Gut Microbiome Testing 101

An X-ray can evaluate our bony structures. An ultrasound can assess our organs or soft tissue. But outside of a clinical research setting, there is no verifiable method to examine the microbes that live in and on us.

That’s where at-home gut microbiome tests come in. A growing number of companies now offer a way to sequence the gut microbiome through a DIY stool swab. But what do these tests tell us about our health? Do they truly give us a glimpse into the microbial world within—or are their claims outpacing the science?

As a microbiome science company led by leading academics and researchers in the field, this is our evidence-based perspective on gut microbiome tests.

Most at-home tests analyze the gut microbiome, where the vast majority (95%) of our body’s microbial life resides.¹ 

The gut microbiome is a worthy site of study considering the critical role it plays in nearly every biological function of the body, including digestion, mood, and immunity. Collectively, its bacteria can fend off infection, maintain a strong intestinal lining, and help break down food into functional byproducts—some of which have impacts well beyond the gut.^2,3 (Butyrate, a fatty acid formed by the microbial fermentation of fiber, supports the production of T cells in the immune system, for example.)⁴

The composition of the gut microbiome is mind-bendingly complex and expansive. If you laid out the lining of the small intestine, it would take up roughly half of a badminton court, while the large intestine houses more microbial density than any other organ.^5,6 

The gut microbiome is also highly individualized, evading blunt categorizations like “good” or “bad,” “healthy” or “unhealthy.” At a high level, a resilient gut will contain a variety of bacteria that work together to allow your body to undergo critical functions.⁷ Think of your gut like a company: It’s stronger when it employs workers with different skills and talents, who are ready to tackle potential problems with a unique perspective.

While your poop is often written off as waste, it actually contains up to 54% of bacterial biomass by weight (the rest is carbohydrates, fiber, protein, and fats).⁸ Instead of flushing this valuable health metric down the drain, gut microbiome testing companies collect it and use it to analyze your internal workforce. 

After purchasing a microbiome test online (typically $150-$300), you’ll be sent a kit for your stool sample. This will contain instructions on how to collect your poop (mess-free) and mail it back to the company. (Note: Due to local regulations, New York, Maryland, and Rhode Island do not allow certain gut microbiome tests without the consent of a healthcare provider.) From there, the company will send your sample to a lab for processing. 

This is where each test starts to differ: Every company will have its own methodology for “sequencing” the sample, or labeling its microbial parts using a technique known as shotgun genomics. In simple terms, fecal kit sampling using shotgun genomics aims to extrapolate a complete picture of your microbiome using a relatively small isolated sample. 

Most companies do so by breaking down your stool into its constituent microbial DNA, multiplying these parts, and comparing the resulting genome to a “normal” microbiome. (However, the technology they use affects the number and types of bacteria recognized in the sample, and some bacteria may be missed while others may be over-represented. We’ll dig into this more below.)⁹ 

Companies will then cross-check to see how the microbial composition of your sample compares to their internal models to compile an assessment of your gut health.

Some companies now utilize more advanced methods, such as metatranscriptomic or metabolomic sequencing, which measure not only which bacterial/microbial genes are present but also how these genes function and which duties they perform in the gut.

About 2-6 weeks after sending in your sample, you’ll receive your gut health report card. It will likely give you an overall “score” based on the bacterial species and strains that were statistically significant in your sample. 

Gut microbiome tests are not meant to diagnose health conditions or tell you about your risk of developing a condition in the future. (You’ll need to see your doctor for that.) 

Instead, they use information about your gut bacteria (and potentially archaea, viruses, and fungi) to paint an overall picture of your gut health. In addition, many microbiome tests recommend foods, supplements, or probiotics that may be best suited for your microbial composition. 

Many people use these suggestions in the hopes of losing weight, gaining energy, improving mood, or having more comfortable, consistent digestion.

We’ll cut to the chase: the majority of the scientific community is in agreement that while gut microbiome tests are exciting in theory, they lack precision and utility in practice.¹⁰  

As it stands today, the technology of these tests is not quite advanced enough to provide an accurate readout of the gut microbiome. 

On top of that, there is no consensus among microbiologists and researchers on what a “healthy” microbiome actually looks like (healthy subjects can vary considerably in their gut microbial composition), so the clinical utility of these tests is limited.¹¹ 

The gut microbiome is also constantly changing (even within a single day), so one snapshot captured through one small stool sample may not provide a complete picture of your gastrointestinal health. 

If you asked our team of scientists about gut microbiome tests at a dinner party, these are the pros and cons they’d likely tell you:

Pros:

• • They foster curiosity about personalized microbiome care.

Gut microbiome testing kits can encourage citizen science, foster curiosity about the gut microbiota, and potentially generate awareness of the microbes that live within us. They also show that we all react differently to foods and supplements based on our gut microbiota composition.

• • They are convenient.

Fecal samples are more convenient than other methods of microbiome exploration, such as tissue-specific biopsies, luminal brushes, and surgeries. (However, they aren’t always the most reliable measurement of gut health.)

