The Organic Acids Test: Focus on Gut, Oxalate and Mental Health Markers

Adapted from episode 74 of The Perfect Stool podcast and edited for readability.

Today I’m going to be introducing you to a test that I use with a lot of my clients called the Organic Acids Test and explaining the markers on the test that can tell you about your gut health, excess oxalates and your mental health and give you some insight into how to interpret this test. And then in a future post, I’ll finish it off to discuss the other markers on the test that address your detoxification status, energy production and more.

So the Organic Acids Test is a test I use with most of my clients because in addition to giving insight into gut health issues and having the only reliable marker of invasive candidiasis, it also offers insight into bacterial overgrowths in the gut, other fungi, markers of mitochondrial health and energy production from all the macronutrients (carbs, fat and protein), detoxification markers, markers of excess oxalates, B vitamins, vitamin C and CoQ10 status and the state of your neurotransmitters (serotonin, dopamine, epinephrine or adrenaline, norepinephrine or noradrenaline and more). So it’s an amazing test to get a read on what’s going on in someone’s body and where problems could be arising. It’s also a urine test that can be done at home and can be ordered in most states without a doctor’s order, so that makes it easy and accessible. As far as I know, it is primarily offered by two labs – Great Plains and Genova. The Genova one is called the Organix with an x. But the markers on each are a little bit different. I generally prefer the Great Plains one because it includes oxalates, which aren’t on the Organix, and it has many more markers for fungi, including environmental molds.

So a little history on this test first as I understand it. One of my mentors on this test, Dr. Daniel Kalish, shares this history in most of his videos. He’s been working with Richard Lord, PhD for years to learn about this test and others and how to interpret them and to pass on Dr. Lord’s complex understanding of the body, and I’ve taken a course with videos and webinars from both of them on amino acids and B vitamins. But basically Richard Lord, in addition to developing the GI Effects test, was the first person to think of taking these organic acids tests normally given to infants to make sure they don’t die in the first few days or weeks of life due to certain genetic SNPs or single nucleotide polymorphisms, aka gene mutations, and apply them to adults. So while an infant with a homozygous form of a certain gene (meaning two copies of a mutation) might have extreme effects ranging from severe disabilities to death, adults who are heterozygous (meaning just one copy of a mutation) or only have one polymorphism impacting a given condition (as multiple genes can impact things), may have much more mild effects that only come to light when there are environmental factors at play like a poor diet, lifestyle or just the effects of aging. So the organic acids are metabolic byproducts in urine, meaning the end products of digestion by you or your microbes. And the markers point to the ways in which gut health or other root cause issues are causing dysfunction in the body and at the cellular level. I generally recommend this test to clients also struggling with complex issues like autoimmunity, fatigue, brain fog or mental health problems or who show symptoms of systemic candida infections like sugar cravings, a white coating on their tongue or recurrent yeast infections.

I’m going to be discussing markers on a sample Organic Acids Test, so you’ll want this open as you continue to read. So the first set of markers, 1-9 are yeast and fungal markers. The primary one to determine if someone has invasive candidiasis is number 7, Arabinose, which is the only fungal marker on the Organix. I will generally recommend taking action on that if someone is symptomatic and it’s above the yellow and orange bars, which represent one standard deviation around the mean, which is the black line in the middle. If someone isn’t symptomatic but has a number near the top of the range, like in this example, I will let it go. But if someone had bacterial dysbiosis/SIBO and had a high marker on Arabinose, like this, I would make sure I educated them on antimicrobial products that covered both bacteria and yeast, like most herbals do.

Another set of markers that are different from the candida markers are the furans – 2, 4 and 5. These three are markers of aspergillus, which is typically an environmental mold. When I see those elevated, I recommend mold testing in someone’s house. Number 6 can point to candida or aspergillus.

Then number 9, tricarballylic is associated in particular with a fumonisins, which are a toxin produced by the fungus F. verticillioides (vertasiliodees), which come from corn products contaminated with this omnipresent toxin. So generally when I see that elevated, I suggest people reduce corn-based products other than fresh corn. In this case, eating organic probably doesn’t matter, as it’s an equal opportunity toxin.

Then I’ll go briefly over the remaining markers. So number 1, citramalic, can point to elevated Saccharomyces species or Propionibacteria overgrowth. Although one of the most common probiotics and one I use a lot is called Saccharomyces Cervisiaie subspecies Boulardii (S boulardii for short), some people can have an immune reaction to this strain.

And then number 3, 3-Oxoglutaric, is also a marker of yeast overgrowth. That’s one I commonly see elevated. And 8, Carboxycitric is a general yeast/fungal marker.

