Choosing a Stool Test
Stool Testing Techniques: Culture vs. PCR and Beyond
To recap on culture vs. PCR testing. For those looking to get to the root of their health issues, a stool test can offer important insights. Many health issues can be traced back to the presence of pathogenic microbes or parasites, lack of beneficial microbes or lack of general diversity. However, it is important to know the difference between the types of testing available and how to use them.
Generally speaking, if you go through a GP or hospital (or LifeLabs if you are Canadian) for a stool test it will be what is called a “Stool Culture.” This technique is considered the least reliable form of stool testing. In order for culturing to work the microbes in the stool must be alive. When patients are given stool culture kits they are often producing the sample at home and then delivering it hours later. Even if it is produced at the lab, the technicians may not start analysis until much later. The longer the sample is exposed to air the more microbes will die-off – making False Negatives a common occurrence for this technique.
Different Types of PCR Testing
We already know that culture based testing is more or less useless to us. But what about the different types of PCR testing. Which is right for you? The answer will depend on which stage of your journey you are at, what you want to learn about yourself and level of data you want.
16S Nex-gen
The Next-Gen sequencing of 16s RNA is now the most widely used type of PCR testing both for research and for supporting clients through health issues.
The 16s tests we have access to include Ombre or Biomesight. Next-Gen is great for picking up on a wide array of microbes at the species level. It's less intensive for the labs than the other PCR tests I will mention, which is why it has a lower price point. Approx $200CDN for Biomesight for example.
Unlike shotgun sequencing this type of testing doesn't tell you what functions the microbes are using - it will only predict the function based on the microbes present. For example, biomesight gives you predictive information on whether your microbes are breaking down oxalates or producing butyrate based on which are present.
This is a good test to use when you are either following up on previous testing, you know that your pathogen levels are down and you are ready to focus on balancing commensal and beneficial microbes.
You can always add on a stool chemistries test if you want more information on your digestive and immune function.
Results from 16s testing takes approximately two weeks.
Real-time PCR
Real-time PCR (such as Diagnostic Solutions GI Map) is better for identifying specific microbial pathogens. The lab has to input the microbes and virulence factors they're looking for and then analysis hones in on that. It excels at identifying pathogens, especially H-pylori. This is a good place to start if you are new to testing in general as you will get information on bacteria, fungi, parasites, viruses, digestive and immune function. This type will give you genus and species level information, but not strain level.
If you are trying to get a reading on parasites you'll need to do this test around the full moon.
If you want more information on beneficial microbial counts and diversity you would have to do another type of test simultaneously.
This test has add ons available for Calprotectin (Inflammation) and Zonulin (Leaky Gut).
Results take approximately 2-3 weeks.
Shotgun Sequencing
Shotgun metagenomic sequencing, unlike 16S rRNA sequencing, can read all genomic DNA in a specimen rather than just one particular area. Shotgun sequencing can simultaneously identify and profile bacteria, fungi, viruses, and a variety of other microorganisms, which is useful for microbiome research. It also tells you what functions the microbes are using. For example, are they actively making ammonia, histamine or other compounds.
The tests using this method include Nirvana, Microbiome Labs BiomeFX, Viome. An unfortunate side to working with these labs is they don't share the raw data from your results, so you only get to see what they deem as important.
You won't see markers specific to accessory organ digestive function nor immune function with this type of testing. Although they do tell you if your microbiome is metabolizing more proteins vs. carbohydrates.
Results take longer for this testing and it tends to cost more. Results take on average 4-5 weeks.
Checkpoints for choosing your test:
Does the company provide raw data instead of their own interpretation?
Do you retain full control of your microbiome data instead of it being sold off? I never work with microbiome labs that sell your data.
Do you want genus or species level data or strain level data?
Do you want virulence factors for a specific microbe? Telling you whether it's behaving as a pathogen vs. a commensal
Cost: from lowest to highest in price ---> 16s, Real-time, Shotgun
Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol. 2019 Jan;17(2):218-230. doi: 10.1016/j.cgh.2018.09.017. Epub 2018 Sep 18. PMID: 30240894; PMCID: PMC6391518.
Gupta, S., Mortensen, M.S., Schjørring, S. et al. Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing. Commun Biol2, 291 (2019). https://doi.org/10.1038/s42003-019-0540-1
Peterson et al; Front. Microbiol., 15 July 2021
Sec. Evolutionary and Genomic Microbiology
Volume 12 - 2021 | https://doi.org/10.3389/fmicb.2021.670336
Jian C, Luukkonen P, Yki-Järvinen H, Salonen A, Korpela K (2020) Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling. PLoS ONE 15(1): e0227285. https://doi.org/10.1371/journal.pone.0227285
