Tech, testing and trends behind the skin microbiome

In recent years, the focus on the skin microbiome has intensified as consumers and companies alike are realising the opportunity for its application across industries – from beauty to medical, and everything in between. To get to this stage, there have been decades of intense research and development to make this all possible.

Recently we were joined by Tom van den Bogert, Project Manager Metagenomics, at BaseClear, a microbial genomic and DNA laboratory. We picked his brains on the role of the microbiota testing to understand the current landscape, where the future lies and what this means for consumers.

In the first part of the interview, we focused on the technical elements. Exploring the current landscape, technical developments and challenges for the industry. Stay tuned for his perspective on what this means for consumers and the personal care industry in part two – read it here.  

So firstly, at the heart of expanding our knowledge around the microbiome is microbial testing. Can you explain this to us? What is the current state of the technology? What are the limitations?

The current testing is primarily split between two different methods. The first, which tends to be widely used within the industry, is the 16S rRNA gene based approach that enables identification of different bacteria using a single gene –  as the 16S rRNA gene varies between bacteria we are able to identify them.

This is the most used method for skin samples as, when using this technology, the first step is to amplify the gene which enables us to work with very small amounts of the sample – skin samples do not have many microbes so we are always dealing with extremely low quantities of bacteria and thus DNA.

Another method is using metagenomics. In this method, we extract DNA but, instead of focusing on a single gene, the focus is on determining all of the genes from the different bacteria. The difficulty here is that for metagenomics you need more DNA – a lot more than the 16S rRNA gene based approach.

This approach has a lot of potential for skin sampling and research as by extracting the full array of genes from the bacteria on the skin, the metagenomics allows us not only to see ‘who is there’, but also what their potential function is. This is important as while bacteria on the skin may currently be called the same, the research and testing may show they are in fact capable of influencing the skin in different ways, on different people.

This method is much more multi-dimensional than a 16S rRNA gene based approach. It unlocks a lot of potential for beauty and personal care treatments and creams and how this influences our skin for specific conditions or outcomes.

When talking specifically about skin care, what are the biggest challenges?

One of the main challenges of skin sampling is the low quantity of bacteria, or microbes, on the skin. With such small samples, ensuring unbiased analysis is a challenge. We need to find technologies that can analyse much smaller samples and develop testing methods to understand how products change the microbiota on the skin.

Determining this is a big challenge for the skin care industry. What works for one individual, may not work as well for another. This also opens up a potential for a huge market for personalised products – whether for the skin, or more broadly for health and wellbeing.

While the lessons we can learn using a 16S rRNA gene based approach are becoming more clear and can be used for consumer analyses, the data obtained from metagenomics is far more vast.

For research purposes, metagenomics is a great tool to gain much more information, but translating this to lessons or recommendations for the individual as a user of a certain product, requires, in my opinion, dedicated experts that guide consumers through the data or at least generate visualisations that present the data in understandable manner. There are several companies doing this well, but generally we are not quite there.

With the current methods, will consumers soon have access to this testing?

Yes – this is already being done in the labs and by certain companies such as MyMicroZoo in the EU and ubiome in USA that offer gut microbiota analysis – there is a lot of interest in this.

However, the questions around what this actually means for people, which we receive often, are completely justified – this crosses an interesting threshold. For science, there are clear answers to these questions, however for consumer health and wellbeing these answers are more uncertain.

Health, and how this is defined, may vary from person to person so without specific guidance, over-interpretation of the data may occur and raise more concerns or questions than answers. Simple visualisations are crucial to inform the consumers and facilitate consumer education.


Considering the amount of variables that impact the microbiome, analysing the data coherently and consistently must be a challenge?

Yes, the microbiome itself is a community or a network, but influenced by environmental variables, including our diet, physical activity, or the skincare products we use, to name just a few. Accurate predictions on how the microbiota and we as their carrier are influenced by these environmental factors is very interesting, but challenging.

That said, with every piece of research or test, we learn something new and in the end this helps to move towards models that help understand and predict the complex interactions between us as the carrier, the microbiota, and our environment.

“The deeper we dive, the more information we get and the aim is to understand the mechanisms of how the bacteria interact with the host. This is truly where the future lies. “

Is there a difference between the testing of the gut and skin microbiome?

There is. The gut microbiome is more diverse and more abundant compared to the skin – skin samples are much smaller. Also, with the skin there is a desire to further the depth and resolution of sampling, so we are aiming for analysis at the species and preferably strain level.

In the gut research, we found that strains of bacteria can have different functions. This is a real area of opportunity and learning for skin research.

So essentially, not only is skin sampling harder due to the comparative lack of bacteria on the skin, we are also wanting more and more information from limited samples to provide learnings from the role and impact of the bacterial strains.

We are continually pushing this further. From a scientific perspective, we always want more! The deeper we dive, the more information we get and the aim is to understand the mechanisms of how the bacteria interact with the host. This is truly where the future lies.


The skin microbiome is marked as one of the biggest trends in personal care. Do you see this trend as well?

Yes, we do see the huge attention on skin at the moment. When it comes to skin research, we are involved in research ranging from determining the effect of live bacteria or bioactives from microbes as cosmetic ingredients, to complete clinical trials to evaluate the effectiveness of medicines on skin ailments where the microbiota may play an important role. There is so much potential here, but we do need to keep in mind what is possible, and what is not.

This is a discussion I have quite often with other researchers: what can we deduce from our research? It is very important to consider this and ensure there are no false or misleading conclusions.

On a scientific level, we are constantly trying to improve the approaches. Different technologies and small adjustments can potentially change the outcome of the analysis. Keeping this in mind is crucial when there is such an interest in the microbiome and high-quality research takes time.

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