Then the next section is the bacterial markers. So the first four (10-13) when elevated, point to bacterial overgrowths characteristic of SIBO or small intestine bacterial overgrowth. In combination with SIBO symptoms like bloating, constipation, diarrhea or soft stool, elevated markers here are a good indication of SIBO, since I generally don’t put much stock in breath testing. But of course when you see that, it’s best to get a stool test so you know if there are other things at play like parasites, or specific pathogenic bacteria like Enteroinvasive E Coli or H pylori, for example. Just treating with antimicrobials when you choose the wrong ones can leave someone with an overgrowth of something even more dangerous.

The other thing about these first four bacterial markers is that they are also metabolites of fruits and veggies and their polyphenols in the urine. So if they’re really low, that’s also not great, because it means that someone isn’t eating the proverbial rainbow as they should be. Polyphenols feed the good gut bacteria, so you want some moderate to higher level of them within normal. And then the last marker DHPPA is a marker of Lactobacilli, Bifidobacteria, and beneficial strains of E. coli, so elevations here are not generally concerning.

The final section on microbes is specific to species of Clostridia that can be pathogenic. Now there is a whole range of Clostridia, many of which are not just beneficial but essential to healthy gut function. So there’s the class of bacteria, Clostridia, which consists of many known butyrate-producers, including the genuses Eubacterium, Roseburia, Butyrivibrio, Coprococcus, Ruminococcus and Clostridium. So you see there’s the genus Clostridia or clostridium in the singular and the class clostridia. Butyrate producers like clostridia are essential to healthy barrier function in the colon, for keeping it anaerobic and feeding the colonocytes, or cells lining the colon. But there are pathogenic clostridia as well under the genus clostridium, like C. difficile, which is responsible for almost 500,000 cases of acute, chronic diarrhea and almost 30,000 deaths a year in the US.

Marker 17, 4-cresol is a marker specific to overgrowth of C. difficile (but also another clostridium called C. scatologenes). However, if you don’t have symptoms like diarrhea, your C. diff is likely still being kept in check by other bacteria, but it’s an important consideration in picking antimicrobials, because you don’t want to start killing off the other bacteria that are keeping it in check before reducing it. But when this marker is elevated, it impacts an enzyme called dopamine-beta-hydroxylase, or DBH in the brain, which converts dopamine to norepinephrine, which will show up later in the test as elevated homovanillic acid or HVA. High urine values of 4-cresol are associated with the most severe clinical symptoms in autism, multiple sclerosis, neurotoxicity, hallucinations, and other neurological and psychiatric disorders, but at lower levels can show up as symptoms of low norepinephrine, like anxiety, depression, ADHD, memory problems, headaches, sleeping problems, low blood pressure and low blood sugar.

Then marker 15, 4-hydroxyphenylacetic acid, can be a marker of various types of Clostridia overgrowth as in SIBO, but also a marker of any type of small bowel disease or possibly elevated because of celiac disease.

Then marker 16, HPHPA, is indicative of another group of clostridia overgrowing, which can cause a derangement in neurotransmitter balance, so I often see issues with neurotransmitters like dopamine and serotonin off when this marker is high. The same is true for 4-cresol as well.

Finally, marker 18, 3-indoleacetic Acid, is elevated when another group of clostridia is overgrown, and very high amounts of this metabolite, which is derived from tryptophan, can indicate that there is a depletion of tryptophan needed for other physiological functions. And tryptophan is the precursor to serotonin, our feel good hormone, which when too low leads to anxiety, depression and problems sleeping, because serotonin is the precursor to melatonin.

So you can see how the bacteria and yeast can start to impact your mental health, and this test really shows you the connection between them.

So the next page of the test shows the Krebs cycle or citric acid cycle, which is the cycle by which your body produces energy. So it’s showing you all the conversions between different organic acids that are on this test. When you have high levels of these organic acids, what you’re seeing are breaks in that cycle, and hence, in the production of energy.

Then below that is a model of the amino acids being turned into the catecholamine neurotransmitters, which are dopamine, epinephrine and norepinephrine – so you see how phenylalanine, an essential amino acid, meaning you have to get it from food, is converted to tyrosine, which converts to DOPA, then dopamine. That then converts to norepinephrine and epinephrine, and you see to the side of the arrow going to norepinephrine the enzyme that catalyzes the conversion, dopamine beta hydroxylase and the nutrients necessary for that conversion, copper and vitamin C. And then the metabolite of norepinephrine and epinephrine is vanillylmandelic acid, or VMA, and the metabolite of dopamine is Homovanillic acid, or HVA. We’ll look more closely at all this when we get to the neurotransmitter section.

