Organic Acid Testing for Gut Dysbiosis and Beyond, with Dr. Jeff Moss

Organic acid testing is very popular in some functional medicine circles. I am open to it, but have had some reservations. Dr. Jeff Moss comes on the podcast today to discuss organic acid testing and provides some very important insights that satisfy my reservations and some key insights regarding how and when to use this test.

Dr. R’s Fast Facts

What are OA (organic acids)?

  • OA are metabolites of amino acids

Big picture thoughts on OAT (organic acid testing)

  • Interpreting findings to show/treat deficiencies tends to result in poor outcome
  • Better to use them to determine metabolic imbalances: gut, blood sugar, inflammation, stress, and potentially protein insufficiency, for example

OAT for GI: bacterial and fungal dysbiosis. What does the clinical research say?

  • Have studies been done comparing those with IBS, IBD…to healthy controls?
    • Yes, for Crohn’s
  • SIBO… to healthy controls?
    • None for SIBO
  • Candida/fungus…to healthy controls?
    • Yes, D-arabinatol is the marker
  • C. difficile… to healthy controls
    • Yes, good data
  • Have studies shown treatment and subsequent improvement correspond to improved test results?
    • Not much data here. Most for C. Diff and candida (D-arabinatol)
  • Is there any way to determine regionality? Are OA more indicative of small intestine or large intestine?
    • No

Interpretation, look for trends

  • Look globally for imbalances to determine system of dysfunction, and do not attempt to treat each individual marker
    • For example: If you find imbalances in multiple systems, treat first the system that is exhibiting the most dysfunction

Best tests

  • Genova and Great Plains

Is organic acid testing better then SIBO testing or traditional stool testing?

  • No, does not replace a stool analysis or SIBO breath test
  • Can help suggest need for stool testing or SIBO breath testing
  • OAT should not be a frontline test


  • There is some coverage for conventional medical providers
  • LabCorp and Quest offer some markers, but Dr. Moss is unclear on ranges and quality
Organic Acid Testing for Gut Dysbiosis and Beyond, with Dr. Jeff Moss - RusioPodcast JeffMoss
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Prelude … 00:00:40
Episode Intro … 00:03:53
What are Organic Acids? … 00:04:49
Testing Organic Acids … 00:07:23
What Organic Acids Can Tell Us … 00:09:40
Validity and Accuracy of Testing … 00:12:23
Organic Acid Testing and Dysbiosis … 00:14:41
Establishing Helpful Interventions … 00:17:40
Treating the Microbiota … 00:23:00
SIBO and the Low FODMAP Diet … 00:23:31
(click gray Topics bar above to expand and see full outline/time stamp)
SIFO and Fungal Issues … 00:25:14
Using Genova and Great Plains … 00:26:45
Interventions and Before & After Testing … 00:28:53
Diets and Pharmaceuticals … 00:32:58
Gut Health and Inflammation … 00:36:44
When is Testing Necessary? … 00:41:59
Imbalances and Where to Start … 00:43:38
The Next Steps After the Organic Acid Test … 00:46:14
Testing, Insurance, and Billing Options … 00:48:04
Episode Wrap-up … 00:50:25

Download Episode  (Right click on link and ‘Save As’)

Organic Acid Testing for Gut Dysbiosis and Beyond, with Dr. Jeff Moss.


Dr. Michael Ruscio: Hey, guys. Today we had Jeff Moss on the podcast. He’s been on the podcast before. He’s a repeat guest, and we talked about organic acid testing. And there were a few really key takeaways. Now, organic acid testing is something that in some circles is really popular. And I’ve had almost the opposite view, where I’m certainly open to it, but I’ve not found it to be supremely helpful.

You may notice that there are quite a number of tests that I have not found to be supremely helpful, which you can only arrive at that conclusion when you’re able to question if a test is helpful or not. And, unfortunately, and with all due respect, I think some providers are so excited about having some data to treat that they lack objectivity.

And they’re very hard-pressed to be able to say, “Well, this test didn’t really tell me anything I didn’t kind of already know or didn’t help me to perform a treatment that I couldn’t have done without the test to begin with,” which is a really key distinction that I think if more of us made in functional medicine, we would really see the movement become much more efficient and much more cost-effective.

But coming back to some of the key takeaways. One, the organic acid testing should not be a frontline test. That was a key point. Two, it does not replace SIBO breath testing or traditional stool testing, but rather, it can be used as a second line test to help then verify or to support whether or not further testing into something like SIBO or stool testing could be recommended.

This may run counter to what you’ve heard elsewhere, so this is why I think this episode can be very helpful. It helped satisfy some of the reservations that I’ve had about the testing. And with the way that Dr. Moss outlines the testing should be used, it actually fits in with my model. I’m not sure if I would use it per se because I think I can just skip right to the SIBO and the stool testing based upon the way I have things set up in my clinic in terms of our paperwork and my clinical intuition and everything else.

But the way Jeff recommends it being used, I think makes a lot of sense, and it can help, hopefully, many of us better position this test as, again, not a frontline test but a secondary test that may prompt further specific testing.

So with no further ado, we will jump in. Just one quick side note: I may seem a little bit slow today. I just got back from a wedding. And, gosh, it was a two-day event, and I don’t know if you’ve ever had a hotel room that you just do not sleep well in at all. But two nights of just atrocious sleep, and, gosh, I’ll tell you that just beats the bag out of me. One night, I can handle, but two nights of terrible sleep plus a wedding with bad food and drinking. So I am feeling a little bit mentally slow today. Hopefully I pull out a somewhat decent episode. But bear with me if I’m seeming a little bit slow.

