If you’re reading this, you’re probably seeking to answer the question “what are the best stool tests in 2024?” You’re not alone if you’re finding it challenging to decide what the best stool test is to take a closer look at your gut microbiome and digestive health. I’m here to help you understand the different types available so you can make an educated decision. After all, stool tests are expensive, so you really don’t want to order the wrong one! The best stool tests use best-in-class technology and cover a range of gut health markers.
Stool testing has evolved so much over the last 15 years, which is about as long as I have been having stool tests done for myself. I’ve personally seen the evolution of what’s available and unfortunately, there are still many tests available that have outstayed their welcome. Slick marketing often trumps clinical quality when it comes to stool tests that are available. I am incredibly particular when it comes to pathology testing because I’ve personally experienced wasted money more than once before I became a practitioner.
It’s important to keep in mind that microbiome science is relatively new, and stool tests available to the public are even newer. Although there is a lot we know about the microbiome, there are also many things we are yet to discover, so it’s important to keep in mind that stool tests DO have limitations. I will expand on this later, but I want to set expectations early on.
Currently, it's also not easy to get everything we want from one single test that also uses best-in-class technology for each aspect of digestive health being measured. The only one that currently achieves this is Co-Biome from Microba - available only to Australians at the moment.
Please note that - as more tests become available - I will be updating this article. My goal is to help you make the right choice for your personal situation. I hope you find it helpful!
What are stool tests looking for
There are quite a few different things we can investigate via stool testing when it comes to your health:
- The microbiome, which is the ecosystem of microbes in the gut that have a strong influence on our health - it’s mostly bacteria that are reported on and fungi
- Parasites and pathogens
- Digestive health - nutrient absorption
- Inflammatory markers
- Gut-immune function
- Leaky gut (intestinal permeability) - though the markers for this are controversial
- Post-biotics such as the short chain fatty acids that bacteria produce to influence our health
Keep in mind that all stool tests are different - not all of them offer the above. Many of the tests available only investigate the microbiome.
Most stool tests of this type are a single collection and are done at home.
Why you may benefit from a stool test
If you have chronic digestive complaints or a condition that is strongly believed to have a link to gut health, then a stool test is a good choice. If you have the former, then I suggest ordering a test that will assess both your microbiome AND the digestive and inflammatory markers.
Digestive conditions such as IBS, IBD, acid reflux (GERD) are definitely worth getting a stool test for.
Non-digestive conditions or symptoms such as depression, anxiety, insomnia, joint pain, chronic fatigue syndrome, autoimmune conditions such as Anklyosing Spondylitis, skin conditions such as rosacea, eczema or psoriasis are also good candidates for stool testing.
Overview of the types of microbiome stool tests available
Culture-based testing is the traditional type of testing where the microbes first have to be grown successfully from the stool sample in order to be identified and measured. This presents significant problems because many species cannot be grown outside the gut, so it gives an extremely inaccurate or limited view of someone’s microbiome. This is the testing I had done around 12 years ago through Bioscreen in Melbourne which started my journey with stool testing. In a way, it actually was helpful for me because the treatment the doctor gave me alleviated some symptoms I wasn’t expecting it to - that was the big lightbulb moment where I personally realised that there’s really something to this whole gut-brain connection. Culture-based testing is now considered old-fashioned and is quickly being replaced by DNA-based testing. I personally feel that culture-based testing should not be used. The historical dominance of culture-based testing is one of the reasons why there is still a widely held belief that species in the Lactobacillus genus and Bifidobacterium genus are extremely important for an individual to have a healthy microbiome.
DNA-based testing is more modern, does not require culturing and there are 3 major subtypes currently available to the general public - PCR, 16S and Shotgun metagenomics. Some tests such as Co-Biome will actually use more than one of these types of DNA testing to take advantage of their individual strengths. DNA testing has become more accessible and affordable over the years to consumers outside of research settings.
Which type of DNA testing is best?
Each type has its own strengths and weaknesses. As already mentioned, some stool tests such as Co-Biome will strategically use a number of these methodologies on the same test which is an excellent approach. I highly recommend that anyone with chronic digestive complaints orders testing which covers all the bases as much as possible - this may involve ordering testing from two different labs.
qPCR (quantitative PCR) is great for parasite detection but not other aspects of the microbiome, meaning its usefulness is limited to this specific area. These tests generally only report on a pre-determined list of microbes rather than reporting on everything that’s present. This gives a very inaccurate view of the overall state of the microbiome, similar to culture-based testing.
16S RNA gene sequencing is a more affordable option compared to metagenomics, but its accuracy at the species level isn’t as good as metagenomics and doesn’t report on fungi, archaea (eg. Methanobrevibacter spp.) or parasites.
Metagenomics is the most expensive of the widely available DNA-based methodologies, but it will detect more microbes than 16S and can drill down to species level and often, the strain too. It will also report on fungi and archaea. If you’re going to invest any money in stool testing, I recommend using the best technology option available which is metagenomics.
What are the limitations of stool testing?
Not everything that is a factor in your gut health or general health can be tested with a stool test. For example, we can’t determine if there are anatomical or movement abnormalities present that are affecting you. We also can’t measure the effect of your nervous system functioning on your digestive heath, with the exception of Secretory IgA and fecal elastase levels. These factors need to be assessed via clinical examination and specialist testing. For example, I have had two clients run Biomesight 16S stool testing and barely anything abnormal was detected in their results. Which is a good indication that you can have a “perfect on paper” stool test result while you have troublesome digestive symptoms.
