Microbiome testing: What is it, how does it work, and is it regulated?

Last Updated : 31 July 2025

Key takeaways:

• The human gut is home to trillions of microbes, the so called human gut microbiota. Together with the substances they produce, they make up what’s called the human gut microbiome.
• Microbiome testing kits can provide insights into the gut microbiota; however, research shows they lead to inconsistent results.
• The science behind microbiome-based dietary recommendations is still developing, so caution is needed regarding personalised advice.
• Data privacy policies often varies between companies, and microbiome data may not be adequately protected under current regulations.
• Consumers should be mindful of marketing claims and potential conflicts of interest in microbiome testing services.
• Microbiome testing kits should not be relied upon for medical decisions without medical supervision. Currently, these tests are best used for general curiosity rather than definitive health assessments.

The gut microbiome has become a hot topic in health and wellness, with increasing evidence linking gut bacteria to digestion, immunity, mental health, and even chronic diseases. This growing awareness has led to a surge in microbiome testing kits, marketed directly to consumers as tools for understanding gut health and making personalised dietary and lifestyle choices.

But how reliable are these tests? Can they really tell you what to eat or predict health outcomes? And what should you know about privacy concerns, ethical issues, and regulatory challenges? This article breaks down the science behind microbiome testing, answering key questions to manage consumer expectations.

What is microbiome testing?

Your gut is home to trillions of bacteria and other microorganisms. These microbes are crucial for human health, having well-established links with digestion, immune function, mental health, and weight management. This collection of microbes is known as the “human gut microbiome.”¹ Changes in the microbiome may be linked to health conditions such as obesity, allergies, digestive disorders, cognitive issues, and cancer.²

Microbiome testing kits have become popular as people look for ways to understand and improve their gut microbiome. These tests claim to analyse the bacteria in our gut and provide personalised insights, often including dietary and lifestyle recommendations. For healthcare professionals, analysing the microbiome has also the potential to improve diagnoses, predict the risk of disease, and understand treatment responses.³

But how reliable are the tests currently available to the general public (without medical prescription)? And what should you know before buying one?

Fig. 1 – Human genetic testing vs. microbiome testing

How does microbiome testing work?

Microbiome testing kits are sold in two main ways: directly by companies or through medical labs. Most at-home microbiome testing kits involve collecting a stool sample and sending it to a lab for analysis. The lab extracts and sequences the microbial DNA in the sample and identifies different bacterial groups and in what proportions they’re present. The company then generates a report detailing your gut microbiome’s composition and, in some cases, suggests personalised dietary and lifestyle recommendations. However, interpreting these results is more complicated than it may seem because the gut microbiome changes daily and over time with age, diet, health status and environmental factors.

Fig. 2 – The microbiome testing process

Who does microbiome testing?

Microbiome testing has gained attention for a variety of reasons. Over the past decade, healthcare professionals and researchers have explored the microbiome using advanced, cutting-edge techniques, often as part of broader studies on the gut microbiome and its link to health and disease. This growing body of research has been leveraged by industry players to develop commercial testing kits, now marketed to health-conscious consumers seeking personalized insights and lifestyle guidance. As such, individuals should approach microbiome testing with a clear understanding of its current limitations and the rapid evolving state of the science.

Are microbiome testing kits worth it? Do they work?

A study comparing six different microbiome testing kits available on the European market (without medical prescription), including five from European companies and one from the United States, revealed significant inconsistencies in results. To mimic a real consumer experience, the researchers sent a unique stool sample from a healthy adult to each company and compared the results. A panel of 21 experts, including scientists, healthcare experts, and industry specialists, reviewed the reports to assess their accuracy and usefulness.⁶

Significant issues with the reliability of 6 microbiome testing kits included in non-exhaustive benchmarking analysis were revealed:

1. Different kits provided conflicting conclusions about the same sample’s microbial diversity: some companies labelled the sample’s bacterial diversity as “excellent,” while others rated it as “average” or even “unfavourable.”
2. The proportions of bacterial groups varied between reports: some reports labelled the proportion of a certain bacterial strain as “high,” while others called them “low.”
3. Because microbiome testing is not a standardised process, results can vary significantly across different tests: microbiome testing kits differ widely in their design, analytical methods, and interpretation of results. This leads to contradictory findings and makes it difficult to compare outcomes across tests.

These discrepancies highlight the challenges in making meaningful conclusions from microbiome testing kits. There is currently no industry-wide standard for microbiome testing, leading to inconsistent results.

How accurate is microbiome testing?

Many microbiome testing companies use terms like “bacterial diversity,” “dysbiosis index,” or “gut health index” in their reports – but often without clearly defining what these mean or how they’re calculated. This lack of transparency makes it difficult to understand whether our microbiome is actually diverse or whether certain bacteria levels are truly “optimal” or “unfavourable.”⁶

Experts stress the need for greater clarity in how these tests are conducted. While companies simplify reports to make them easier to understand, they should also provide links to more detailed scientific explanations. This would not only help healthcare professionals evaluate the strengths and limitations of the results but also give consumers better insights into their own gut microbiome.⁶

Another concern is the dietary advice included in many microbiome test reports. Companies often claim that their recommendations are personalised based on microbiome composition. However, experts question the scientific reliability of these suggestions. Some recommendations are too generic – such as “eat more vegetables” – advice that applies to everyone, regardless of their microbiome profile. Even more confusing, some reports contain conflicting recommendations. For example, one test advised avoiding garlic due to certain bacteria in their gut, only to later recommend eating more garlic because of the presence of another bacteria.⁶

What should you keep in mind when receiving your microbiome test results?