All right. We’ll get to the show now, guys. Thanks.

Episode Intro

Hey, everyone. Welcome to Dr. Ruscio Radio. This is Dr. Ruscio. Today, I am here with Dr. Jeff Moss, who has been on the podcast before. And today, we are going to talk about organic acids. So, Jeff, thanks for coming back on the show.

Dr. Jeff Moss: Thanks for having me. Much appreciated.

DrMR: Always good to have you here. And for people that don’t know much about Jeff, I’ve been a big fan of Jeff’s work for a while because, amongst other things, he has a great product line at his company Moss Nutrition. But he also does a very good job of reviewing evidence in a very evidence-based, non-biased fashion which, unfortunately, is fairly rare.

And so, I thought who better to come on the podcast to discuss organic acids than Jeff, also because he has recently put together a course on organic acids. And knowing Jeff’s methodical, evidence-based, and non-biased way of going through information, I thought he’d be able to give us a very good narrative on the topic of organic acids.

What are Organic Acids?

And so, Jeff, before we get into some of the details, can you tell people, who may not be familiar with what organic acids are, what they are?

DrJM: Basically, what they are, are they’re metabolites of amino acids for the most part. Some are not, but most are metabolites of amino acids. As the name suggests, they are acids. And you’d expect basically an acid metabolite of amino acids. They appear in the urine. Traditionally, they were used for years to detect basically inborne errors of metabolism—severely ill neonates, where there were life and death situations going on due to genetic inadequacies, genetic polymorphisms, and get some idea of what to do about it.

Probably the one scenario in this case we’re all familiar with is fetal ketonuria. That’s the one organic acid we’ve probably all heard about is routinely tested on all neonates. And so, like I said, it’s been known for years in the neonatal intensive care units. Well, probably about 20 years ago, over at Metametrix, Alexander Bralley and Richard Lord starting looking at the literature.

And they had the idea, “Well, yes, we are seeing these in very severely ill people, but can we also see aberrations in organic acids production in chronically ill patients. Granted, we’re not going to see the extremes that we might see with a very ill neonate. But nevertheless, we will see imbalances. And can they give us information, not about just acute illness, but can they give us information about what’s going on in chronically ill people and what to do about it?“

So that’s basically the basis of what Bralley and Lord—how they formed their work and, in turn, they formed the profile which had been used by Metametrix for several years and recently has been inherited by Genova. Metametrix was purchased by Genova.

For sake of completeness, I should mention that Genova is not the only lab doing organic acids profiles. For years, they were. There are other labs that are doing it now. One I know of fairly well. I don’t know a lot about their profile. I know some about it. That’s the Great Plains Lab. I heard they were doing excellent work, and I think there may be one or two others also.

But right now, it’s my understanding most practitioners using organic acids, the Genova/Metametrix profile is still the predominant profile being used.

Testing Organic Acids

DrMR: Gotcha. Okay. Now, I definitely want to make our focus how we can use organic acids for gut testing, things like dysbiosis. But before we launch into some of the niche topics of the gut, were there any big-picture takeaways that you uncovered as you were going through the literature review and in the creation of your course?

DrJM: The creation of the course really came as a response to the difficulty in interpretation that many of my customers are reporting. Traditionally, the way the profile is being used is purely a tool to detect micronutrient deficiency. By using it for that, basically, the recommendations, the traditional recommendations were to take micronutrients.

And the response was less than optimal, mainly for two reasons. Number one, we run this profile in usually a very sick individual. The profile is not inexpensive, so it’s not a first-line test that we’re going to do. This is a test we’re going to do where we’ve done our usual diagnostic. We’ve done our usual interventions, lifestyle supplementation, etc., and it didn’t work.

And so, we’re usually using this as second-line diagnostic for the exceptionally ill patients. And for the most part, the first-line interventions for most of these people has already been micronutrients. So to basically now run the test and just, well, let’s give more micronutrients, the feedback was less than optimal. People were very dissatisfied.

I heard this enough. I saw it in my own efforts with my own patients, with my own family in using organic acids and using it just to let’s supplement more micronutrients, the clinical outcome was just not there. Even more frustrating was that not only did the patients not notice significant symptomatic improvement based on the interventions recommended.

Also, we ran follow up organic acids—another expense. And the test hadn’t changed; the results hadn’t changed. So we had dissatisfaction on two levels. They didn’t feel any better, and the follow up testing didn’t change.

What Organic Acids Can Tell Us

DrMR: And I’ve seen exactly that, Jeff. Not to cut you off, but I just want to support that’s some component of what I’ve seen exactly. So I’m really happy to hear you saying both of those things.

DrJM: Exactly. So I decided actually to go back and go beyond what is typically recommended, to go back and really read Lord and Bralley’s textbook in their organic acids section, which is quite expansive. I think it goes well over 100 pages. And what I learned is that there’s a lot more to this test than just micronutrient deficiency.

And then from there, I started looking at as much research as I could find on the analytes that are being tested, the organic acids being tested and the research independent of the Lord/Bralley textbook. And I found out that what it really tells us—yes, it can tell us about micronutrient deficiency, which generally will not exist in most people running the test on because we’ve already given them micronutrients.

What it’s usually going to tell us is basically key metabolic imbalances, insulin resistance, chronic inflammation, acid alkaline imbalance, toxicology, and, as you mentioned, gut dysfunction. But also, one other thing that I learned also is that since most of these analytes are amino acid metabolites, it can also tell us about amino acid deficiency, so macronutrient deficiency. So it can tell us a lot more.

