to test for yeast and fungal overgrowth in the general population.
There are studies that connect these markers to bacterial overgrowth in humans. However, when interpreting these markers, it’s important to keep in mind that factors and conditions other than bacterial overgrowth/dysbiosis can increase them. For example:
- Benzoic acid can increase with elevated benzoate intake, elevated benzoate production by gut bacteria, a urinary infection, or liver or kidney issues with the benzoate-hippurate conversion [10, 11, 12, 13].
- Hippuric acid tests are used to check for occupational exposure to toxins such as toluene [14, 15]
- 4-hydroxybenzoic acid increases after consuming almonds, strawberries, green tea, and gingko or oregano extract [16, 17, 18, 19, 20, 21, 22]. 4-hydroxybenzoic acid levels also increase after ingestion of parabens — these are additives used as preservatives in foods, cosmetics, and pharmaceuticals .
- Indican can increase on diets high in protein and low in fiber [24, 25]. Vegetarians generally have lower indican levels . Indican levels also increase in malabsorptive disorders, such as celiac disease and hypochlorhydria (low stomach acid) [26, 27, 28].
- Phenylacetic acid can increase with the ingestion of certain foods and drugs, exercise, gut dysbiosis, chronic alcoholism, and in a metabolic disorder called phenylketonuria [29, 30, 31, 32, 33, 34].
- Phenylproprionate can increase in phenylketonuria 
- 3,4-Dihydroxyphenylpropionate or DHPPA is listed by one company as beneficial, by the other as signaling bacterial overgrowth. DHPP is produced in the breakdown of caffeic acid by gut bacteria [36, 37, 38, 39, 40]. It’s production slightly increases after ingestion of caffeic acid sources, such as coffee, mate, and many types of spices, fruits, and vegetables .
- 4-hydroxyphenylacetic acid can increase in a genetic disorder called tyrosinemia. In addition, people on vegetarian and Mediterranean diets tend to have higher levels [41, 42, 43, 44, 45, 46].
Because of all these confounders, it’s important to discuss any abnormalities with your doctor, who will interpret the results based on your medical history, signs, symptoms, and more reliable test results.
Causes of Yeast and Bacterial Overgrowth
The use of antibiotics is a common cause of changes in the microbiota. The effect will depend on the dosage, length of treatment, and the type of antibiotic .
Changes in the microbiota can allow fungi or bacteria normally present in the gut to grow out of control, which then often cause issues such as diarrhea. This is the case for different species of bacteria, such as Clostridium difficile, and of the yeast Candida albicans .
In some cases, the imbalance can also allow microorganisms that cause diseases to reproduce and cause an infection .
That’s why you should only take antibiotics as prescribed by your doctor.
Our body responds to stress by releasing hormones. Our microbiota responds to these hormones by releasing active compounds into the blood .
Some studies suggest that high levels of stress can diminish the amount of the beneficial bacteria, Lactobacillus and Bifidobacterium, in our gut. It may also lower the natural protection of the gut, making it an easy target for infection-causing microorganisms like E. coli or Y. enterocolitica [47, 49].
While the mechanisms here are certainly plausible, larger studies are needed to confirm the link between stress and microbial imbalance.
When we eat an excessive 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. Studies suggest that microbes can use the protein to produce metabolites that our body’s usually don’t produce. This is especially true of animal protein [50, 47].
High Carbohydrate and Sugar Diets
A large amount of refined sugar in the diet causes fermentation to occur in the gut. Studies also suggest that sugar in excess can change the production of bile acids and their use by our gut bacteria, altering the gut environment and the microbiota balance .
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. Some research suggests that large amounts of sulfate may change the gut environment, thus helping the growth of microorganisms that cause disease .
4) Lowered Immune System Response
In the gut, a very close interaction between our immune system and microorganisms takes place. Researchers found that 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 [53, 54].
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) .
- Antipsychotics: A study suggests that the use of atypical antipsychotics like risperidone, changes the gut microbiota in women but not men .
- Metformin: diabetes medication, like metformin, that lower blood glucose levels can change the microbiota, possibly by affecting the bile acids available .
- Opioids: The use of opioids can cause constipation and modify the gut environment .
- Statins: certain drugs that help lower cholesterol levels can either cause constipation or act as laxatives [59, 60].
Ways to Decrease Bacterial and Yeast Overgrowth
Antibiotics That Kill Clostridium Bacteria
Overgrowth of certain bacteria, such as Clostridium difficile, can have serious consequences. Standard therapy for controlling C. difficile includes antibiotics like metronidazole, vancomycin, or fidaxomicin .
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 .
2) Probiotics and Prebiotics
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 [63, 64].
Prebiotics are fiber 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 study with 142 patients with a previous infection .
Remember,always speak to your doctor before taking any supplements, including prebiotics and probiotics, because they may interfere with your health condition or your treatment/medications!
3) Fecal Microbiota Transplantation
In cases where the microbiota has been severely affected, gut bacteria from a healthy donor can be transplanted into the patient’s gut, where they replace the unstable microbiota. Studies suggest that this may be effective to stop infections by C. difficile .
4) Regular Exercise
Although excessive exercise can generate physical stress and may damage the microbiota, regular exercise helps keep a varied and stable microbiota. Studies have found that small but significant changes in the microbiota happen when a person begins working out [67, 68].
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.
The reference ranges have not been verified in independent clinical studies. In other words, we don’t know if they are reliable. If something does come back flagged, discuss the relevance of the result with a medically trained health professional. Your doctor will interpret your results, taking into account your signs, symptoms, medical history, and other test results. They will order further, more reliable tests if needed.
Markers of yeast and bacterial overgrowth are the most exciting part of the organic acid test (OAT). Mainly because we are just beginning to understand our microbiome and the effect it has on our bodies and metabolism. However, this also means that these markers are experimental — no clinical studies have verified or validated their use and their ranges.
While there are studies that have linked most of these markers to yeast and bacterial overgrowth, they are few and small in scale. Much larger and well-designed research is needed to establish how useful and informative testing each of these markers is in the general population.
Many of these markers can increase due to causes other than microbial overgrowth, including certain foods and metabolic disorders. Therefore, results should be interpreted with caution by a qualified medical professional. Your doctor will interpret your results in conjunction with your signs, symptoms, medical history, and other test results, and they will order further tests if needed.
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:
- Organic Acid Testing
- OAT: Mitochondrial Markers
- OAT: Nutrient Deficiencies & Methylation
- OAT: Detoxification & Oxalates
- OAT: Neurotransmitters
- OAT: Amino Acid Metabolites
Learn more about OAT with the CEO of SelfDecode Joe Cohen and Dr. Tommy Wood: