Did you know that each teaspoon of stool contains around 100 billion microbes (1)?
That’s right. Your stool is rich with that much diversity and complexity.
There is so much bacterial DNA found in just one teaspoon of stool that it would require 100,000 of today’s highest-capacity thumb drives to store all the data.
The magnitude of this microbial world within us is astounding and has fueled a surge of interest and research in recent years.
The Complexities and Realities of Stool Testing
In 1956, only one publication on stool testing existed. Fast forward to today, and the research on the topic has dramatically changed, with a staggering 170,186 results on PubMed covering stool tests.
With this surge in interest comes a market (financial) opportunity, leading to the proliferation of direct-to-consumer (DTC) stool tests.
These tests, often costing hundreds of dollars, are widely used by integrative practitioners.
If you are on the internet, you likely have been marketed to by companies who promise to "sequence your gut microbiome" to give you "valuable insights into your general wellbeing".
Some of these companies even say they can tell you about your "cognitive health", "inflammation response" and "metabolic health" by examining your gut microbiome.
But the question remains: Are they valid? Do they help in targeting treatment?
Are these companies actually able to deliver what they are promising?
Or are they a waste of money?
Microbiome: The Ecosystem Within Us
The gut microbiome is the community of microorganisms, including fungi, protozoa, bacteria, and viruses, living in the gastrointestinal (GI) tract. These microorganisms perform essential functions such as:
Strengthening gut lining integrity
Shaping the intestinal epithelium
Harvesting energy
Protecting against pathogens
Regulating the immune system
Focusing on the gut microbiome, bacteria are the most abundant, with two dominant phyla—Bacteroidetes and Firmicutes—making up approximately 95% of the microbiome in healthy individuals.
The relative abundance of these organisms varies widely among individuals (1).
Stool Testing: Methods and Limitations
Stool testing includes a range of methodologies, each offering insights into the microbial community living within us.
Culture: Traditional method for bacteria (and some archaea and viruses). It involves growing bacteria on specific media and counting them.
PCR Panels: Also known as polymerase chain reaction. Amplifies specific DNA fragments to detect known organisms—think “DNA photocopier”; it makes lots of copies of a small piece of DNA so scientists can have enough material to study. PCR has a high sensitivity and specificity but is limited to known bacteria.
Enzyme Immunoassay (EIA): Detects substances microbes produce in stool samples. It is faster but potentially less specific than other methods. It is commonly used for detecting H. pylori, Giardia, and C. difficile.
Amplicon Sequencing: This technique sequences partial genomes of selected organisms. It is like copying and reading a specific, important chapter of a big book (DNA) to understand more about the story (the organism).
Shotgun Sequencing: This method sequences the complete genomes of all organisms. It is suitable for novel organisms or parts of the DNA that are tricky to study. However, it is more expensive than other methods.
Metatranscriptomics: Examines messenger RNA (mRNA) to study gene expression—not just the genes alone. mRNA is like a message or a recipe that tells the microbes what to do and how to behave.
We Don’t Know What The Ideal Microbiome Is
Despite advancements in stool testing, there are still significant limitations to using and interpreting stool tests in clinical practice:
First, as mentioned above, the microbiomes of healthy people are significantly diverse.
“This means there is no standard microbiome biome that can be used as a “reference range” like we have for common lab tests like cholesterol levels and blood sugar.”
Additionally, the microbiome is dynamic and constantly changing, affected by factors such as medications, environment, and diet.
How do we interpret one “snapshot” that may have shifted by the time the results have come back?
This dynamic nature of the microbiome, combined with its diversity, complicates interpretation and analysis.
Furthermore, the collection of stool samples may not fully capture the intricacies of the gut microbiome, as microbial communities vary along the length of the gastrointestinal tract. The microbes in the stool do not reflect the microbes higher in the digestive tract.
Do We Use ANY Stool Tests At Modrn Med?
Yes, we routinely screen people who have symptoms that warrant stool testing. This can include diarrhea, bloating or blood in the stool.
However, we believe that stool testing can be put through insurance through a reliable commercial lab like quest or lab corp. We do not believe that direct-to-consumer microbiome tests or “comprehensive stool testing” that look at different microbes are currently useful given our limited knowledge as a medical community.
Conclusion
We are still in the infancy of microbiome research. While there are potential clues in stool testing, significant limitations exist. The field has not yet matured to the point where microbiome testing can be a reliable clinical tool. For now, understanding and interpreting these tests require caution and professional guidance.
Questions? Let us know below. We're happy to address them on our social media for everyone to benefit.
Citations:
Allaband C, McDonald D, Vázquez-Baeza Y, et al. Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol. 2019;17(2):218-230. doi:10.1016/j.cgh.2018.09.017
Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823-1836. Published 2017 May 16. doi:10.1042/BCJ20160510
Magne F, Gotteland M, Gauthier L, et al. The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients?. Nutrients. 2020;12(5):1474. Published 2020 May 19. doi:10.3390/nu12051474
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