So basically, what I came to conclude was that what this is going to tell us is basically why didn’t the initial diagnostic and intervention work. What did we miss? What environmental stressors did we miss? In these sick people, we have to understand the common sense that you can get sick for reasons that have nothing to do with what you put in your mouth.

When they didn’t respond to the intervention, could it have been that there are other stressors that we missed? Organic acids can tell us that. Such as, did we miss a toxin? Did we miss something going on with the gut? Did we underappreciate the role of loneliness, of worry, of lack of sleep in creating symptomatology?

And also, the metabolic imbalances. What did we miss there as a result of these environmental stressors? We thought, Oh, we fixed the insulin resistance. But maybe we didn’t. Organic acids can tell us this. “Oh, we fixed the neurotransmitter imbalances.” Maybe you didn’t. Organic acids can tell us this. “We got rid of all the toxins.” Maybe you didn’t. You thought you fixed the gut, but maybe you didn’t. That’s what organic acids can tell you.

Validity and Accuracy of Testing

DrMR: Well said, Jeff. And I’m really happy to hear you connect some of those dots, because I’ve, for many years now, not been a huge proponent of deficiency testing for nutrient deficiencies, because whenever I treat them I am almost always disappointed with the outcome, with the result.

And my thinking, and I grow more steadfast in this belief with every passing several months, is that the best testing is not testing that’s going to necessarily uncover insufficiencies, but rather things that are interfering with normal function in the body, like a gut infection or like dysbiosis or like insulin resistance or some inflammatory burden. So we’re definitely on the same page there.

DrJM: Well said. Well said. Exactly.

DrMR: Now, as we get into the organic acid testing for things like dysbiosis, I really want to pick your brain with what the clinical research says. And I have a few kinds of specific questions, so instead of giving you one broad question, I can try to break it down into mini chunks. And there’s just one thing I wanted to offer for the audience quickly, which is—and this is a concept we’ve covered numerous times—but just because a test shows you a high or a low doesn’t mean that marker is actually clinically meaningful or that the treatment of that marker will result in a positive outcome.

And something I was just writing about for the next edition of our clinical newsletter, The Future of Functional Medicine Review, was how many of the forms of free T4 have actually been shown to be very inaccurate. And there’s actually a handful of methodologies for T4 that have been shown to be accurate. And I did some checking around, and one of the more commonly ordered free T4 methodologies offered by LabCorp, for example, is not an accurate form.

And so, this is important because you may be seeing a low free T4 on a patient, using an inaccurate methodology, thinking that this person needs to either take more T4 or do things to help boost their T4 production. You do those interventions and the person feels no different.

Organic Acid Testing and Dysbiosis

So it’s important to make sure that the testing we’re using is accurate and has clinical validity to it. And so, that’s where I really want to try to dig into some of the details here, Jeff, to see if we can really ferret out what the evidence shows for the use of organic acid testing for dysbiosis.

And so, I’m wondering, firstly, in this line of questioning, have there been studies done comparing those with either IBS or IBD to healthy controls and showing that there’s a significant imbalance shown in those with IBS or with IBD compared to healthy controls using organic acids?

DrJM: Well, first of all, I haven’t looked at all the literature on all the organic acids. What I have looked at is what they’re using in the Genova profile.

DrMR: Gotcha.

DrJM: With that in mind, there’s about a half a dozen, actually about seven or eight different analytes that they’re looking at. And yes, in the literature I was able to find some trends in terms of mainly inflammatory disorders, issues related to certain imbalances of resident microflora and presence of overt pathogens. Much of the research actually in terms of overt pathogens has been done with C. difficile.

And the organic acids profiles, the analytes using a Genova test are quite indicative of C. difficile. Now, I will say this: a lot of people mistakenly think that you can use the organic acids as an easy substitute for a stool analysis. Even though they’re both expensive, the inconvenience of the stool analysis is such that we’d rather get all the information from the urine-based organic acids. And I will say this: it’s not a substitute.

Basically, what the organic acids will show you are trends, suggestive information. From there, it does need to be verified with a stool analysis. With a combination of both tests, you can feel confident that you’ve discovered a key factor in the patient’s case presentation and get some reliable information on what do you do about it.

So, yes, it will show trends. Specifically, there was some good research on Crohn’s disease, some actually the analytes being lower. Again, some infective situations, microbial imbalances where some will be high.

Again, it is indicative, but you have to look at the overall trends, not only in the microbial section, the bacterial section, but you still have to look at the entire profile in terms of all the trends, looking for the imbalances in terms of inflammation, insulin resistance. Then, you can go ahead and get the best idea of what’s going on.

In short, what I’m trying to say is to start cherry-picking individual analytes and say, “Well, this means this and this means that,” that will lead you astray and will lead to frustration.

Establishing Helpful Interventions

DrMR: Gotcha. And I think that’s a really key point that you make which is, again, sometimes it’s easy to look at maybe we have seven bacterial dysbiosis markers, and you see one that’s elevated. It doesn’t always—and, again, if you disagree with this, please let me know.

But in my experience, treating one marker in isolation of looking at the entire context is usually a fool’s errand, because we want to look at the overall body of data, how the patient presents, what the lab work shows and look at all this information to establish what the ideal intervention may be and not simply look at, well, we have one bacterial dysbiosis marker that’s marginally elevated and we’re just going to keep treating that one marker. And I think that does sometimes happen in functional medicine. But it sounds like what you’re saying is we want to look broadly at all the data to try to establish what intervention may be the most helpful.

