The gut feeling – where it all began
For years, we have known that the billions of bacteria, fungi, and other microorganisms that live within us – known collectively as the microbiome – help in myriad ways to keep our bodies healthy. On the flip side, an unbalanced microbiome can foster or even directly drive a disease state. How do commensal microbes exert their beneficial and harmful effects on the health of the host? Small molecule metabolites are one of the primary mechanisms for the interaction between microbial and host cells, as well as among the organisms within a microbial community. Naturally, at Metabolon, we are focused on discovering these mechanisms through the power of metabolomics, to help our clients understand how the microbiome functions in health and disease and how new treatments can restore balance to an unhealthy microbiome.

The gut has been the long-time hotbed of microbiome research, and with good reason: each of our intestinal tracts harbors several pounds of microbes that can affect everything from weight management to brain function and even the effectiveness of certain cancer therapies. Metabolon has been at the forefront of illuminating how small-molecule metabolites – known collectively as the metabolome – mediate these effects and how those insights can translate into new treatments for diseases that involve the gut. But what about the microbiome of other body locations, particularly our largest organ – the skin?  

The microbiome of our body’s largest organ
Like the gut, the skin is an immunological barrier where conditions ranging from acne to psoriasis and atopic dermatitis can result from either unchecked microbial infection or inappropriate immune system activation. We know from gut studies that an individual’s microbiome, as well as genetics and environmental exposure, can strongly influence his or her predisposition to these disease-prone states. Importantly, while not as numerous as those of the gut, skin-resident microbes offer a similar or even greater level of phylogenetic diversity, depending on the skin site. Finally, just like in the gut, the skin microbiome also displays immense interpersonal variation, even among healthy individuals. Therefore, merely enumerating who comprises the microbiome, i.e., the species present at a given skin site, is not enough to understand skin conditions and diseases. At Metabolon, we believe metabolomics – measuring the small-molecule signatures of the microbiome’s activity – will produce critical insights into what a healthy skin microbiome is doing and how balance can be restored to unhealthy skin.

Delving into the skin metabolome
In the past, studying the skin metabolome has required invasive techniques such as a punch biopsy. Recently, though, Metabolon has been able to obtain high-quality, highly relevant metabolomic data using commercially available skin tapes combined with a proprietary sample preparation process and our Precision Metabolomics™ platform. The result has been reproducible, authenticated identification and measurement of several hundred metabolites, at least several dozen of which have a strong microbial contribution, in addition to the hundreds of lipid analytes quantified on our pre-existing skin lipid panels. (The linked poster shows an example dataset.)

To accelerate our understanding of skin health, the challenge now is to combine these new metabolomic and lipidomic data streams with host genetics and microbial metagenomics across a range of skin conditions in diverse populations. Skin and immune conditions are immensely multifactorial, so we need to cast a wide net, in terms of both study size and what we measure in those studies. Underpowered studies, as well as those that focus on only a few well-known analytes or gene variants, represent a missed opportunity to leverage the discovery power of high-throughput ‘omics technologies, including metabolomics. On the other hand, the stage is now set for a well-designed study to crack the code of a single skin condition through smart analysis of these large datasets. This knowledge will transform our ability to correct that particular skin condition with treatments such as live microbes or their beneficial products. It will also set a scientific standard that will drive new insight into the next skin disease, and so on into the future.

To learn more about how metabolomics can help you accelerate your understanding of skin health with our Precision Metabolomics platform, contact us at

Part of this blog post was adapted from Lisa’s Speaker Interview for the upcoming Microbiome Movement Skin Health & Dermatology summit.