Functional Medicine Tests Demystified

Adapted from episode 99 of The Perfect Stool podcast and edited for readability with your host, Lindsey Parsons, EdD, Gut Health Coach. 

Today, I’m going to be describing all the different functional medicine tests I use and when and why I choose certain ones, including stool, blood, urine, and even hair tests, which cover things like organic acids, fatty acids, amino acids, heavy metals, and nutrient levels. As you read, it might be useful to open up my Rupa Health Lab Store*, and open up the tests I’m talking about so you can see what I’m referring to. On every test, after selecting it, if you scroll down and select View Report, right under Sample Report, you can see an example of the test report.

Which functional medicine stool tests do you like the best?

To start with, the primary stool test I use is the GI Map from Diagnostic Solutions. Like most functional medicine stool tests, the GI Map uses polymerase chain reaction or PCR testing to quantify the microbial DNA present your stool. This is newer technology than culture-based tests, which favors the microbes that grow well in culture, and is no longer a valid measurement technique given the newer PCR technology available. The GI Map, like other tests, covers commensal bacteria and bacteria that may overgrow. This includes Methanobrevibacter smithii, one of the two primary microbes involved in IMO or intestinal methanogen overgrowth, and Desulfovibrio species, which are overgrown in hydrogen sulfide SIBO. Additionally, the test includes bacterial and viral pathogens, quantities of the two major phyla in the gut: bacteroidetes and firmicutes, quantities of yeast, fungi, parasites. Intestinal health markers are also part of the test, including markers for fat in the stool, pancreatic enzymes, beta-glucuronidase (which relates to estrogen dominance and heightened risk of breast and colon cancer), fecal occult blood, secretory IgA (your gut immune defense system), and anti-gliadin IgA (a marker of gluten intolerance). Finally GI Map tests include levels of Eosinophil Activation Protein, a marker of gut inflammation, and calprotectin, a marker of active inflammatory bowel disease.

Pros for the GI map are that among bacteria it tests, it includes Helicobacter pylori, along with its virulence factors, which indicate whether the strain you have could cause stomach cancer or ulcers, whereas this is an add-on test for some other companies and doesn’t include virulence factors. You can also get the H. pylori profile as a separate test, incidentally, from Doctor’s Data for $131. The other big pro is that it’s lower cost at $381, if you get it from my Rupa Health Lab Store* (or a little less for my active clients if they get it directly through me), which is less than some other functional medicine stool tests.

The biggest cons for me about the GI Map are that it doesn’t measure the different short-chain fatty acids in stool. Additionally, it does not compare the levels of the other important phyla, namely proteobacteria and actinobacteria. In addition, Lucy Mailing, one of my gut health mentors, sent a stool sample split in half to Diagnostic Solutions and got two very different results on calprotectin, so the reliability of that particular marker is somewhat in question. Although arguably, one part of the stool could concentrate certain things, so it’s hard to be sure this questions the reliability of that marker for Diagnostic Solutions. I have generally seen it correlate well with clients diagnosed with IBD.

The Genova GI Effects Comprehensive Profile is the second stool test that I’d be most likely to order if doing a functional medicine stool test. I’d be more likely to choose this one if there were no symptoms of H. pylori like reflux, nausea, constipation, or if someone had done a prior PCR stool test for H. pylori and it was negative. I might also choose it if I suspected there was an issue with producing sufficient butyrate, like when I see loose stool, unresponsive to antimicrobials or antibiotics or with IBD. It’s also one that Lucy Mailing has found reliable in her split stool experiments.

With the GI Effects, there is a 3-day stool sample and a 1-day stool sample option for the same price, so if clients are game for taking stool samples for 3 days, that would likely be more accurate.

What are the key differences between the GI Effects and GI Map tests?

The main differences between the GI Effects and the GI Map are that there are 5 markers for fecal fat on the GI Effects as opposed to only one on the GI Map, plus all the short-chain fatty acids. This is helpful for assessing if there is a gut barrier issue in the colon as well as dysbiosis. The GI Effects also provides a marker for the products of protein breakdown, indicative of incompletely digested protein in the colon, which could come from low stomach acid, for example. The GI Effects shows you the relative abundance of all the major phyla of bacteria, yeast and archaea in the gut, which I like because people often have overgrowths of proteobacteria.