DrJM: Right. The key thing to remember, number one, is we’re treating people, not the lab tests. There’s a temptation to treat the lab test. For every marker, analyte that’s outside the norm, we’re going to do an intervention, give a pill, a supplement, a dietary recommendation, etc. The value of the profile is to base a suggestion—overall picture. Let me give you an example.

All right, let’s say we have imbalanced microflora, and the profile tells us that. Well, unless you have an absolute pathogen, and even with absolute pathogen, there’s another question that needs to be answered. Is this just an issue of an attack, basically something that is so pathogenic that it overwhelmed all coping systems? Rarely the case. If you have somebody who just came back from Africa, maybe. Or they just drank water out of the Ganges River, maybe. But that’s not what we’re seeing.

What we are seeing is usually imbalances of resident microflora or even pathogens that have created problems because of a coexisting disturbance in gut lining metabolism, in the functioning of the gut lining of leaky gut, of gut integrity. And gut integrity is not just a matter of what you put into your mouth. Gut integrity is also an issue of your thoughts.

It’s an issue of the toxins you’re exposed to. It’s an issue of too much exercise. It’s an issue of over-exercise. It’s an issue of too much time on the computer. And yes, it is an issue of diet. And that’s what the organic acids can tell you is do you need to just go and kill things? Because they’re pretty smart organisms and, generally speaking, they’re going to adapt to any of our efforts to try to kill them.

What our best effort is going to be in terms of getting long-term reduction in symptomatology is, yes, we’re going to have to apply antimicrobials in combination with efforts to restore overall gut health so that the ones that we don’t kill—and we never kill them all—will go back into a dormant state, which they probably were in, in the first place. Most of the people we’re treating, they didn’t get these infections overnight.

These organisms they were probably exposed to years ago but were living in a dormant state because they could not gain control, if you will, due to overall balance of resident microflora, acidophilus, bifidus, etc., and overall metabolic health. But because of other stressors that come into play, gut health declined to the point where these dormant pathogens could now become active.

Our goal is to kill as many as we can, and the ones that we can’t kill, basically, improve health so they go back into a dormant state.

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Treating the Microbiota

Well said. And that’s actually one of the things that I talk a lot about in the book and is incorporated into the self-help section of my book, which is not rushing to the strongest treatments. In the majority of the cases, we want to lay a foundation, because there are many factors that can help resolve dysbiosis that don’t involve actually coming in and blasting the microbiota with antimicrobials. And so, yes, it is important to look at the greater context of not just firing in there with antimicrobial agents.

SIBO and the Low FODMAP Diet

And this is actually a good transition to the question of looking at SIBO in organic acid testing, because one of the methods of dietary change that can be helpful for SIBO, at least based upon some inferential data, is something like a low FODMAP diet.

So we may not need to go in there and, again, fire in with antimicrobials. Someone may have adequate resolution of inflammatory markers and symptoms by merely limiting fermentable foods as the low FODMAP diet does. So with that as kind of the foundation into this next question, has there been any research looking at organic acids in small intestinal bacterial overgrowth?

DrJM: Not that I could find. Not that much. We can basically learn from the organic acids whether are there imbalances of pathogenic organisms or commensal organisms, resident organisms. Can we tell from the organic acids where they are? Have they migrated beyond large intestine into the upper large intestine and into the distal or even sometimes small intestine? No, not really. This is not a replacement for the breath testing. No question about that.

DrMR: Yeah, that makes sense you wouldn’t be able to tell regionality from a urine test. That makes sense. Ok.

DrJM: No. But again, I think you point out, and certainly, you have been at the forefront of the SIBO situation. And no matter what the findings are, as you’ve pointed out and in my own reading, the low FODMAP diet is going to be the foundation no matter what you find on the organic acids test.

SIFO and Fungal Issues

DrMR: Sure. Sure. Now, one of the things that we’ve talked about on the podcast before, Jeff, is this new entity—and I think Dr. Satish Rao is doing some fascinating research in looking at small intestinal fungal overgrowth. And one of the areas I’m curious to see if we can get a peek at or maybe an indirect measure, kind of the best we can do until we have a more formal test, for SIFO, might be looking at some of these organic acids.

Now, I’m sure there’s been nothing published on SIFO because it’s so new. But what can you tell us about looking at yeast or Candida? Have there been trials showing that maybe people that have documented Candida compared to healthy controls and have they correlated organic acids with that? Can you tell us what some of the vetted clinical data shows regarding yeast, Candida, fungus?

DrJM: Yeah. There’s one analyte on the Genova profile that’s a d-arabinitol, which is an organic acids metabolite that is produced by fungal forms, Candida primarily, but other fungal forms also. And it’s quite diagnostic. When elevated, you can pretty much assume that there is a fungal issue, probably Candida, but not necessarily Candida or it may be Candida and something else.

Again, can we make any conclusions about regionality? No, we can’t. But it is a very strong indicator that there are fungal issues and certainly would want to follow up with stool analysis.

Using Genova and Great Plains

DrMR: Okay. So let me ask you another follow up, because in looking at the Genova panel and then the Great Plains, it seems that Genova consolidates the yeast and the fungus to arabinitol. But then, if you look at Great Plains, they have nine different markers. Now, again, I want to be careful in saying—more markers in my opinion does not mean it’s a better test. We really have to be careful about that in functional medicine, because many of these nine may have little to no validity at all.

Have you looked at all to see are there other yeast and fungal metabolites that are well validated beyond the one that Genova is using?