So the next page, page 3, starts with the oxalates. And you can see on this example test that there are two oxalate markers that are officially high, and I just want to point out that once you see the orange/yellow bar reduced in size to the left like that and the scale ending, you know the levels are so high that they’re off the chart. Then you should look at the scale and the number you got on the test to get a sense of how high. Oxalic acid or oxalates are a naturally-occurring compound in plants, and they’re especially high in berries, nuts, legumes and dark green leafy vegetables like spinach. So when I see someone put down on their intake form that they eat a green smoothie each morning, I’m always thinking yikes, there could be an oxalate issue. Oxalates are also produced as waste by our bodies, as well as coming from our diet. If the oxalates bind to calcium in our digestive tract, it will be pooped out and won’t cause an issue. But often as people try to eat healthier, they often fill up on high oxalate foods and eliminate dairy, and then they start to get these issues like urinary tract infections or UTIs, because oxalates are little crystals that can make cuts in your urinary tract. They can also deposit crystals in your joints causing joint pain, be deposited in your bone and cause osteoporosis, be deposited in the kidney and form kidney stones, be deposited in the eyes and cause cuts and pain and in the muscles, blood vessels, brain and heart and cause problems in all those places. They can contribute to muscle pain in fibromyalgia, and oxalate deposits in the breast tissue have also been associated with breast cancer. Another source of high oxalates can be a bile acid deficiency. Bile is what helps break down fats, so when it’s deficient, the excessive undigested fatty acids in the diet will be poorly absorbed and they will bind to calcium, preventing it from binding to oxalate and eliminating it. High oxalates in the GI tract can also reduce absorption of calcium, magnesium, zinc and other essential minerals.

So oxalic, marker number 21, is the primary marker of excess oxalates in the diet, but can also be elevated due to dysbiosis from aspergillus, penicillium and possibly candida, or from high doses of vitamin C. However, my favorite oxalate expert, Susan Owens, believes that it’s the other way around: high oxalates can cause elevations in candida and bacteria. There can also be genetic causes of high oxalates. The other two markers, gycolic and glyceric, if low, rule out genetic causes for high oxalates. While oxalates are best known for causing kidney stones, I see lots of clients who have what I believe to be oxalate-related problems who have never had a kidney stone. Some of the most common manifestations I see in my practice are UTIs, joint pain and interstitial cystitis, or frequency or urgency with urination.

High glyceric acid, number 19, may be due to microbial sources such as yeast (aspergillus, penicillium, candida) or due to dietary sources containing glycerol/glycerine, or due to genetic factors.

High glycolic acid, number 20, can also be from overgrowths of fungi and yeast in the GI tract, including aspergillus, penicillium and candida, from dietary sources of glycerol or glycerine, and from a wide variety of bacteria. And glycolic acid can also come from fruits and veggies. According to Susan Owens,  when glycolic is elevated, you should look for a B6 deficiency due to ongoing infections, like gut infections, because your body will create endogenous or internal oxalates if you have a lack of B6.

If you’re concerned about oxalates and how to lower them correctly (and mind you stopping all high oxalate foods suddenly is not the way unless you suddenly want have an oxalate dumping event where oxalate crystals start coming out of your body everywhere), you can check out Susan Owens’ web site There’s also a Facebook group called Trying Low Oxalates.

For now I’m going to skip to the neurotransmitters and save the energy production markers for the next post. So skip to the bottom of page three and maker 33, HVA. This is your marker of dopamine. When this marker is very high, it means you’re going through some type of high emotional or internal stress and using lots of your neurotransmitters. When it’s below the mean, it indicates your dopamine production is low. This will happen with long-term antidepressant usage if it’s an SSRI or selective serotonin reuptake inhibitor, because serotonin and dopamine compete for resources in the body and SSRIs increase serotonin. It can also happen when you’re protein deficient, because you need phenylalanine, which converts to tyrosine, to make dopamine. So long-term vegan or vegetarian diets can lead to a dopamine deficiency. You can also have issues with missing co-factors like vitamin B6 that are necessary for dopamine production. Chronic stress can lead to this, but it can also be genetic. When dopamine is very low, you’ll see profound fatigue or physical exhaustion, difficulty concentrating, compulsive behaviors, loss of satisfaction, addictions, cravings, sensation-seeking behaviors including pain-inducing behaviors like cutting, or drugs, sex addictions, or food compulsions, like sugar cravings, because eating sugar temporarily causes a dopamine rush). Low dopamine has also been linked to Parkinson’s, restless leg syndrome and ADHD.

