Organic Acids Tests: Can They Assess Gut Health

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Organic Acids Tests

Can They Assess Gut Health or Other Conditions?

If you’ve been suffering from gut issues or a chronic illness, and your standard lab tests keep coming back “normal,” what should you do? Some functional medicine doctors recommend a urine test called the organic acids test (OAT). They say it can reveal the underlying cause of your symptoms.

Is this test right for you? In short, I don’t recommend this as your first go-to test for gut health—or any health—diagnosis. The organic acids that the test measures can suggest certain conditions, especially with a skilled interpreter when looking at multiple markers together. Overall, it’s best used as a “big picture” test. Treating for any single marker, as I’ll discuss, is problematic. It can’t replace other gut health tests like a stool test or a SIBO breath test. Let’s cover what you should know about organic acids testing, so you can decide whether it’s worth your valuable resources.

What is the Organic Acids Test (OAT)?

Organic Acids Tests - metabolismUrine Test to Analyze Your Metabolism

An organic acids test—in a nutshell—evaluates the organic acids that are excreted in your urine, to get a metabolic picture of your overall health.

Organic acids (also known as metabolites) are products of our body’s metabolism. Metabolism is a process that breaks down food to give you energy.

How Organic Acids Testing Works

Organic acids aren’t readily reabsorbed by your body, so they’re found in the urine in high amounts. If you have a metabolic imbalance—say, an inflammation-related condition in your gut—this may show up as abnormal organic acids on your test.

Labs use combined techniques called chromatography and mass spectrometry to obtain your test results. Chromatography separates the acids out, and mass spectrometry breaks apart the compounds (using a process called ionization) and analyzes them.

Issues OAT Can Uncover

Metabolic Dysfunctions

Conditions One Expert Looks For

In my podcast with Dr. Jeff Moss, who is very knowledgeable about using organic acids test in the clinic, the big takeaway was that organic acids test can help you see the metabolic big picture. Here are a few metabolic imbalances he looks for:

  • Organic Acids Tests - AdobeStock50037472WebgutstomachinfectionIBSceliacInsulin resistance
  • Mitochondrial dysfunction
  • Ketosis or poor carbohydrate metabolism
  • Acid/alkaline imbalance
  • Inborn errors of metabolism (generally for newborns)
  • Chronic inflammation
  • Gut dysfunction
  • Amino acid deficiency (macronutrients)
  • Toxicology
  • Neurotransmitter imbalances

A skilled interpreter can use their knowledge of important markers to find the missing pieces in your earlier treatment. This could be environmental toxins, insulin resistance, possibly a genetic condition. And they can help treat you from there.

Gut Dysbiosis

What can the organic acids test reveal about your gut? If your gut is out of balance, we call this gut dysbiosis. A stool test is more diagnostic of gut issues (because markers are directly linked to the gut). However, the organic acids test can give you threads to follow up on.

OAT Marker(s) What Gut Conditions They Suggest
D-arabinitol Candida
Hippurate (low), citrate, glutamine, cysteine IBD (Crohn’s, Ulcerative Colitis)
P-cresol C. difficile


Candida is a naturally occurring fungus in your mouth, gut, and on your skin. But if your system is out of balance, Candida may grow out of control. An organic acids marker that can suggest pathogenic Candida is called D-arabinitol. (1)(2)(3) If your clinician sees this elevated marker on your test, they may suspect a fungal overgrowth. However, you will still need to verify with a stool test. You won’t be able to tell where the fungus is.

IBD: Crohn’s Disease & Ulcerative Colitis

Crohn’s disease is a type of inflammatory bowel disease (IBD) that leads to inflammation in your digestive tract. Its causes are still unknown.

Ulcerative colitis is a separate type of IBD that leads to inflammation in your colon. Together with Crohn’s, they are the most common types of IBD. Both are considered chronic autoimmune conditions.

Some organic acids have been studied in Crohn’s patients versus ulcerative colitis and healthy controls. In these studies, differences were noted between the metabolite “fingerprint” of a healthy person and someone with an inflamed gut. But findings don’t always agree on all the markers (4)(5)(6)(7) For example, a few found the marker for hippurate low in Crohn’s disease, but not all.

A study looking at multiple immune-related inflammatory diseases (including IBD) saw organic acid associations across these diseases, particularly from the citrate family. (8) Cysteine and glutamine are a few other markers that may flag in IBD. (9)(10)(11)

Your takeaway? Your clinician may be able to get an overall picture that your gut is inflamed from a constellation of markers. But the data sometimes conflict. Again, you’ll need to follow up with something like a stool test. Calprotectin is a useful stool marker for IBD.

Clostridium Difficile (C. Diff)

  1. difficile (recently reclassified Clostridioides difficile) is another naturally occurring bacteria in the gut that can overgrow when your gut is out of balance, usually from taking antibiotics. Overgrown C. diff can become particularly virulent, causing toxins, diarrhea, inflammation, and more.

Organic Acids Tests - AdobeStock76635780WEBgutibsSIBOdiarrheaGreat Plains Laboratory uses the p-cresol marker to identify C. diff in its organic acids testing. Some early studies indicate support for this marker, although I wish some of them were more high-quality studies actually indicating the marker in human urine. (12)(13)(14)

Again, a stool test will be needed to verify these results. Even Great Plains Laboratory itself notes, “Toxigenic stool culture, which requires growing the bacteria in a culture and detecting the presence of the toxins, is the most sensitive test for C. difficile, and it is still considered to be the gold standard.” The rationale for the urine culture? It’s faster!


So you’re thinking about getting the test. What are some common things to watch out for?