DrJM: Here I want to plead actually ignorance. I started out with the Metametrix/Genova profile, and it’s what I’ve been working with and what I’m used to and what most practitioners are working with. However, I’m in the process—I’m pretty much winding down developing my course on the Genova profile. Of what little I know about the Great Plains profile, I am very impressed.

And where I’m at right now, I need to learn more, particularly about these other markers. My guess is there’s something there, but I really don’t know. So I’d have to say because I’ve traditionally used only the Metametrix/Genova profile, is it the best profile? I can’t say that right now. So I’m going into this question of what Great Plains is doing with very much of an open mind and very much anticipating learning more. They teach a course on it. I want to take the course on it and learn a lot more.

I guess we’re all students. We’re just on a different point on the spectrum, and this is the next area of learning where I have to go is learning more about what Great Plains is doing.

DrMR: Gotcha. So maybe at some point several months from now we’ll have you back on, once you’ve had a chance to go through that and you can give us your summary on that, because I’d be curious to get your thoughts.

DrJM: Sure.

Interventions and Before & After Testing

DrMR: And also, I appreciate your honesty. And you’re right. We’re always learning more and you can never know everything. So totally understandable. There’s one other question—one or two others—regarding some of the clinical intervention data. Do you know of any studies that have looked at, okay, here we’ve found someone has an imbalance on their organic acid testing? Now we are going to treat them for the imbalance and then retest and show that subjective or maybe even other objective measures have improved after the treatment? Is there any data like that that you know of?

DrJM: Some. It depends on the analyte. Not a lot. I didn’t find much of in terms of before-and-after testing that would correlate a specific clinical presentation with before-and-after testing and a specific intervention. Probably the main things I saw were pathogens, quite frankly. C. difficile, D-arabinitol for Candida, where I saw the most distinct before-and-after type research that had a specific finding, a specific set of clinical symptoms and they did this intervention and here’s what the test showed.

Certainly, with a lot of the others, there is going to be suggestive information, but, again, not controlled research studies. One of the things also that complicates interpreting the test in such a fashion is that by the time you get to this point on running this test, on the types of patients that we’re talking about, there’s no book, there’s no chapter, there’s no protocol for these types of people. They are their own illness, a study of one.

And therefore, to basically—with these people, to say that we can generalize and create specific groupings where we can do this type of controlled research, gather 10, 20, 30 people who have a similar presentation, that’s generally not what we’re going to see with these patients. So that’s another reason you’re not going to see this kind of controlled before-and-after studies.

The patient is going to be their own control, if you will. Basically, you use the information as best as you can from the organic acids with all your other diagnostic information, including what you learn from your initial intervention. Again, this is not a good initial intervention diagnostic. It works best when you’ve done your usual things first. And when it didn’t work, do this and correlate it with your initial diagnostic, what you already know what did and didn’t work, and then you can come up with a unique understanding of this particular individual.

And ultimately, what’s the ultimate judge? It’s not in terms of what the research says. Ultimately, the patient becomes—it’s a case study of one. If they get better, then you know it worked. And then, all right, they felt better. Then you go back and run a test. Did the results change? Yes, they did. No, they didn’t. It’s nice when they change. But now, we get into the issue of patient individuality.

Some patients, their normal, optimal level, based on unique issues of age, of genetics, nutrigenomics, genetic polymorphisms, all kinds of issues that are important, that we may not from a practical standpoint be able to entirely elucidate, is that some of the values may never change. And that’s why I emphasize we run this test to basically resolve chief complaints. We don’t run this test to create perfect tests. You’ll never create a perfect test in these people.

The test may not be within optimal findings ever. As long as the patient feels better and you’ve got some type of relative permanence in terms of case presentation, you’ve done your job. End of story.

Diets and Pharmaceuticals

DrMR: Yeah. Well said, Jeff. And just to kind of piggyback on that, something I think is important for all of us to keep in mind as providers, or if you’re a patient trying to, I guess, evaluate how much farther you want to go with a particular provider, is to remember that, in many cases, you don’t need a test in order to undergo a treatment for dysbiosis.

There are many different dietary interventions, for example, an elimination diet or a low FODMAP diet, that really do not require any lab testing to guide. And also, coming up another level on the intervention ladder if you will, things like probiotics or enzymes.

Much of that, again, in my opinion, is steered by someone’s presentation and does not require lab testing to guide or to steer. Then, even going a level further, looking at things like potentially antimicrobials, herbal antimicrobials that is, or things like elemental diets.

And neither one of those really requires very specific lab markers to steer. Now, you can make the case for pharmaceuticals because they can be helpful to distinguish between bacteria or fungus, so you know whether or not to administer an antibiotic or an antifungal agent. And also, within antibiotics, if you’re looking at SIBO, you have your hydrogen SIBO compared to your methane SIBO, and there may be different antibiotics that work better for each one of those.

So when you get to the level of pharmaceuticals, knowing at least what you’re dealing with can be helpful. But even that doesn’t require painstakingly meticulous data. You just want to establish is this person hydrogen predominant or methane predominant or do they have neither and they have a fungal issue.

So it’s just important to keep that in mind, because one of the biggest hang-ups I see in my conversations with practitioners is they only treat based upon labs. And it’s really unfortunate, because many of the good treatments, especially in nature and functional and complementary medicine for dysbiosis, don’t really require lab testing.

So if you’re shackling yourself to only treating or only using those interventions based upon lab tests, you’re really doing yourself and your patient a huge disservice.