The next marker, VMA, is indicative of low levels of epinephrine and norepinephrine. Because they are converted from dopamine, there are similar root causes and symptoms of low levels, with the addition of a lack of Sam-e or S-adenosylmethionine, a well-known supplement used for depression, which is needed for the conversation of epinephrine and norepinephrine to VMA. Common genetic polymorphisms in the MAO and COMT genes can also cause a reduction in VMA. VMA values that are below the mean but which are much lower than HVA values are usually due to issues with an enzyme called dopamine beta hydroxylase or DBH due to the Clostridia metabolites HPHPA, 4-cresol, or 4-hydroxyphenylacetic acid, which we saw on the first section, or the mold metabolite fusaric acid (the one that comes from moldy corn). So again you see how the bacteria and fungi interact with the neurotransmitters and can cause mental health issues. There are also certain pharmaceutical drugs that can lead to low HVA values, as well as consuming aspartame, or deficiencies of the cofactors vitamin C and copper. If you have low VMA due to Clostridia metabolites or a genetic DBH deficiency, you should not take supplemental l-phenylalanine, l-tyrosine, or L-DOPA.

The next marker, 35, represents that ratio of the two above, so if it’s high, you can see there are conversion issues from dopamine to norepinephrine and epinephrine. Again, this points to a lack of cofactors like vitamin C or copper or the other causes I mentioned above.

The next marker, 36, DOPAC, is an intermediate in the metabolism of dopamine and when elevated, it can be from supplementing with l-phenylalanine, -l-tyrosine or L-DOPA, or because of factors that inhibit the DBH enzyme as I mentioned above. Because if you go back to the image on the bottom of page two, you’ll see that the DBH enzyme is helping convert dopamine to norepinephrine and epinephrine, and if it’s sluggish, then the dopamine will be shunted off to DOPAC, which converts to HVA. So that’s one way to see if DBH is likely an issue.

Then 37, the HVA/DOPAC ratio, will tell you if that final conversion is off, which can point to a lack of Sam-e, needed for the conversion, or a sluggish COMT enzyme, which catalyzes the conversion.

Then markers 38-40 are all about tryptophan metabolism. Tryptophan is an essential amino acid that is the precursor to serotonin. So when you see marker 38, 5-Hydroxyindoleacetic acid or 5-HIAA high, it means you’re using up a lot of serotonin, which can deplete tryptophan, which is needed for the formation of all proteins in the body except collagen, and can be caused by stress or SSRI usage. Levels below the mean may indicate low serotonin production related to long-term tyrosine usage or usage of ADHD medications, antidepressant usage, recreational drugs, a deficiency of tryptophan from a long-term vegan or vegetarian diet, poor absorption, and/or missing co-factors or an inherited deficiency. When you’re low on this marker, you’ll see anxiety, panic attacks, insomnia, chronic pain and digestive imbalances and constipation (because serotonin is involved in moving the intestines, assimilation and absorption, particle transport and fluid discharge in the GI tract). Also, serotonin is released as you eat and is nature’s natural appetite suppressant. So low levels will increase food cravings and lead to overeating and weight gain.

Then marker 39, quinolinic, points to faulty tryptophan metabolism, where tryptophan is being diverted into the kynuerate pathway because of stress or infections, and it eventually turn into quinolinic acid, which is neurotoxic. This will lead to decreased serotonin and its symptoms. The most common source of infections are viral, parasitic, fungal or bacterial infections in the gut or body in general, and the second most common sources of inflammation are chemicals and heavy metals impacting the liver as well as autoimmune disorders. There’s a diagram of this on the top of p. 7. High levels of quinolinic have been implicated in Alzheimer’s, autism, Huntington’s disease, stroke, dementia, depression and schizophrenia, and high levels are also highly correlated with the degree of arthritis impairment. 

Marker 40, kynurenic, will be elevated if you’re inflamed, are defending against a pathogen or are deficient in B6 and the result will be a decrease in serotonin. Kynurenic is also produced in the liver, so if it’s low from the liver, that points to a B6 deficiency, but if it’s low because of the brain and stress, it points to neuroinflammation. If you see both kyurenic and quinolinic high, you know there’s inflammation impacting the brain. Then you need to find the source of the inflammation. However, if you see low B6 on marker 51 and high kyurenate but low quinolinate, it’s likely a low B6 problem, not neuroinflammation.

So I’m going to finish the remaining OAT markers in a future blog post, but that gives you a great insight into how the OAT can show you how bacterial and fungal infections in the gut or dietary issues, which can lead to mental health and physical health issues.

So if you’re dealing with either gut issues or mental health issues or chronic all over body problems, the good news is that this stuff is quite fixable. I work with clients using this test to reveal these issues and their root causes and educate you on how to fix them. If you want to talk to me about what you’ve been dealing with and see if I think I can help, you can set up a free, 30-minute breakthrough session with me. I’ll ask you about what you’ve been going through and I can let you know if I think I can help you. I’ll tell you about my 5-appointment gut or autoimmune healing program and you can decide it that seems like a good fit for you. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

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