Cons:

• • Stool isn’t necessarily the best sampling medium.

Concerns about gut microbiome test kits begin with their collection method.¹² While fecal samples are convenient, they are an imperfect proxy for a well-rounded picture of intestinal microbiota.

Different sections of the gastrointestinal tract have unique properties, so relying on a stool sample to survey the microbiome as a whole is generally inaccurate.¹³  The microbial composition of your GI tract can also vary significantly from your stool, and this variance will change with age.^14,15 The part of the stool that your sample is taken from also matters. Unintentional contamination issues can occur during the collection stage, too.¹⁶

• • • Results lack critical nuance.

So much of the gut microbiome is yet to be explored. Researchers only started sequencing the gut microbiome in earnest over the last two decades, and it’s too soon to know what a “healthy” one looks like (if it exists at all). The inherent qualities of microbes—enormous genetic diversity, rapid evolution, and complex interdependence—mean that it’s challenging to categorize them.^17,18

It’s also important to remember that the microbiome is an ecosystem that exists within a bigger ecosystem—the human body—and is contextualized by factors unique to us as individuals, as well as the environment we live in.¹⁹

All of this is to say that your gut microbiome is unique to you. It’s as singular as your fingerprint, and assigning it a score or number does a disservice to its fascinating nuance.

• • • Test kit recommendations are outpacing microbiome science.

At this time, we do not know enough to associate the presence of certain microbes in the gut with reliable recommendations about nutrition or supplements.

This is partially due to the sheer scale and complexity of these microbes. There are 300 to 500 bacterial species that reside in the gut (and an untold number of strains within those species).²⁰ The impact that these microorganisms and their metabolites have on our biology is complicated and heavily context-dependent. This is further complicated by evidence of horizontal gene transfer in the human gut microbiome, in which microbes “inherit” traits from other microbes outside of their immediate lineage.²¹

Any advice on “optimizing” the gut microbiome also needs to be considered with respect to other lifestyle factors—including diet, exercise, and general health status. When thinking about putting together a “treatment plan,” a range of laboratory readouts (i.e., blood lipid, blood sugar, inflammatory markers, etc.) are critical factors to acknowledge as well. 

• • • Different testing companies use inconsistent methodologies.

As previously mentioned, sequencing technologies often vary across companies. The gut microbiome testing space lacks a regulatory body, so company laboratories don’t have standardized technical and analytical procedures or reference databases.¹⁰ This means that the results you get from one company could vary widely from the results you get from another.

• • • These tests come with ethical concerns.

Lastly, ethical concerns with these technologies can’t be ignored. Gut microbiome tests are not regulated by the FDA, and so they are not subject to adverse event reporting. Though many companies will state that their tests are not diagnostic, some marketing claims can imply—and lead the consumer to believe—that the results are scientifically accurate and clinically relevant when that has not been substantiated. 

Under the guise of a “customized” plan, consumers may then go on to spend money on a slew of probiotics and supplements. This can pose harm when the results are inaccurate or come with nutrition advice and/or food supplement recommendations that are clinically unproven. It can also result in some consumers self-misdiagnosing, delaying seeking medical treatment, and/or substituting non-medical supplements for prescription medications. 

Additionally, through the purchase and use of these tests, individuals may be financing the collection of their personal health data to be monetized by others.²² 

At this time, we believe you’re better off skipping gut microbiome tests and spending your money on tools that are known to improve microbiome health—no matter your starting point—instead.

This isn’t to say that there will never be a role for direct-to-consumer testing in the gut microbiome space. The scientific landscape is progressing rapidly, and next-generation tests may focus more on function (what the microbes are doing), rather than simply which microbes are present, helping to bring more clarity and precision.

Products may also evolve to be more “predictive” by employing functional and longitudinal sequencing techniques alongside other novel technologies—such as AI and machine learning—to help generate patterns, trends, and ultimately, lifestyle recommendations. 

Before this becomes a reality, further regulations and scientific developments will be needed. In the meantime, we’d advise against making diet and lifestyle changes using the results of gut microbiome tests alone. Remember: your microbiome is unique to you—a veritable universe far more expansive than any one report can reflect. 