Stool tests also don’t measure the small intestine microbiome. There are obviously similarities between the small and large intestine microbiomes in an individual, however they are not the same. This is mostly because the small intestine and large intestine have differing anatomical and physiological features which may favour the growth of different species. I have personally observed that species that would be expected to show up on a stool test based on an individual having SIBO or an autoimmune condition that flares with starch consumption - such as Klebsiella spp. - are just not there. I’ve also observed that people who have methane detected on a breath test may show zero M. smithii on a stool test that does report on it.
Technically, stool tests are measuring the fecal microbiome which may not be wholly representative of the microbiome in different areas of the large intestine. However, stool testing is still believed to be a good high-level representation of the microbiome as a whole and is currently the least invasive option since no colonoscopy is required to obtain a sample.
Results of a stool sample that has been split and sent to two different labs may differ because different technologies and libraries are used for sequencing - or identifying - the species. If a split sample is sent to the same lab for two different analyses/reports, we should expect reproducibility between the two reports - there is one stool test (GI Map) where this was found not to be the case with digestive markers which is concerning. This is one reason I don’t recommend GI Map or Nutripath GI Mapping (the Australian equivalent).
Some tests report on substances such as short chain fatty acids OR the potential to produce them based on the bacteria identified. SCFAs measured directly may not be representative of their activity in the gut - for example, a high butyrate in a stool sample may actually mean the butyrate is being excreted in the stool and not utilised (which may happen in significant dysbiosis). In tests where the potential for producing SCFAs is measured rather than the actual amount, this measurement can be misleading. A highly unhealthy microbiome - often due to antibiotics - may lose the ability to produce butyrate as part of “gut hypoxia” which is akin to a gut injury. The presence of microbes that produce butyrate doesn’t necessarily mean they are producing it - the potential is there, but it may not be happening.
Lastly, from a wider context, it’s important to remember we are still in the infancy of microbiome research - that means that we can’t always accurately deduce the impact of various microbes and should never look at individual species in isolation. The microbiome is an ecosystem after all.
The stool tests I use and recommend
Where possible, ordering a test that combines digestive markers with a metagenomic-based microbiome assessment is the best choice. The first two in the list below are my top recommendations, although I know they are not available to everyone. US and Australians are well covered by the top two recommendations.
For those in other countries, you will most likely need to order two stool tests - one that offers either metagenomic testing (preferred), 16S (second choice) for the microbiome and a second test to cover the digestive markers.
Some labs also do not offer the “raw data” to enable a further deep dive into the microbiome - this is usually done by uploading a file to a third party service. This may only be required for a particular set of people rather than everyone. It’s certainly a risk to “over-analyse” microbiome results and forget there is a lot more to health than the levels of some bacteria.
Combination tests
As far as I am aware, these tests don’t automatically provide the raw data, however they are still my top recommendation for most clients
- US testing: Genova GI Effects (I usually ignore the culture-based results section) with Microbiomix module added on OR Microbiomix with GI Effects Fundamentals
- AUS testing: Microba Co-Biome - available in Australia only at present
Microbiome-only
The below are all metagenomics tests except Biomesight which is 16S
- Genova Microbiomix (note this doesn’t include any digestive markers unless you order the GI Effects with Microbiomix added on)
- Microba - an Australian test that is sometimes available to other countries
- Thorne Gut Health Test - available only to US residents, provides raw data
- Biomesight - UK based and available mostly worldwide
- myBIOME (Synlab) - European lab using Microba technology
Tests I don’t recommend
These are the tests I don’t recommend using - either because they use out-of-date techniques, they don’t use the best DNA-based technology or there have been questions raised about the accuracy of some markers.
- GI Map
- Nutripath GI Mapping
- CDSA
- Maldi-TOF based tests (since they still rely on being able to culture or grow the microbes in the lab)
- Culture-based testing such as Bioscreen (AU) and particular sections of some tests such as GI Effects (meaning I disregard the results from those sections)
What about breath tests?
Breath tests are commonly used to investigate SIBO, however there are some issues with these tests. They don’t measure the microbiome directly, they are measuring gases produced by bacteria (and methanogens) after the individual swallows a substrate such as glucose, fructose or lactulose. Lactulose is known to speed transit time and glucose usually only detects SIBO that is quite high in the small intestine (since glucose is mostly all absorbed by the time it reaches the middle section of the SI). So, fructose is my preferred option - you can watch a video from naturopathic microbiome expert clinician Jason Hawrelak PhD about this topic and what he observed in his own clinic. You can also read more about how I’m testing and treating SIBO in 2024.
What to do if your budget is limited
If your budget is limited, my suggestion is firstly to order a stool test rather than a breath test as that will give you much more information than a breath test. A good clinician should be able to tell if you have SIBO based on your history, symptoms and other non-digestive conditions you may have eg. rosacea, autoimmunity.
Secondly, I would see what digestive function tests your doctor can order that are appropriate to you and are often included on the combination tests. Examples here are fecal elastase and calprotectin.
My experience of the Co-Biome Meta Explore test
I recently did an Instagram Live talking about why this is my stool test of choice and taking you through my own results. Check it out below:
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I also offer a stool test interpretation service.
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Diet is the number one most important factor to improve your microbiome diversity which is associated with better health outcomes. I designed the recipes in C'mon Gut Happy to be delicious and to maximise microbiome-nourishing ingredients.
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