Treating Single Markers is Ineffective

Many functional medicine practitioners recommend their patients supplement with micronutrients to address markers that showed up on the test: nutrient deficiencies like vitamin C, B-vitamins, or other imbalances.

Unfortunately, it’s not as simple as treating the deficiencies directly. For one thing, if some deeper metabolic condition is driving the deficiencies, you won’t typically see results by treating the symptoms. For another, if you have a chronic illness, you’ve probably already tried that and it didn’t work. It’s well-known that many deficiencies (think anemia) occur secondary to gut dysfunction (15)(16)(17)(18).

Dr. Moss (mentioned above) who uses organic acids testing with his patients, confirms that taking micronutrients to treat markers just doesn’t work. His patients didn’t feel better, and retesting showed no improvement. So what does work? Understanding and treating for broader conditions.

You Need a Skilled Interpreter (and Baseline Info)

Certain metabolites have been linked to specific conditions, such as metabolic disorders and gut dysbiosis. But organic acids research is still new. That means data can conflict. To make useful recommendations, your clinician should combine an understanding of current research with their deep knowledge of you.

As I mentioned, this should not be a first test. Your doctor will hopefully have taken you through other diagnostics and treatments before getting to this point.

If they’ve gotten baseline knowledge about your health already, putting that together with organic acids markers can help your clinician figure out what you might be missing.

Organic Acid Testing Does Not Help Diagnose IBS

Organic acids testing also does not currently help in diagnosing irritable bowel syndrome (IBS). Research is too thin.

Organic Acids Tests - constipationgutpainTwo studies identified a distinct organic acids profile in IBS patients vs. healthy controls. But they were both problematic.

  • In one, the IBS patients had many other conditions muddying the data. (19)
  • In another, many of the markers they looked at aren’t measured in the organic acids testing we have today. (20)

A third IBS organic acids study did show that the low FODMAP diet reduces urinary histamine (a marker of immune activation) in IBS patients. (21)

I recommend the low FODMAP diet as part of my first steps to try healing IBS. If you’re having symptoms, you can simply try this non-invasive treatment to see if it helps.

Organic Acids Testing Does Not Replace Stool Test, SIBO Breath Test

You may be able to tell from an organic acids test that your gut has an imbalance of pathogens. However, because the metabolites are in urine, you won’t be able to tell what part of the large or small intestine they are coming from. So this is not a substitute for a stool test or the small intestinal bacterial overgrowth (SIBO) breath test.

OAT may help you to spot the suggestion of a fungal overgrowth or Crohn’s disease. However, this is not definitive. Organic acids only suggest trends in digestion, and you will need to verify with a stool test to be certain.

Main Labs that Offer It

Well-known options for organic acids testing are:

1. Genova Diagnostics

Genova acquired Metametrix, the original developer of the organic acids test, (who based their markers on the research of their scientists J. Alexander Bralley and Richard S. Lord).

The lab offers multiple organic acids tests, with varying cross-sections of markers. One specializes in gut dysbiosis, the Organix Dysbiosis Profile. It is more targeted but also more limited.

Their detailed profile is called Organix Comprehensive and measures 44 different markers.

2. Great Plains Laboratory

Organic Acids Tests - alz test tubes adobe stockGreat Plains Laboratory’s Organic Acids Test (OAT) is the other most popular offering. Their test measures 75 different markers. Although not the original developers of the test, they also seem to be pushing the research forward.

3. LabCorp, Quest, & Others: May Not Offer Full Profile

LabCorp does not provide details about their organic acids markers, nor does Quest Diagnostics.

There is no universal standard for markers or ranges, but most clinicians currently refer to the Genova profile.

Genova and Great Plains Laboratory are the two most established providers of the test and your best bet for testing.

Insurance Coverage

Not all insurance covers this test. It’s helpful to have an MD order, but it’s not a guarantee of coverage.

When Should You Use OAT?

After You’ve Tried Everything Else.

Overall, my recommendation is to use organic acids testing as a later step to identify systemic dysfunction. Right now, the research isn’t far enough along to use it as a way to diagnose conditions, but it may give you clues.

In terms of gut health, make sure you’ve really done everything else first. Changing your diet and lifestyle first can take you far, then adding steps like probiotics and potentially antimicrobials (see my book Healthy Gut, Healthy You for a step-by-step gut health roadmap). These crucial steps can resolve many imbalances.

And tests like functional stool tests will give you more definitive information in cases of pathogenic infection. That being said, if you have tried everything and are stumped, organic acids testing could reveal a systemic trend that you and your doctor might have missed.

Organic Acids Tests - Probios BGAlso, don’t forget that many gut imbalances can be remedied without needing any testing. How? A comprehensive probiotic protocol can clear SIBO and fungus, combat H. pylori, reduce leaky gut, and improve symptoms like gas, bloating, diarrhea, constipation and abdominal pain. Here are the probiotics I use in my office.

In summary, organic acids testing is interesting and may be helpful, but most people will not need to perform this test.  If you are struggling I would recommend pursuing competent advice (a good book, program or clinician) instead of testing.

What do you think? I would like to hear your thoughts or experience with this.

Dr. Ruscio is your leading functional and integrative doctor specializing in gut-related disorders such as SIBO, leaky gut, Celiac, IBS and thyroid disorders such as hypothyroid and hyperthyroid. For more information on how to become a patient, please contact our office. Serving the San Francisco bay area and distance patients via phone and Skype.


I care about answering your questions and sharing my knowledge with you. Leave a comment or connect with me on social media asking any health question you may have and I just might incorporate it into our next listener questions podcast episode just for you!