International consensus on microbiome testing in clinical practice

At-home intestine microbiome checks are gaining recognition to personalize food regimen and microbiome-directed remedies based mostly on which microbes dwell within the intestine, fend off illness, and monitor the efficacy of interventions that modulate the microbiome. Nonetheless, the direct utility of microbiome checks to diagnose or handle well being situations is hindered by the unknowns within the microbiome (e.g., the ), the absence of matched well being ranges for microbiome composition and features, the inadequate laws and frameworks for shifting microbiome analysis from bench to bedside, and restricted expertise of most healthcare professionals to use microbiome advances.

A brand new worldwide consensus published in The Lancet Gastroenterology & Hepatology recommends find out how to standardize the framework for growing and utilizing microbiome testing in scientific observe.

The skilled panel concerned a multidisciplinary group of 69 clinicians, microbiologists, microbial ecologists, and computational biologists with experience within the microbiome from 18 nations. A Delphi course of was used to attain consensus on 5 key points on microbiome checks.

First, relating to normal rules and minimal necessities, the consensus highlights that laboratories that commercialize microbiome checks ought to adhere to high-quality requirements. It’s also important that people from totally different disciplines with experience in intestine microbiome are concerned. At each stage, from check prescription to interpretation of outcomes, clients should concentrate on the at the moment restricted proof for this testing. When modifications in affected person therapy based mostly on the testing are made, they need to be supervised by the referring well being skilled.

Second, the prescription for a microbiome check needs to be made by a licensed healthcare supplier (e.g., physicians, pharmacists, and dietitians), however no private trainers, coaches, homeopaths, osteopaths, nutritionists, dietary therapists, or food regimen consultants. Self-prescription by sufferers is discouraged, and no suspension of therapy or change within the standard food regimen earlier than testing is really helpful. Scientific metadata needs to be collected to supply context to the microbiome check outcomes and to manage for variables that will affect intestine microbiome traits, together with private affected person options (e.g., age, gender, physique mass index, and intestine transit time) and present and previous medicines and illnesses or medical situations. Earlier than testing, the brand new consensus acknowledged the significance of a stool assortment package with genome preservative, testing inside a really helpful time-frame, and storage of fecal samples at -80ºC within the laboratory. The microbiome evaluation from samples totally different than feces ought to adhere to out there scientific proof and requirements.

Third, intestine microbiome profiling ought to use amplicon (e.g., 16S rRNA) or whole-genome sequencing. Whereas typical microbial cultures or polymerase chain reactions could assist determine particular pathogens, they aren’t really helpful for microbiome evaluation and can’t be used as a proxy for microbiome testing. When profiling the microbial group, microbiome checks ought to incorporate ecological measures (i.e., alpha and beta range measures) and full taxonomic profiling, in contrast with a matched management group.

Fourth, the report of the microbiome check ought to embody the affected person’s medical historical past and the check protocol, together with stool assortment, DNA extraction, and post-sequencing analyses. Taxa and clusters related to human well being should be constantly reported alongside alpha and beta range measures with the deepest potential taxonomic decision. On the similar time, specific dysbiosis indices (e.g., Firmicutes/Bacteroidetes ratio) and composition on the phylum stage needs to be excluded in microbiome testing stories as they don’t seize the variation within the intestine microbiome throughout the similar host and between hosts and there may be insufficient evidence to ascertain a causal relationship between particular dysbiosis indices and host well being.

Fifth, a standard definition of dysbiosis just isn’t out there at this level. Importantly, post-testing therapeutic recommendation by the testing supplier is strongly discouraged; this job is the duty of the referring healthcare supplier who requested the testing. The latter additionally displays the panel’s opinion that buyers’ or sufferers’ direct requests for microbiome testing needs to be discouraged. This can keep away from testing with out clear indication or consciousness of limitations.

Concerning the relevance of microbiome testing in scientific observe, the consensus states that there’s inadequate proof to suggest the routine use of microbiome testing broadly. Whereas microbiome knowledge is likely to be useful within the administration of a number of issues, devoted research are wanted to advance the sector.

Regardless of the mentioned execs and cons of microbiome testing, a recent perspective article of commercialized microbiome testing kits from Europe and USA firms highlights that there’s a house for using microbiome checks for wholesome people (not sufferers) to fulfill their curiosity about how their fecal microbiome seems to be like in a given time level. This evaluation could also be accompanied with normal dietary or life-style suggestions directed to the buyer with out the help of a healthcare skilled. In distinction to microbiome testing kits supposed for scientific use and diagnostic, this utility has much less stringent regulatory wants, don’t have to reveal a particular scientific profit and can’t embody medical claims within the closing report, which needs to be despatched to a microbiome-specialized well being skilled for interpretation.

To sum up, microbiome checks are more and more out there because of the diminished prices of microbiome sequencing and the evident position performed by the intestine microbiome in well being and illness. Earlier than microbiome checks turn into built-in into scientific observe, microbiome science should shift from descriptive to mechanistic approaches involving host physiology options and control for confounders that hinder the causal reference to human illnesses. Present challenges that microbiome analysis faces embody methodological variability, incomplete understanding of which microbiome gamers are concerned in well being and illness, and the big inter-individual variability within the intestine microbiome that hinders personalizing pharmacological and non-pharmacological interventions based mostly on the outcomes of a microbiome check.

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.