There is still a culture section on the GI Effects which feels a bit dated, so I basically ignore that section, unless it happens to catch yeast; in which case, it’s helpful because if anything is found growing in culture, they do provide a sensitivity section of that microbe to various antibiotics and antimicrobial herbs, which can guide can help determine which herbal preparation to choose. The GI Effects also include Reflex Subtyping for Blastocystis hominis, because only subtype 7 is considered pathogenic, and subtype 4 has even been shown to even be beneficial in studies (as an add-on test). So this might be a good follow-up stool test for someone who originally did the GI Map and got a positive result for blastocystis. The GI Effects will run you $507 in my Lab Shop, so as I said, it is more expensive, which is one reason I usually recommend the GI Map for most people.

Those are the two primary stool tests that I use, but sometimes, rarely, I come upon someone whose symptoms all scream H. pylori and nothing else, like if they have no bloating but they’re constipated and have reflux or nausea, or if money is a real issue. In that case, I may choose to recommend just the H. pylori profile from Diagnostic Solutions or use it as a follow-up test after working with someone on H. pylori.

When should I consider using a SIBO breath test?

Sometimes, I choose to use SIBO breath testing with people, perhaps when their primary symptoms scream SIBO to me but nothing else, like with lots of bloating, and then either loose stool or constipation. Reflux may also be an issue. If they have loose stool, I’ll recommend the trio-smart, as it’s the only test that includes all three gases, hydrogen, methane and hydrogen sulfide, especially if they have visceral pain and sulfury-smelling stool. That’s $349 if you get it directly from the manufacturer. If someone’s stool is loose but doesn’t smell at all, then I generally assume it’s likely hydrogen and a SIBO/IMO breath test either with lactulose or glucose is best. That’s $261 in my lab shop, but honestly, you can find it cheaper elsewhere if you’re using glucose as the measuring substrate. However, you can get it with the lactulose from my shop, as they have a physician review service in the ordering that allows for lactulose, as it’s only available with a prescription in the U.S.

Glucose and lactulose, by the way, are the substances that people drink before taking the test. Lactulose is definitely more useful if you’re looking at IMO and constipation, as IMO can be anywhere in the digestive tract and glucose is absorbed early in the digestive tract. If someone has loose stool and bloats immediately after eating, then glucose may be the better choice. If they have alternating constipation and loose stool, then lactulose is probably the better choice. 

However, I will say that I don’t use breath testing that often; I generally use a combination of a stool test, symptoms and history to decide whether it’s likely a case of SIBO or IMO or neither. Now I should mention that there is also something called the Food Marble, which is an at-home breath testing machine. For someone with super recurrent/recalcitrant SIBO or IMO, I often wish I had suggested they order this at the beginning, as it would be more helpful because you can retest and the equipment includes two glucose kits and costs as much as one SIBO/IMO test. But you can’t get lactulose without a prescription if you’re using the Food Marble, so it’s not so great for IMO in the large intestine, unless you’re not in the U.S. and can get lactulose. And you never quite know who is going to have a tough case of IMO until you’re usually one stool test and at least a couple rounds of antimicrobials into the problem. One other nice thing about the Food Marble is you can also get a food intolerance test kit for the other things you can test on breath, like lactose, fructose, sorbitol and inulin, which many people are sensitive to. You should reach out to me at to order a Food Marble, if you’re interested, as I can get you a discount.

Finally, when someone has recurring symptoms of SIBO that seem to come back after trying antibiotics like rifaximin or antimicrobial herbs, generally with diarrhea or loose stool, then I also think of the ibs-smart test, which tests for the antibodies for vinculin and CdtB, which tells you whether your IBS or SIBO is the result of food poisoning and will be an ongoing issue for you, necessitating prokinetics and lifestyle interventions to help you manage it and delay recurrences. You can get that for $220 direct from the manufacturer.

What do you think of food sensitivity testing?