DrJM: You make a wonderful point, Michael. I think what you’re taking about, based on our years, even if you haven’t had that many years but based on your learning experience, we develop a kind of clinical common sense. And that’s what I hear you talking about. Again, use that first. It seems common sense to me and to you if you have some type of GI problem and gut microbial imbalance that you start out with the diet first. To me anyway, it seems like common sense. And that’s I think what you’re talking about.

What I’m saying is do the usual things first. And then if you’re stumped. “This patient, the usual things aren’t working. This patient doesn’t seem to fit common sense.” Then run the test. Use it as an adjunct. And basically, it’s going to give you some ideas, “Aha! That’s what I missed. I know there’s something I missed here.” And maybe the reason that you missed it and the reason the patient didn’t respond is because of allostatic load principles that it’s going to be cumulative stressors that create the problem.

Let’s say there’s five stressors. In many patients, if you get three out of five, it’s enough they’ll feel better. But not all of them. Some patients, you may have gotten four out of five and nothing changes. Organic acids will help you identify that fifth one that you missed.

Gut Health and Inflammation

DrMR: So with that in mind, Jeff, you were mentioning earlier that you can interpret, or try to interpret this test ,not so much based upon one individual marker, but looking for trends. So I’d be really curious to get your perspective, especially if you’re a clinician that suspects a problem in the gut, and you’re trying to make sure that we optimize a person’s gut health. How are you looking at this in terms of interpreting the organic acid testing to try to not get lost in all the details but take away the clinical actionable? How do you interpret this broadly?

DrJM: First of all, I look at the gut, not just in terms of as an isolated entity—what’s living in it and what we put into it. I see it as a metabolic organ that’s connected to everything else, that is affected by other stressors that immediately relate to what you put into it or to what’s living in it.

For example, how much is psychological stress going to play a role in creating production of inflammatory mediators, which will, number one, decrease gut integrity through direct impact of the inflammatory mediators? Also, production of inflammation will lead to increased insulin resistance and a catabolic physiology where you get increased gluconeogenesis.

Now, popular thinking was that gluconeogenesis, the conversion of amino acids to sugar, the body just robs skeletal muscle to basically… And we get sarcopenia, where the amino acids, primarily branch chains, are taken from off the peripheral musculoskeletal system to make sugar. What we also know is that the gut lining is also robbed of protein amino acids to make more sugar.

And even go one step beyond that, the body not only robs muscle and gut lining to make more sugar, the body also, to make inflammatory mediators that are primarily protein-based cytokines, C-reactive protein, TNF-alpha, etc., etc. Does the protein just come from muscle? No. It also comes from the gut lining.

So what created that inflammation that’s robbing the gut lining of its structure of the protein amino acids? And what is creating inflammatory mediators that are directly attacking the gut lining? Is it your thoughts? Is it a toxin? Is it too much exercise? Is it too little exercise?

All right, let’s talk about is the patient over-exercising? Maybe we missed that. What I would do is I’d start looking at the mitochondrial function section, looking for overall trends. And I talk about all of this in my class. I’m looking at—one key metabolite is beta-hydroxy butyrate in the carbohydrate metabolism section.

If it’s elevated, what does that tell us? We know traditionally that’s a ketone body. And that generally goes up when we have insulin resistance. It’s classically known as a diabetic indicator. But it also tells us that the patient is insulin resistant. Insulin is not working, and so that means we have decreased energy production, increased inflammation, and this catabolic physiology.

So I’m looking for these overall trends and getting him back to the gut. Again, what are the environmental stressors that came into play that I missed? What did I miss? Did I get a good enough history on toxicology? Did get a good enough history on stress physiology, etc., etc.? And, since I’m seeing an indicator of insulin resistance, yes, I thought I treated that with my initial intervention. I saw the elevated glycosylated hemoglobin. I saw the elevated blood sugar, and I thought I fixed it. But maybe you didn’t. That’s how I use the test.

Dr. Ruscio Resources

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And finally, if you’re a healthcare practitioner looking to learn more about my functional medicine approach, you can visit All of these pages are at the URL, which is D-R-R-U-S-C-I-O dot com, then slash either ‘gethelp,’ ‘gutbook,’ or ‘review.’ Okay, back to the show.

When is Testing Necessary?

I want to pose a hypothetical example to make sure that I’m kind of capturing that correctly. But before I kind of toss that out there, just again for the audience to reiterate, remember that a lot of this may be addressed from your initial interventions. So if someone comes in and they haven’t changed their diet and you’re looking at all these markers that are skewed, they may improve from an elimination diet and also reducing carbohydrate load and maybe getting them on some vitamin D and a fish oil, especially if they’ve had a really kind of standard American diet.

Again, I think Jeff makes a great point, which is using this as a frontline test may really not be a good idea, because there are many imbalances that will rectify themselves as soon as you did what you were going to do anyway. And again, coming back to this efficient, cost-effective model of functional medicine, if we can prevent ordering one test, that adds up. I think we’re all on the same page there. I just want to reiterate that because I think that’s important.

DrJM: You make an excellent point. Don’t even run the test if you haven’t changed their diet. Do you really want to run a 350-dollar test to tell them they’re eating a lousy diet? You already knew that.

DrMR: Right.

DrJM: So don’t even run the test unless you’ve done the basics. Unless you’ve done the diet, you’ve done the vitamin D, all the usual things. The test is too expensive to basically tell you that you didn’t do the basics. That’s not the patient’s issue; that’s your issue.

DrMR: Exactly. Well said.