While microbiome testing can be a fascinating tool, it’s important to approach the results with a critical mindset. Here are key points to keep in mind:

1. Commercial tests available to consumers, without the supervision of a healthcare professional, should not be used to diagnose or predict disease: some reports suggest links between microbiome composition and health risks, but these are often based on correlations – not proof that certain bacteria cause or prevent disease. While certain bacteria may be more common in people with specific health conditions, this doesn’t mean they directly contribute to illness. Without proper context, these associations can be misleading and create unnecessary anxiety. If a test suggests that your gut bacteria make you prone to a certain disease, take that information with caution and consult a healthcare professional before making any health decisions.
2. Look for transparency and scientific backing: companies should clearly explain how they analyse microbiome data and provide references to peer-reviewed research. If a report lacks scientific evidence or uses vague terms such as “gut health index” without further specification, it may not be as reliable as it seems.
3. Be sceptical of dietary recommendations: while some tests claim to offer personalised nutrition advice, recommendations should be taken with caution and consulted with a healthcare professional.
4. Avoid over-interpreting your results: the gut microbiome is complex and constantly changing. A single test provides only a snapshot in time and may not reflect long-term health status and risk factors.

How is microbiome testing regulated in the EU?

Microbiome testing falls into a regulatory grey area. Many at-home microbiome tests don’t follow regulatory standards and results are often sent directly to consumers without the need for a medical prescription. Only one test reviewed carried a CE (Conformité Européenne) marking, which shows a product meets EU safety and quality standards — but even that was under older rules, with none meeting the newer, stricter requirements yet.⁶

What privacy concerns should consumers be aware of surrounding microbiome testing?

When it comes to microbiome testing, it’s not always clear how companies handle consumer data. Here are key questions to keep in mind:

• Who has access to my data? Microbiome testing companies collect and store sensitive biological data, like age or health status, but not all are transparent about how this data is used, stored, or shared.
• Is my microbiome data protected under privacy laws? Unlike genetic data, microbiome data is in a grey area when it comes to regulations like General Data Protection Regulation (GDPR), making it unclear how well it is safeguarded.
• Can I control how my data is used? Before using a microbiome testing kit, check the company’s privacy policy to understand where your data is stored, whether it’s shared with third parties, and if you can request to remove any human genetic data before analysing microbiomes. To build trust, consumers should be able to easily find companies’ privacy policies — both online and in the testing kits.

What are the ethical issues surrounding microbiome testing?

Knowing more about the microbiome can easily be perceived as a way to empower individuals by encouraging informed self-care.⁴ However, it also raises several ethical issues that require careful consideration:

1. Impact of health information: microbiome characteristics given by these tests cannot be associated with the risk of developing diseases. Without sufficient evidence and guidance from healthcare professionals, such associations can lead to unwarranted anxiety or inappropriate lifestyle changes.
2. Data privacy: experts warn that microbiome data, like personal health data, needs protection to prevent misuse and safeguard consumer privacy.
3. Ethics in data collection: while collecting consumer data for test interpretation raises ethical concerns and despite the above-mentioned limitations of commercially available microbiome testing kits, experts say that if it’s fully anonymised and follows privacy rules, data collected through these can help advance research and ultimately improve clinical practice.
4. Repeated testing recommendations: some companies suggest repeating microbiome tests regularly, however it should be noted the test results are likely to be unreliable over time due to a lack of standardisation.
5. Cost and accessibility: despite paying high prices for testing kits, consumers often don’t get access to their own microbiome data, raising questions about who really owns it.
6. Product recommendations: after sending out microbiome test results, some companies recommend buying food supplements. But without enough knowledge, it’s hard to know if these products are really necessary or just clever marketing.

Conclusion

Gut microbiome testing has great potential for healthcare, but several challenges remain. These include a lack of clear rules and standards, and confusion between commercial tests meant for consumers and clinically supervised alternatives. Other issues include unreliable results, inconsistent practices, and a lack of training for healthcare professionals to understand the data. Developing validated tools and quality checks can help make tests more reliable; benefiting consumers, companies, and research, and making it easier to use microbiome data in the future.

One step in this direction is the development of in vitro diagnostic tests. These are tests that go through rigorous checks to ensure they produce accurate, reliable results that can guide medical decisions.
Some European researchers and companies are already working on developing and validating such tools for microbiome testing. These developments are done in close collaboration with clinicians, in specific clinical conditions or indications. This shift would not only build confidence among healthcare providers and patients but also help integrate microbiome science into routine medical decision-making.

This article was developed in collaboration with the Human Microbiome Action project. This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 964590.