I’ll also briefly mention that I put the Grain Zoomer test by Vibrant Wellness in my Rupa Lab Shop* because I have had a number of clients who are eating strictly gluten-free and have gotten a positive anti-gliadin IgA on the GI Map. In this case, it usually indicates there’s some cross sensitivity to grains, so if they’re positive and there’s no gluten slipping in, then I recommend this test to see if they’re reactive to other grains–that’s $304. If they’re eating grain-free too but are eating dairy, then I may recommend the Dairy Zoomer test by Vibrant Wellness instead to see if they’re reacting to dairy. I don’t generally do food sensitivity testing, but sometimes there’s clearly inflammation in the gut that’s coming from something, and if you get that positive anti-gliadin IgA, you know it is food-mediated, then you know there is some cross-reactivity between gluten and other grains or dairy–that’s also $304.

What does an Organic Acids Test cover?

Another test I use frequently is the Organic Acids Test. I typically use the Mosaic version, which changed its name recently from Great Plains Lab. Episodes 74 and 77 of my podcast go into great depth on the interpretation of this test, so if you want more details, check those out. I usually add that in for gut health clients if I hear symptoms of fungal overgrowths or candida, like heavy antibiotic use, a turn in health after antibiotics, a white coating on the tongue, frequent UTIs or urgency, vaginal yeast infections, or household mold issues, because there are multiple markers on that test for fungal overgrowths.

I also add in the Organic Acids Test if I hear about anxiety or depression, as there are markers for neurotransmitters. It also covers markers in the urine of bacteria and specifically, clostridia overgrowths, as well as oxalates, Krebs cycle metabolites, markers for energy production from fatty acids, carbs and proteins, and markers for the status of various B vitamins, vitamin C, and CoQ10. Markers of detoxification include two markers that assess glutathione sufficiency, which is your master antioxidant. So, it’s also useful for people with low energy, chronic fatigue, likely toxic exposures, poor liver function, etc. That’s $337 in my Rupa Lab Store*.

What does the Genova NutrEval® test for?

Now for clients who have health issues that go above and beyond gut stuff and maybe some light mental health issues, like chronic fatigue, any type of autoimmunity, any type of inflammatory bowel disease, or fibromyalgia or complex, long-standing health issues, I often suggest the NutrEval®. There are two versions, FMV or plasma, and I think plasma is preferable for the most accurate amino acid levels. The NutrEval  is both a blood and urine profile that evaluates over 125 biomarkers. It includes an Organic Acids Test, the Genova Organix version, which is similar to the Mosaic OAT but only has 3 markers for yeast and fungal overgrowths. Then on top of that, you get all of the amino acids, all of the fatty acids, so you can see if people are low in Omega 3’s or over supplementing–and sometimes, you find they’re low in Omega 6’s.

The NutrEval also accounts for some minerals, including copper, zinc, magnesium, potassium, manganese and selenium, measured in the best way recommended, as well as heavy metals, including lead, mercury, arsenic and cadmium. It has markers for all of the B vitamins, vitamin D, CoQ10 and markers of oxidative stress that relate to fat-soluble and water-soluble antioxidants. So it’s an amazing all-over-body test that helps you figure out where functionally something is going wrong in the body. That’s $507 in my Rupa shop*. So for an extra $170 you get a lot more stuff over the Organic Acids Test.

The last test that I have used with people before is the Doctor’s Data Hair Elements test, which measures all of the essential elements, meaning minerals, in hair, and then all of the potentially toxic elements, 17 in all. I would use this with extreme hair loss or with known or suspected toxic exposures, or perhaps as a follow-up to check for removal of toxins that were identified on the NutrEval. I actually have a podcast coming up on minerals and hair and tissue mineral analysis so stay tuned for that one. The nice thing about this test is at $137, it’s very inexpensive but gives you a lot of information.

So those are the primary tests I use with clients, just to give you an overview. You can order them yourself in my lab store*, but if you’re thinking of working with me, I give clients a slight price break, so best to have me put in the order for you.

If you’re struggling with  bloating, constipation, diarrhea, soft stool, acid reflux, IBS, IBD or any type of chronic disease, etc. and want to get to the bottom of it, that’s what I help my clients with. You’re welcome to set up a free, 30-minute breakthrough session with me (Lindsey). We’ll talk about what you’ve been going through and I’ll tell you about my 3- and 5- appointment health coaching programs in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. 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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