1. Dupont, H. L., Jiang, Z. D., Dupont, A. W., & Utay, N. S. (2020). The intestinal microbiome in human health and disease. Transactions of the American Clinical and Climatological Association, 131, 178–197.
2. Spragge, F., Bakkeren, E., Jahn, M. T., Araujo, E. B. N., Pearson, C. F., Wang, X., Pankhurst, L., Cunrath, O., & Foster, K. R. (2023). Microbiome diversity protects against pathogens by nutrient blocking. Science, 382(6676). https://doi.org/10.1126/science.adj3502
3. Blackwood, B. P., Yuan, C. Y., Wood, D. R., Nicolas, J. D., Grothaus, J. S., & Hunter, C. J. (2017). Probiotic Lactobacillus species strengthen intestinal barrier function and tight junction integrity in experimental necrotizing enterocolitis. Journal of Probiotics & Health, 05(01). https://doi.org/10.4172/2329-8901.1000159
4. Luu, M., Weigand, K., Wedi, F., Breidenbend, C., Leister, H., Pautz, S., Adhikary, T., & Visekruna, A. (2018). Regulation of the effector function of CD8+ T cells by gut microbiota-derived metabolite butyrate. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-32860-x
5. Helander, H. F., & Fändriks, L. (2014). Surface area of the digestive tract – Revisited. Scandinavian Journal of Gastroenterology, 49(6), 681–689. https://doi.org/10.3109/00365521.2014.898326
6. Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body. PLoS Biology, 14(8), e1002533. https://doi.org/10.1371/journal.pbio.1002533
7. Dogra, S. K., Doré, J., & Damak, S. (2020). Gut microbiota resilience: Definition, link to health and strategies for intervention. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.572921
8. Rose, C., Parker, A., Jefferson, B., & Cartmell, E. (2015). The characterization of feces and urine: A review of the literature to inform advanced treatment technology. Critical Reviews in Environmental Science and Technology, 45(17), 1827–1879. https://doi.org/10.1080/10643389.2014.1000761
9. Levitan, O., Ma, L., Giovannelli, D., Burleson, D. B., McCaffrey, P., Vala, A., & Johnson, D. A. (2023). The gut microbiome–Does stool represent right? Heliyon, 9(3), e13602. https://doi.org/10.1016/j.heliyon.2023.e13602
10. Hoffmann, D. E., Von Rosenvinge, E. C., Roghmann, M., Palumbo, F. B., McDonald, D., & Ravel, J. (2024). The DTC microbiome testing industry needs more regulation. Science, 383(6688), 1176–1179. https://doi.org/10.1126/science.adk4271
11. Shanahan, F., Ghosh, T. S., & O’Toole, P. W. (2021). The healthy microbiome—What is the definition of a healthy gut microbiome? Gastroenterology, 160(2), 483–494. https://doi.org/10.1053/j.gastro.2020.09.057
12. Tang, Q., Jin, G., Wang, G., Liu, T., Liu, X., Wang, B., & Cao, H. (2020). Current sampling methods for gut microbiota: A call for more precise devices. Frontiers in Cellular and Infection Microbiology, 10. https://doi.org/10.3389/fcimb.2020.00151
13. Donaldson, G. P., Lee, S. M., & Mazmanian, S. K. (2015). Gut biogeography of the bacterial microbiota. Nature Reviews. Microbiology, 14(1), 20–32. https://doi.org/10.1038/nrmicro3552
14. Hillman, E. T., Lu, H., Yao, T., & Nakatsu, C. H. (2017). Microbial ecology along the gastrointestinal tract. Microbes and Environments, 32(4), 300–313. https://doi.org/10.1264/jsme2.me17017
15. Grieneisen, L., Blekhman, R., & Archie, E. (2023). How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome. Gut Microbes, 15(1). https://doi.org/10.1080/19490976.2023.2178797
16. Weiss, S., Amir, A., Hyde, E. R., Metcalf, J. L., Song, S. J., & Knight, R. (2014). Tracking down the sources of experimental contamination in microbiome studies. Genome Biology, 15(12). https://doi.org/10.1186/s13059-014-0564-2
17. Van Rossum, T., Ferretti, P., Maistrenko, O. M., & Bork, P. (2020). Diversity within species: Interpreting strains in microbiomes. Nature Reviews. Microbiology, 18(9), 491–506. https://doi.org/10.1038/s41579-020-0368-1
18. You, C., Jirků, M., Corcoran, D. L., Parker, W., & Jirků-Pomajbíková, K. (2021). Altered gut ecosystems plus the microbiota’s potential for rapid evolution: A recipe for inevitable change with unknown consequences. Computational and Structural Biotechnology Journal, 19, 5969–5977. https://doi.org/10.1016/j.csbj.2021.10.033
19. Porras, A. M., Shi, Q., Zhou, H., Callahan, R., Montenegro-Bethancourt, G., Solomons, N., & Brito, I. L. (2021). Geographic differences in gut microbiota composition impact susceptibility to enteric infection. Cell Reports, 36(4), 109457. https://doi.org/10.1016/j.celrep.2021.109457
20. Quigley E. M. (2013). Gut bacteria in health and disease. Gastroenterology & Hepatology, 9(9), 560–569.
21. Borodovich, T., Shkoporov, A. N., Ross, R. P., & Hill, C. (2022). Phage-mediated horizontal gene transfer and its implications for the human gut microbiome. Gastroenterology Report, 10. https://doi.org/10.1093/gastro/goac012
22. Ahmed, L., Constantinidou, A., & Chatzittofis, A. (2023). Patients’ perspectives related to ethical issues and risks in precision medicine: A systematic review. Frontiers in Medicine, 10. https://doi.org/10.3389/fmed.2023.1215663