Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges

Abstract

Background: In recent years, human microbiome research has flourished and has drawn attention from both healthcare professionals and general consumers as the human microbiome is now recognized as having a significant influence on human health. This has led to the emergence of companies offering microbiome testing services. Some of these services are sold directly to the consumer via companies' websites or via medical laboratory websites.

Methodology: In order to provide an overview of the consumer experience proposed by these microbiome testing services, one single faecal sample was sent to six different companies (five based in Europe and one based in the USA). Two out of the six testing kits were commercialized by medical laboratories, but without any requirement for a medical prescription. The analyses and reports received were discussed with a panel of experts (21 experts from 8 countries) during an online workshop.

Results: This workshop led to the identification of several limitations and challenges related to these kits, including over-promising messages from the companies, a lack of transparency in the methodology used for the analysis and a lack of reliability of the results. The experts considered the interpretations and recommendations provided in the different reports to be premature due to the lack of robust scientific evidence and the analyses associated with the reports to be of limited clinical utility. The experts also discussed the grey areas surrounding the regulatory status of these test kits, including their positioning in the European market. The experts recommended a distinction between regulatory requirements based on the intended use or purpose of the kit: on the one hand, test kits developed to satisfy consumer curiosity, with a clear mention of this objective, and no mention of any disease or risk of disease, and on the other hand, in vitro diagnostic (IVD) CE-marked test kits, which could go deeper into the analysis and interpretation of samples, as such a report would be intended for trained healthcare professionals.

Conclusions: Recommendations or actions, specific to the context of use of microbiome testing kits, are listed to improve the quality and the robustness of these test kits to meet expectations of end users (consumers, patients and healthcare professionals). The need for standardization, robust scientific evidence, qualification of microbiome-based biomarkers and a clear regulatory status in Europe are the main issues that will require attention in the near future to align laboratory development with societal needs and thus foster translation into daily health practice.

Keywords: Direct-to-consumer tests; In vitro diagnostic; Microbiome testing; Regulatory status.

Fig. 1

Two different regulatory statuses, depending on the intended use, need to be proposed for the microbiome testing placed on the European market. In terms of intended use, two different microbiome testing kits can be proposed, but currently, the distinction between these two different purposes is still unclear and undefined. In conclusion of a multistakeholder workshop, two different frameworks to separate the microbiome testing kits intended for consumer curiosity only and the microbiome testing kits intended for clinical use and diagnostic were proposed. Microbiome testing kits, designed to satisfy consumer curiosity, can be purchased over the counter (as is currently the case) and are being proposed to the general population. The sample to be analysed is collected at home and sent directly to the company offering the analysis. Based on the results and analysis, general recommendations (dietary or lifestyle recommendations) can be made directly to the consumer, without the assistance of a healthcare professional. However, no health claims or health recommendations can be made in the report. On the other hand, microbiome testing kits intended for clinical use should be regulated as in vitro diagnostic medical devices that comply with the currently applicable regulation on the medical devices (Regulation (EU) 2017/746 of the European Parliament and of the Council of 5 April 2017 on in vitro diagnostic medical devices and repealing Directive 98/79/EC and Commission Decision 2010/227/EU). These devices are intended for a diagnostic purpose and should therefore require a medical prescription. The sample can be collected at home and brought directly or sent to a medical laboratory. In this context, medical claims can be included in the report, which should be sent to a doctor or health professional