DrJM: This is designed basically after you’ve done all the basics, if they’re still not responding and you’re stuck. You’re really stuck, not that you just didn’t bother to change their diet. Then it makes the cost worthwhile.

Imbalances and Where to Start

DrMR: Completely agreed. And now, to throw out that hypothetical. Let’s say someone performs a test, and, of course, they’re probably going to see imbalances in more than one system. So let’s say they’ve got maybe two to three dysbiosis markers that are flagging. They’ve also got a marker or two of carbohydrate metabolism and also a couple for neurotransmitter metabolism.

This begs the question of where do I start, because they’re exhibiting some gut stuff, some metabolism stuff, some emotional neurotransmitter stuff. Now, I’m assuming and this just seems practical, but you would look back at your patient and make a note of, “Well, are they exhibiting a lot of GI dysfunction and not much in the way of stress, anxiety, insomnia, blood sugar dysregulation?” And if so, we’ll pierce more deeply into gut interventions.

However, if they’re somewhat devoid of gut interventions and they seem like a type A, or they have some stress in their life, or they’re not sleeping enough, or we didn’t really give them very strict dietary recommendations, then you would go there.

So I’m assuming that part of how you treat these findings is based upon what the person quite simply is presenting with. But is it more complicated than that?

DrJM: No, that’s basically it. It’s nice—we like to have broad-based generalizations, “When you see this, do this.” I know we like to do that. By the time you’ve run this test, you’ve done all the usual things. Again, it’s an n-of-1. They’re a unique case, and you really have to go based on a specific patient presentation.

For example, you may run this test and you see, “My god, they can’t produce energy.” Mitochondrial function is just trashed. They’re clearly insulin resistant, and we have to support energy production. But if your patient says, “Every time I take a supplement I get a stomachache,” well, we’re going to have to start out with the gut. Get them to the point where they can tolerate the supplements and utilize the supplements and absorb the supplements.

So these are some situations where you really have to go based on, not the hardline issues, but the soft-line issues of just the realities, a practicality of patient compliance. And again, particularly when gut function comes into play, even though it’s a secondary issue, the symptomatology may be such that you’re going to have to start there and do the best you can.

The Next Steps After the Organic Acid Test

DrMR: Gotcha. Gotcha. Now, as we’re bringing this more toward a close here, there’s a few more questions I wanted to ask you. You mentioned this earlier—and I’m glad you said it—which was would you say this test—the organic acids test—can replace a SIBO breath test or traditional stool and maybe blood antibody testing? And you already marked that these do not replace those.

DrJM: No.

DrMR: But it sounds like you’re saying that you could order this test and then use the organic acid results to help steer where your more specific testing should then be ordered.

DrJM: Yes. Again, we’re assuming you’ve already done your initial screen, which would maybe involve a routine blood chemistry, first morning urine pH, acid alkaline issues, all your basic laboratory testing. But now, we get into some of the secondary testing issues, suggesting that requires a good amount of money, some effort on the part of the patient. The breath testing is somewhat laborious. It takes three to four hours, so compliance becomes an issue.

When we come to these factors with these advanced tests, we have to pick and choose carefully for many reasons and which ones we’re going to recommend. Yes, under those circumstances, organic acids can be a good gross screen on how to prioritize that advanced type of testing. Obviously, you may not be able to do it all for reasons of money, let alone anything else.

So how do you prioritize which test you’re going to do next? Are we going to run, again, a SIBO test? Maybe we have to run some type of look for heavy metals or some type of looking for chemicals. Maybe we have an endocrine imbalance. Maybe we have to run some type of endocrine profile. Yes, the organic acids will help you prioritize those choices, those decisions.

Testing, Insurance, and Billing Options

DrMR: Are you doing any of these tests through insurance? For example, I know that you can do d-lactate, benzoate, and indican through LabCorp, maybe also even through Quest. So there’s a few that you can order through insurance.

So any knowledge about using other labs, like LabCorp or Quest, or if you’re using Genova, any feedback or commentary on insurance billing options through Genova?

DrJM: Well, the real issue, even if you could go to these other labs for the certain isolated tests, you have to understand unlike blood chemistry, there’s no uniformity in terms of either the testing procedure or interpretation of the test. Unlike a blood chemistry, everybody, all labs basically do it about the same and the interpretation is the same basically worldwide.

For example, worldwide, we pretty much know that 30 nanograms per deciliter is the cut-off for 25-hydroxy D. That’s generally accepted. When it comes to the organic acids, there are no universally accepted norms. And Genova’s profile is pretty much the norms that they have determined.

So what you might get from LabCorp, number one, it may be a different technology. But number two, their range may be totally different. And, again, most everybody, whether they should or shouldn’t, but most everybody is using right now Genova as an interpretation standard, mainly because of the work of Lord and Bralley, who’ve done really the most clinical work on the subject through their teaching and their textbook over the years.

So to start, all of a sudden, we’ll have this test done with this lab and this test done with that lab would probably give questionable value diagnostically. From an insurance standpoint, my experience with the Genova profile is that it has been covered in some states, mainly when MDs order it.

The feedback I have gotten when other licensed practitioners have ordered the test, no matter where they’re located, reimbursement on insurance has been spotty at best. And I hear “no” more than I hear “yes” when it comes to non-MDs ordering the test.

Episode Wrap-up

DrMR: Is there anything else, Jeff, that you think is important before we bring the conversation to a close?

DrJM: If you’re in the type of practice where you’re treating the difficult, chronically ill patient, if you’re getting good success with what you’re doing, don’t change a thing. Keep on doing what you’re doing. But most everybody I know, we get cases that just stump us once in a while.

