All sorts of microbiome tests are now available to consumers, but are they any good? The microbiome is the community of microbes (bacteria, viruses, fungi) that live in and on our bodies. Each body part (e.g., sinuses, gut, vagina, skin) has a different microbiome, but the one that has been studied the most (with stool tests) is the gut microbiome.
A recent study by researchers at the US National Institute of Standards and Technology (NIST) evaluated the performance of seven commercial (sold directly to consumers) microbiome kits or tests that promise to give you an analysis of your gut microbiome (and health advice) by analyzing a stool (fecal) sample that you mail them. The researchers found that the test results do not give you dependable or reliable information about the actual composition of your gut flora.
They also found that for the same stool samples there were major discrepancies among the results from different companies, and even from the results of the same identical samples sent to each company (3 of the same stool sample was sent to each company).They found that the same sample could be labeled healthy vs unhealthy by different providers.
They point out that you can't make conclusions or recommendations on how to improve (gut) health from the results because the results are so flawed. [An earlier study of tests from 31 companies found the same kind of flawed results.]
Why is this happening? This is because there is no government regulation or oversight of the tests - thus the test manufacturers don't have to prove that they are reliable and actually measure what they say they measure. There are no quality assurance requirements. No standardization of tests. [An earlier 2024 study of microbiome tests sold to consumers and manufacturer claims found the exact same thing.]
Bottom line: The tests may sound great, but don't do it! The companies typically just want to sell you their supplements - which you probably don't need!
Instead, try to improve your diet - a diet rich in whole foods and fiber, which will also feed your beneficial gut microbes. This includes fruits and vegetables, nuts, whole grains, seeds, legumes, whole grains. Also, some fish, some dairy, eggs, some olive oil. For example, Mediterranean style diet.
From Medscape: Commercial Microbiome Tests: Unreliable Results
Commercial home tests that analyze stool samples promise insights into a person’s gut microbiome. But how reliable are those results? A study published in Communications Biology delivers a sobering verdict: the tested microbiome analyses do not provide dependable information about the actual composition of the gut flora.
“The study is very elegantly designed and impressively demonstrates how unreliable the tested commercial microbiome tests are,” said Gregor Gorkiewicz, MD, professor of medical microbiome research at the Medical University of Graz, Graz, Austria, in comments to the Science Media Center Germany. “However, this issue has been a much-discussed topic in the medical-scientific community for some time now.”
The study authors’ starting point: numerous publications link the intestinal microbiome to a range of diseases, from metabolic disorders to cancer and even neuropsychiatric conditions. Despite intensive research, there are currently neither approved routine clinical tests nor broadly established diagnostic standards for microbiome analysis. At the same time, companies are developing home tests for laypeople (direct-to-consumer [DTC]).
Those kits operate in a regulatory gray area between medical devices and lifestyle products. Although consumers often receive health-related assessments and individualized recommendations, the tests are not subject to the same validation and quality-assurance requirements as traditional in vitro diagnostics. Against this backdrop, researchers at the US National Institute of Standards and Technology (NIST) evaluated the analytical performance of seven DTC tests.
To exclude biological variability from individual donors, NIST researchers used a homogenized, well-characterized human stool reference material. They ordered three test kits from each provider and filled them with identical sample material. The companies were not informed about the evaluation so that the conditions would be as realistic as possible.
In addition, the NIST team analyzed samples of the same material in its own laboratory using 16S ribosomal RNA (rRNA) amplicon sequencing and whole-genome shotgun sequencing. The team also examined seven additional donor samples to compare the providers’ methodological variance with the biological variance between actual individuals.
“The providers differed substantially in sample collection, buffer/shipping, sequencing approach (rRNA gene amplicon sequencing vs whole metagenome shotgun sequencing), read depth, and reporting cutoffs,” said André Gessner, MD, PhD, head of the Institute for Microbiology and Hygiene, University of Regensburg, Regensburg, Germany, in comments to the Science Media Center Germany. These methodological differences produced markedly different taxonomic profiles. “In some cases, variability between providers is as large as — or larger than — the biological variability between different donors,” Gessner said. “Reproducibility within individual providers was also inconsistent.”
Beyond taxonomic profiles, many providers offer health-related assessments and individualized recommendations. The reference populations underlying those interpretations vary — internal company databases, the Human Microbiome Project, or American Gut— as does the definition of a “healthy” microbiome.
In one instance, identical sample material was classified as “healthy” by two providers but as “unhealthy” by a third. Functional assessments and dietary recommendations differed accordingly. There were also large discrepancies in detecting potentially pathogenic organisms. For Clostridioides difficile, three providers reported detection and four did not.
“The paper addresses the core problem in the DTC microbiome market: consumers receive seemingly precise reports, even though the analytical basis is often not robustly comparable,” Gessner said. “While the authors used homogeneous reference material and replicates, the study does not determine which provider is ‘right’ — only that they diverge greatly.” The results are also not automatically generalizable to all available services, he added.
Gessner summed up the most important takeaways for physicians: “Several medical societies and international expert panels currently advise against the widespread use of microbiome tests in routine diagnostics. Besides the lack of standardization, again demonstrated in the current study, the reason is that concrete treatment recommendations based on microbiome findings are often not yet possible.”
Accordingly, a recent international consensus paper emphasizes that the evidence for widespread routine use of microbiome tests is currently insufficient.