A de-brief from the Microbiome Safety Workshop 2024

Posted on May 17, 2024   by Dr Elizabeth Darby

Dr Elizabeth Darby reports on the Microbiome Safety Workshop held on 24-25 January at the Microbiology Society office. 


In January, the Microbiology Society hosted a Microbiome Safety workshop co-chaired by Prof. Lindsay Hall (University of Birmingham) and Dr Aline Metris (Unilever). With the increased interest and the production of products that “target the microbiome”, this workshop combined the expertise of academics, industry, entrepreneurs, and regulators to discuss how microbiome-modulating products can be assessed for their safety in the future.

As this was the first meeting, it focused on the gut, skin, and oral microbiome because these are often targeted for intervention.

The known unknowns

It became apparent during discussions at the meeting that it is challenging to define safety around the microbiome when there are still many unknowns within the field. For example, we know that everyone’s microbiomes are different. So it is challenging to define a healthy, or normal, microbiome and one that has been negatively impacted. Furthermore, the human body is home to multiple microbiomes (e.g., skin, oral, gut) and what is safe in the context of one microbiome may not be safe for another. 

Why do we need to measure safety?

Interest in the microbiome has been steadily increasing, both from a medical perspective and across the public. It is important now, more than ever, that there is trust in the scientific community. The best way to ensure that, is to have clear messages about what we do and do not know about the microbiome.

If you go into your local supermarket, you will invariably find products marketed at your skin, oral, or gut microbiome. But we don’t know what the long-term effects, if any, are of using these products. Microbiome-modulating medicines, food products and cosmetics must be both safe and fulfil any claims made. The regulation of microbiome-modulating products also differs depending on their status. Medicines are regulated very differently from food supplements, for example. This makes assessing safety challenging as there isn’t one single workflow for all products.

It is important that we can define and assess the safety of these products, though. In the case of probiotic products, for example, they may be given to vulnerable groups. To check safety, it is useful to evaluate and measure short- and long-term risks in both healthy and vulnerable groups and be able to validate the methods used.

At the workshop, many tools were suggested to help assess safety, such as in vitro cell culture, organoids, metagenomic sequencing, AI, and machine learning. It was generally agreed that in vivo animal models provided limited useful data when measuring microbiome changes, and other experiments, such as organoids derived from human stem cells may be more relevant.

It’s all about the host

When thinking about microbiome perturbations, it is natural for microbiologists to focus on differential abundances of species, or taxa, compared to before intervention. But given that there is no “one-size fits all” for microbiomes, it is perhaps more pertinent to measure changes in microbiome function and the impact it may have on the host. After all, microbiomes have been modulated for many years, for instance, by changes in the human diet or by introducing good oral hygiene. So, a change in microbiome composition is not necessarily bad. In fact, the disruption of dental biofilms prevents disease. Therefore, when assessing safety, a holistic approach could be useful where the host is considered, such as by measuring inflammatory markers.

Engaging with the public

Many products that modulate the microbiome will not be classed as medicines. For example, a probiotic may be licensed as food and therefore existing pharmacovigilance methods will not apply, such as reporting the side effects of medication to the Medicines and Healthcare Products Regulatory Agency (MHRA). This is where engaging with the public through citizen science could be powerful.

If there was an optional pharmacovigilance system, which included patient-reported outcomes for microbiome products, it could make tracking long-term causal effects easier. Due to the inherent biological differences between people and their microbiomes, this could be a useful way to pull apart correlations, if enough people subscribed to it.

Future goals

The workshop was a fantastic couple of days of discussion, which focused on the oral, skin, and gut microbiota. Moving forward, it would be great to hold other workshops and involve stakeholders who could represent the fungal and viral components of these communities and microbiota, including animal and environmental microbiomes. Then, as a collective, there can be defined practical guidance for scientists to accurately measure the safety of microbiome-modulating products, in a way which can be directly compared to other scientists and other microbiomes.

The workshop was co-organised by Prof. Lindsay Hall (University of Birmingham), Dr Aline Metris (Unilever), Dr Gabriela Juarez Martinez (UK-KTN), Dr Jay Tiesman (P&G) and the Microbiology Society.