At-home gut microbiome tests are gaining popularity to personalize diet and microbiome-directed treatments based on which microbes live in the gut, fend off disease, and monitor the efficacy of interventions that modulate the microbiome. However, the direct application of microbiome tests to diagnose or manage health conditions is hindered by the unknowns in the microbiome (e.g., the ), the absence of matched health ranges for microbiome composition and functions, the insufficient regulations and frameworks for moving microbiome research from bench to bedside, and limited skills of most healthcare professionals to apply microbiome advances.
A new international consensus published in The Lancet Gastroenterology & Hepatology recommends how to standardize the framework for developing and using microbiome testing in clinical practice.
The expert panel involved a multidisciplinary team of 69 clinicians, microbiologists, microbial ecologists, and computational biologists with expertise in the microbiome from 18 countries. A Delphi process was used to achieve consensus on five key issues on microbiome tests.
First, regarding general principles and minimum requirements, the consensus highlights that laboratories that commercialize microbiome tests should adhere to high-quality standards. It is also essential that individuals from different disciplines with expertise in gut microbiome are involved. At every stage, from test prescription to interpretation of results, customers must be aware of the currently limited evidence for this testing. When changes in patient treatment based on the testing are made, they should be supervised by the referring health professional.
Second, the prescription for a microbiome test should be made by a licensed healthcare provider (e.g., physicians, pharmacists, and dietitians), but no personal trainers, coaches, homeopaths, osteopaths, nutritionists, nutritional therapists, or diet experts. Self-prescription by patients is discouraged, and no suspension of treatment or change in the usual diet before testing is recommended. Clinical metadata should be collected to provide context to the microbiome test results and to control for variables that may influence gut microbiome characteristics, including personal patient features (e.g., age, gender, body mass index, and gut transit time) and current and past medications and diseases or medical conditions. Before testing, the new consensus acknowledged the importance of a stool collection kit with genome preservative, testing within a recommended time frame, and storage of fecal samples at -80ºC in the laboratory. The microbiome analysis from samples different than feces should adhere to available scientific evidence and standards.
Third, gut microbiome profiling should use amplicon (e.g., 16S rRNA) or whole-genome sequencing. While conventional microbial cultures or polymerase chain reactions may help identify specific pathogens, they are not recommended for microbiome analysis and cannot be used as a proxy for microbiome testing. When profiling the microbial community, microbiome tests should incorporate ecological measures (i.e., alpha and beta diversity measures) and complete taxonomic profiling, compared with a matched control group.
Fourth, the report of the microbiome test should include the patient’s medical history and the test protocol, including stool collection, DNA extraction, and post-sequencing analyses. Taxa and clusters relevant to human health must be consistently reported alongside alpha and beta diversity measures with the deepest possible taxonomic resolution. At the same time, particular dysbiosis indices (e.g., Firmicutes/Bacteroidetes ratio) and composition at the phylum level should be excluded in microbiome testing reports as they do not capture the variation in the gut microbiome within the same host and between hosts and there is insufficient evidence to establish a causal relationship between specific dysbiosis indices and host health.
Fifth, a common definition of dysbiosis is not available at this point. Importantly, post-testing therapeutic advice by the testing provider is strongly discouraged; this task is the responsibility of the referring healthcare provider who requested the testing. The latter also reflects the panel’s opinion that consumers’ or patients’ direct requests for microbiome testing should be discouraged. This will avoid testing without clear indication or awareness of limitations.
Regarding the relevance of microbiome testing in clinical practice, the consensus states that there is insufficient evidence to recommend the routine use of microbiome testing widely. While microbiome data might be helpful in the management of several disorders, dedicated studies are needed to advance the field.
Despite the discussed pros and cons of microbiome testing, a recent perspective article of commercialized microbiome testing kits from Europe and USA companies highlights that there is a space for the use of microbiome tests for healthy individuals (not patients) to satisfy their curiosity about how their fecal microbiome looks like in a given time point. This analysis may be accompanied with general dietary or lifestyle recommendations directed to the consumer without the assistance of a healthcare professional. In contrast to microbiome testing kits intended for clinical use and diagnostic, this application has less stringent regulatory needs, do not need to demonstrate a specific clinical benefit and cannot include medical claims in the final report, which should be sent to a microbiome-specialized health professional for interpretation.
To sum up, microbiome tests are increasingly available due to the reduced costs of microbiome sequencing and the evident role played by the gut microbiome in health and disease. Before microbiome tests become integrated into clinical practice, microbiome science must shift from descriptive to mechanistic approaches involving host physiology features and control for confounders that hinder the causal connection with human diseases. Current challenges that microbiome research faces include methodological variability, incomplete understanding of which microbiome players are involved in health and disease, and the enormous inter-individual variability in the gut microbiome that hinders personalizing pharmacological and non-pharmacological interventions based on the results of a microbiome test.
References:
Porcari S, Mullush BH, Asnicar F, et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol. 2025; 10(2):154-167. doi: 10.1016/S2468-1253(24)00311-X.
Rodriguez J, Cordaillat-Simmons M, Badalato N, et al. Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges. Microbiome. 2024; 12(1):258. doi: 10.1186/s40168-024-01991-x.
Jiao N, Zhu L, Zhu R. The search for authentic microbiome-disease relationships. Nat Med. 2024; 30(5):1243-1244. doi: 10.1038/s41591-024-02920-z.