Chronic illness is getting increasingly complex, due to the increased amount of stressors in our lives and the increased complexity of metabolic imbalances and increased age of our patient population. The allopathic world is doing a wonderful and increasingly better job. You look at cancer oncology alone, and the wonderful job they’re doing keeping people alive. They’re wonderful, but there’s a price to be paid for the ability to keep people alive is that we have more people who are sick and who have increased complexity of sickness.

So we’re getting more and more of these patients is what I’m saying. And all I’m saying is don’t be afraid to do the test. I know it seems complicated and I guess it is complicated, but do it. Just run one, and I’m really glad to assist in all of this. Part of my course, when you sign up for my course, call me up with your test. I’ll spend as much time as you need to spend. And certainly, anybody on this call, whether or not you sign up for my class, if you’ve run an organic acids test and you need some help, give me a call.

My main point is that we have an epidemic, a crisis of chronically ill patients, and this is one of the best tests that you can use to really help you create a roadmap—where do I go with this person? Really, my main goal is to get this information out and basically help more people. Because many of these people are just going from doctor to doctor, and they’re just desperate. And this is one of the great tests, and I want to get the word out.

DrMR: Great. Well, Jeff, thank you again for taking the time. It’s always a pleasure talking with you. And, guys, if you haven’t checked out his course, I would definitely check it out. Like I said earlier, I’ve always been impressed with the thoroughness of Jeff’s research, and really the thing that I value the most is really the objectivity. Because I’m sure people out there are frustrated, as am I, with you just get a shtick from everyone you go to. And people just seem to have a hard time with admitting, “Hey, here’s something that I’m interested in. Here’s the strengths. Here’s the weaknesses.”

You more often get, “Here’s a strength. Here’s a strength. Here’s a strength. Here’s a strength.” And you get kind of a very biased perspective. So this is one of the things I really enjoy about Jeff’s work. I’ll anticipate people would enjoy and get a lot out of his course. Jeff, thank you for the work that you’re doing, and I’m sure we’ll have you back on the show at some point in the future.

DrJM: Looking forward to it.

DrMR: All right, Jeff, take care.

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 in 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!

18 thoughts on “Organic Acid Testing for Gut Dysbiosis and Beyond, with Dr. Jeff Moss

  1. Good Afternoon,

    Just read your interview and thought it was great. I am working a primary care doctor with functional medicine background and she mentioned this acid test but we are debating about Great Plains test and Genova? I do notice my insurance is covered by Great Plains. Also, looking to get SIBO breathe test too but few years ago it was negative and not digesting my proteins/fats very well based on Genova Stool test and gut lining is inflamed, excessive gas/bloating building up in my lower gut small/large intestine even with digestive enzymes/HCL/added fermented veggies. , increased tension through my neck to the gut stress. Any other tests that might help.

  2. Good Afternoon,

    Just read your interview and thought it was great. I am working a primary care doctor with functional medicine background and she mentioned this acid test but we are debating about Great Plains test and Genova? I do notice my insurance is covered by Great Plains. Also, looking to get SIBO breathe test too but few years ago it was negative and not digesting my proteins/fats very well based on Genova Stool test and gut lining is inflamed, excessive gas/bloating building up in my lower gut small/large intestine even with digestive enzymes/HCL/added fermented veggies. , increased tension through my neck to the gut stress. Any other tests that might help.

  3. Hello 🙂 I am having difficulty with indigestion. There is not much information in Korea. Please help me. If you answer only one question, it will help my life.😭😭😭 My symptoms are bloating and diarrhea. I saw you write about Sifo. That was very similar to my symptoms, so I was tested for urine organic acids. The results have not yet arrived. But there is something I am curious about. Can I find out sifo for using urine organic acids test???

    1. Hi Kim,

      So sorry to hear you’re not feeling well. As far as SIFO goes, the best test available to diagnose SIFO is a small bowel aspirate via endoscopy, which is pretty invasive. Dr Ruscio has an article about it here:

      If you’re having those symptoms, I would definitely recommend picking up a copy of Dr. Ruscio’s book, “Healthy Gut, Healthy You” as it walks through the exact protocol he uses in his clinic to help his patients overcome all sorts of gut issues. You can find it here:

      Good luck!

  4. Hello 🙂 I am having difficulty with indigestion. There is not much information in Korea. Please help me. If you answer only one question, it will help my life.😭😭😭 My symptoms are bloating and diarrhea. I saw you write about Sifo. That was very similar to my symptoms, so I was tested for urine organic acids. The results have not yet arrived. But there is something I am curious about. Can I find out sifo for using urine organic acids test???

    1. Hi Kim,

      So sorry to hear you’re not feeling well. As far as SIFO goes, the best test available to diagnose SIFO is a small bowel aspirate via endoscopy, which is pretty invasive. Dr Ruscio has an article about it here:

      If you’re having those symptoms, I would definitely recommend picking up a copy of Dr. Ruscio’s book, “Healthy Gut, Healthy You” as it walks through the exact protocol he uses in his clinic to help his patients overcome all sorts of gut issues. You can find it here:

      Good luck!

  5. What is the date of this interview? Great Plains has been doing OAT a long time and has very interesting information and support. I am especially interested in mold mycotoxins at this point. Also, Medicare pays for it if the practitioner is a Medicare provider.

  6. What is the date of this interview? Great Plains has been doing OAT a long time and has very interesting information and support. I am especially interested in mold mycotoxins at this point. Also, Medicare pays for it if the practitioner is a Medicare provider.

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