Using 3D Skin Maps to Study the Relationship Between Microbes, Metabolites, and the Environment

By Amina Bouslimani, PhD

Skin, the largest and most exposed organ of the human body, harbors an incredible diversity of molecules that have a number of origins. Such origins include but are not limited to human cells, microbes that live on the skin, and the surrounding external environment. Our daily routine as well as all of the soaps, creams, and moisturizers that we apply on the skin also contribute to the chemical composition of human skin. This interplay creates a unique chemical niche environment on human skin surface that results in regiospecific ecosystems. But how can we characterize all these chemicals on the skin? And, how do these molecules influence our skin microbiota at each specific body part?

In the Dorrestein lab at the University of California San Diego, we have decided to develop a mass spectrometry based approach in combination with computational tools to study the chemical composition of human skin surface. Together with the Knight lab, we have also planned to identify bacteria that are present on human skin. We have then generated human 3D maps to visualize the body distributions of all molecules and bacteria detected on the skin to finally correlate specific chemical and bacterial communities at each body site.

Two healthy volunteers, a male and a female, were recruited to validate our approach. Skin preparation included avoiding bathing, shampooing, or moisturizing for 3 days before sampling and minimizing the use of personal hygiene products. Over 400 samples per individual were collected from superficial human skin surface using swabs, which represent half of entire human body for each person. At each skin spot, 2 swabs were collected: the first one for molecular analysis by LC-MS/MS (Liquid Chromatography- tandem mass spectrometry), and the second one for bacterial analysis using 16S rRNA sequencing.

Mass spectrometry and 16S rRNA sequencing information collected from hundreds of skin swabs were mapped to a human 3D model. We have generated high resolution 3D topographical maps that capture the molecular and microbial variations across the body (1).

The video below (click link to play in new tab) reveals that many molecules have distinct chemical distributions in different regions of both subjects. In essence, they create unique chemical niches.

Human 3D model

In terms of bacterial identification, more than 800 distinct microbial operational taxonomic units (OTUs) were identified on human skin surface of these 2 volunteers. The image below shows specific body distributions of 3 main genera of bacteria present on human skin surface: Corynebacterium, Propionibacterium and Staphylococcus, highlighting here again a specific and distinct localizations on human skin of both volunteers.


To identify the chemicals detected on skin surface we have used a computational tool named “molecular networking” that enables the interpretation of large scale mass spectrometry data (2). A molecular network was constructed from mass spectrometry data of human swabs, beauty products used by volunteers, human skin cells, human skin tissues and selected skin bacteria strains cultures; to identify and determine the origin of molecules.

Many molecular classes, revealed through molecular networking, were identified on human skin surface such as antimicrobial peptides, lipids and beauty products components utilized on a daily basis by the volunteers. In total ~14% of the spectral features identified could be explained. We showed that the large portion of chemicals detected on the skin result from our hygiene and daily routine, despite the three days moratorium on bath and hygiene products application. Using spatial mapping, we can reveal the body distribution of these chemicals from our daily routine. As shown below, traces of ingredients from male’s shampoo and female’s sunscreen persist and accumulate on the skin.


If we look closely to some spatial colocalizations between skin molecules and bacteria, we can begin to predict the impact of molecules on skin bacterial communities. The image below shows a correlation between body distribution of sunscreen and Staphylococcus, suggesting that beauty products might drive skin microbial community development. Furthermore skin bacteria could change the chemistry of human skin surface. More specifically several free fatty acids that spatially colocalize with Propionibacterium, appear to be the result of lipid hydrolysis by that bacteria and this can be highlighted by the human 3D maps (1). We were also able, using the human spatial maps, to highlight the localization of molecules involved in inflammation such as human alpha defensin and spatially correlate them to a specific microbial communities (1).


3D surface spatial mapping of human skin provides insights into the chemistry of human skin surface that drive microbial community formation. The spatial maps can reveal the lifestyle of people and the chemistries of our daily routine including hygiene and beauty products that we apply on the skin, the food we eat and the clothes we wear, reflecting the skin chemical microenvironment the microbes live in. These maps lay essential foundation for further studies of the interplay between the skin, the microbes that live in and the external environmental factors, with a potential for monitoring variations of skin chemicals and microbes and their influence on human health and susceptibility to disease.



  1. Bouslimani, A.; Porto, C.; Rath, C. M.; Wang, M.; Guo, Y.; Gonzalez, A.; Berg-Lyon, D.; Ackermann, G.; Moeller Christensen, G. J.; Nakatsuji, T.; Zhang, L.; Borkowski, A. W.; Meehan, M. J.; Dorrestein, K.; Gallo, R. L.; Bandeira, N.; Knight, R.; Alexandrov, T.; Dorrestein, P. C., Molecular cartography of the human skin surface in 3D. Proc Natl Acad Sci U S A 2015, 112 (17), E2120-9.
  1. Watrous, J.; Roach, P.; Alexandrov, T.; Heath, B. S.; Yang, J. Y.; Kersten, R. D.; van der Voort, M.; Pogliano, K.; Gross, H.; Raaijmakers, J. M.; Moore, B. S.; Laskin, J.; Bandeira, N.; Dorrestein, P. C., Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci U S A 2012, 109 (26), E1743-52.


Amina Bouslimani, PhD, is Post-doc in the Dorrestein lab. My research is focused on the characterization of molecular and bacterial composition of human skin surface, using a system biology approach, including modern mass spectrometry methods and 3D modeling. Credit Theodore Alexandrov for the generation of 3D models.