Does everyone need a gut test?
No. If you’re healthy, there is no reason you need stool testing, unless you’re just interested to learn more about the microbiome! Even if you’re struggling with chronic health issues, your first step should be getting the major health behaviors in place, as this can often significantly improve symptoms. If you’re still struggling with symptoms once you’ve optimized your diet and lifestyle, it could be worth testing your gut to determine if it’s contributing to your health problems.
What if my GI doc already ran a stool test?
Your doctor’s office is likely only testing that sample for about 0.01% of what they could be testing your gut for. Here’s a typical result from a basic lab stool culture:
No visible ova or parasites
Occult blood: negative
Not only does this result provide little useful information, but it can also lead you to believe your gut is healthy, even if gut pathologies are the underlying cause of your health struggles.
Depending on your symptoms, a GI doc may also run a basic PCR screen for some of the most common parasites, but these are far from comprehensive.
How often should I get a stool test?
For most people, a single test is enough as a screening tool. If the test identifies a parasite or something that clearly needs to be treated, then it is often a good idea to get a follow-up test to confirm that it was cleared.
Some people like to get more frequent tests to be able to track things over time, and this can certainly be interesting and occasionally help generate hypotheses to guide treatment, but it’s important not to get too fussy over the numbers, and instead focus on whether your symptoms and quality of life are improving.
Is qPCR effective for detecting parasites?
Yes. Several recent studies and literature reviews suggest that qPCR detection of parasites is equivalent, and in many cases superior, to microscopy-based parasitology.4–9 Not only can qPCR detect the absence or presence of parasites, but it can also detect parasite load by providing an absolute number per gram of stool. Unlike traditional microscopy, this method does not require stool sampling on multiple days to ensure that parasites are detected and offers more rapid results. That being said, some parasites are still picked up more frequently by traditional parasitology, so combining the two methods is the most thorough way to screen for parasites.
What about the MALDI-TOF with high complexity culture method, isn’t that better than basic stool culture?
In recent years, there has been a resurgence of interest in culture-based methodologies thanks to improvements in culture techniques and a newer detection method called MALDI-TOF. MALDI-TOF uses mass spectrometry of microbial proteins and can identify over 1,400 microbial species without having to purify or isolate them.
The MALDI-TOF method has been shown to have 99 percent accuracy in the ID of common commensal microbes, 100 percent accuracy in ID of common pathogenic species, and high reproducibility across laboratories.1,2 The problem is that MALDI-TOF still relies on successfully culturing the microbe first. And even with high-complexity stool cultures now used in some commercial laboratories, they still miss 95 percent of the microbiome!
Are fecal SCFAs reliable?
Somewhat. Short-chain fatty acids (SCFAs) are produced from the bacterial fermentation of dietary fiber and play important roles in the health of the gut and the rest of the body. However, quantifying them poses quite a challenge. Fecal excretion of SCFAs depends on the rate of absorption, cross-feeding interactions, and gut motility, so fecal SCFAs do not directly reflect SCFA production in the gut. For instance, ulcerative colitis patients have impaired absorption of butyrate, which means they will excrete a greater proportion of the butyrate they produce. One recent study also found that higher fecal SCFA excretion, which is typically thought to be indicative of good gut health, was associated with obesity, hypertension, and cardiometabolic disease risk factors.10 In general though, low fecal SCFAs do tend to correlate with lower SCFA production.
Is zonulin a useful marker of gut permeability?
No. Blood or fecal zonulin has been shown to be elevated in depression, autism, diabetes, metabolic syndrome, PCOS, aging, and celiac disease. However, only a fraction of the patients in these studies have elevated zonulin.11,12 Moreover, many of the studies used to support the clinical use of zonulin testing were not measuring zonulin at all – they were measuring properdin, a zonulin analog.13
Furthermore, zonulin is only weakly correlated with other more validated measures of intestinal permeability, such as the differential sugar (lactulose-mannitol) absorption test and has been shown to fluctuate greatly throughout the day.11,12 Zonulin antibodies in the blood may be more stable and reflective of intestinal permeability, but these obviously will not be included on a stool test.
Does the stool microbiome actually reflect the gut microbiome?
You might recall a study that I reviewed and discussed on Chris Kresser’s podcast, which suggests that stool samples don’t accurately reflect the gut microbiome, and tend to over or underrepresent different genera from even the most distal part of the colon.
But this doesn’t mean that stool testing is useless. Consider that the majority of published research on the human gut microbiome to date is on fecal samples. In fact, given the current lack of human studies on the gut mucosa, a stool sample is likely more clinically useful than a small intestinal microbial biopsy.
If you think about it:
- We know how certain interventions like diet, exercise, and antibiotics affect the fecal microbiome.
- We know which fecal microbiome patterns are correlated with certain diseases
- We have a general idea of which microbes should make up the bulk of a healthy fecal sample
- We have a general idea of which microbes should not be present in large amounts in fecal samples.
This means that while fecal samples are imperfect, they are still a useful proxy for the overall ecosystem and are currently one of the best ways to screen for various gut pathologies.
Summary: tests I currently recommend and use myself and with clients
In summary, comprehensive stool tests and microbiome tests can be very helpful tools, but it’s essential to know which ones are reliable, and how to use the information appropriately. The testing landscape is constantly changing, so I am always re-evaluating different stool testing options and will attempt to keep this article up to date with what is available!
I have no affiliation with any stool testing companies. As of this writing, I recommend:
1) Genova GI Effects Comprehensive Profile
This test provides the most comprehensive look at the overall gut environment, parasites, and gives a decent look at bacterial balance. If you’re new to exploring gut health and are only going to get one test, I’d go with this one.
GI Effects is available through many functional medicine practitioners, or direct-to-consumer via directlabs.com (Click on “Order Tests” and search for “GI Effects”).
I recommend the 3-day stool collection if this is your first comprehensive stool test, as it is slightly more thorough in looking for parasites. Results typically take 2 weeks.
2) Thorne Gut Health Test + Genova GI Effects Comprehensive (or CSAP)
For a deeper dive into gut health, I recommend combining the Thorne Gut Health Test with the GI Effects, or another test that will provide clinical information about the gut environment, like the CSAP (just be sure to ignore the culture section!).
Thorne provides the best and most thorough look at the gut microbiome, with extensive raw data that includes overall bacterial balance and the ability to screen for stealth infections. The Thorne Gut Health test is available directly from their website for $198. Results typically take 4-8 weeks.
Unfortunately, the consumer report from Thorne is pretty limited. If you’d like help exploring and understanding your raw data, this is something that I do as part of my 1-on-1 health consultations.
Have you had comprehensive stool testing? Please share your thoughts or experience in the comments below!