Understanding Microbiome Testing Kits: What They Are and How They Are Used

Published on: Mar 25th, 2025

Microbiome testing is an advanced tool that allows individuals and healthcare professionals to analyse the complex ecosystem of microorganisms living within the human body. These tests assess the composition and/or functionality of bacteria in various microbiomes, including the gut, skin, oral, and vaginal microbiomes. The insights gained from microbiome tests can help identify imbalances, highlight potential health risks, and inform personalized health strategies.

How Microbiome Testing Kits Work

Microbiome testing kits are designed to collect and analyse biological samples to determine the microbial composition within an individual’s body. Traditionally, these tests use faecal samples to analyse gut microbiota.

Once the sample is collected and sent for analysis, the results provide valuable information about an individual’s microbiome composition and/or functionality. These insights can help tailor dietary recommendations, suggest lifestyle modifications, and guide the use of probiotics or supplements to promote overall well-being. Healthcare professionals also use microbiome testing for diagnostic purposes, assessing disease risks, and predicting treatment responses.

Microbiome Testing vs. Genetic Testing

Both microbiome and genetic testing involve analysing biological samples and play a role in personalized medicine. They can serve as companion diagnostics helping to predict treatment responses in precision medicine, thereby guiding more effective and targeted therapeutic interventions.

However, there are fundamental differences between the two:

• Source of Analysis: Genetic tests analyse an individual’s own DNA, while microbiome tests examine microorganisms residing on/in the body. Although interdependencies between a host and its microbiome are very substantial, microbiomes are generally not regarded as being part of the host himself.
• Complexity: Microbiome testing is more complex due to the vast number of microbial genes, compared to human genome. Furthermore, the microbiome’s composition is known to vary significantly between individuals introducing additional complexity.
• Influence of External Factors: Unlike genetic testing, microbiome analysis is influenced by diet, medication, lifestyle, and environmental factors, making personalized data integration essential to accurately contextualize and interpret the results.

Microbiome Testing Kits in Europe: Commercialization Routes

In Europe, microbiome testing kits are available for both consumers and patients. The distinction between the two lies in their intended use, sample collection process, and the level of detail in test reports.

• Consumer Use: Tests are used out of curiosity or for dietary and wellness purposes. Individuals typically collect their own samples, and the reports provide straightforward recommendations and interpretations.
• Patient Use: These tests are typically meant for diagnosing or detecting certain disease or a risk factor for specific conditions. They may be handled by healthcare professionals, however certain medical tests can be used by lay persons (devices for self-testing). The reports are more comprehensive and used for medical decision-making. Such testing kits for medical purposes require certification prior commercialization.

Check out this session of Ask the experts Will you be ready for the new IVD regulation? to get more information on your IVDR readiness.

Regulatory Framework in the EU

Currently, the EU lacks harmonized standards specific to microbiome testing kits. The regulatory classification depends on their intended use:

• Medical purpose: If a test has a medical purpose, i.e., to provide information concerning a physiological or pathological process or state; concerning the predisposition to a medical condition or a disease; to predict treatment response or reactions; etc., , it is classified as an in vitro diagnostic medical device (IVD) or companion diagnostics under Regulation (EU) 2017/746 (IVDR).
• Non-medical purpose: If a test is intended solely for personal interest, dietary insights, or general wellness, it does not fall under IVD regulations.

Do Microbiome Testing Kits Require CE Marking?

CE-marking requirements for microbiome testing kits depend on their intended use:

• General consumer kits: If the test is for lifestyle or dietary recommendations without medical claims, CE-marking is not required.
• Medical kits: If the kit is used for diagnostic, prognostic, or treatment-related purposes, it must obtain CE-marking under the IVDR.

In the EU, IVDs are categorized into four risk classes (A, B, C, D). Microbiome tests typically fall under at least Class B, and self-testing devices fall at least under Class C. Higher-risk classifications require regulatory approval from a Notified Body, including assessment of Quality Management Systems (QMS) and technical documentation.

In this blog post Selection of a Notified Body for Medical Device Development, we discussed in details of how to select a Notified Body.

Conclusion

Microbiome testing is revolutionizing healthcare by offering insights into the complex microbial ecosystems within the human body. Whether used for personal wellness or medical diagnostics, these tests are gaining popularity among consumers and healthcare professionals. As regulatory frameworks continue to evolve, ensuring compliance with EU regulations will be crucial for companies looking to commercialize microbiome testing kits in Europe.

With growing awareness of the microbiome’s role in health, microbiome testing is expected to play a significant role in disease prevention, treatment optimization, and personalized medicine.

Reference

Rodriguez, J., Cordaillat-Simmons, M., Badalato, N. et al. Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges. Microbiome 12, 258 (2024). https://doi.org/10.1186/s40168-024-01991-x