Molecular cartography of the human skin surface in 3D

Molecular cartography of the human skin surface in 3D

Amina Bouslimani, Carla Porto, Christopher M. Rath, Mingxun Wang, Yurong Guo, Antonio Gonzalez, Donna Berg-Lyon, Gail Ackermann, Gitte Julie Moeller Christensen, Teruaki Nakatsuji, Lingjuan Zhang, Andrew W. Borkowski, Michael J. Meehan, Kathleen Dorrestein, Richard L. Gallo, Nuno Bandeira, Rob Knight, Theodore Alexandrov, and Pieter C. Dorrestein

Edited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved March 6, 2015 (received for review December 30, 2014)

PNAS 2015 112 (17) E2120-E2129; published ahead of print March 30, 2015, doi:10.1073/pnas.1424409112

ABSTRACT: http://www.pnas.org/content/112/17/E2120

The research process described in this article represents a good example of the use of interdisciplinary tools to generate a map of molecular and bacterial distributions on human skin:  mass spectrometry, an analytical chemistry tool, polymerase chain reaction and RNA-based sequencing, a biochemical tool, MATLAB and other computational modelling tools were used to analyze and visualize the results.

In this paper, the authors present the result of a comprehensive study of the stratum corneum part of the skin to create a 3D molecular topographical map along with the microbial community composition of the human skin surface.  While previous mass spectrometry analysis have been done on limited areas of the skin, this is the first one that collected data correlating the microbial community with the chemical make-up on the surface (microbiome – chemistry associations).

The Materials and Methods section can be found in the supporting information (14 pages).

RESULTS AND DISCUSSION

General workflow for construction of high-spatial resolution 3D models:

The skin surface of two volunteers, Person 1, a male, and Person 2, a female, was sampled twice at ~400 sites using cotton and soft foam swabs.  Both subjects were asked to refrain from showering and using skin and beauty products 3 days before the swabs to maximize the probability of detecting microbially produced chemicals.

These swabs were analyzed using mass spectrometry and 16S rRNA amplicon analysis (an amplicon is a piece of DNA or RNA that is the source and/or product of natural or artificial amplification or replication events).  Different types of mass spectrometers were used to resolve different size molecules and to aid in identification (LCMS, MALDI-TOF (larger molecules), UPLC – QTOF and tandem MS (smaller molecules)).  PCR and16s rRNA-based sequencing were used to identify bacterial populations.  3D topographical map to visualize distribution of metabolites, peptides, and bacteria was created using UPLC-QTOF and MALDI-TOF along with 16S rRNA amplicon analysis. MATLAB was then used to map the molecular and bacterial inventories onto the 3D topographical computer models of people. Other finer details of the worklow are given in the article and in the supporting information pages which contain the Material and Methods section.

LCMS/MS was used to analyze chemical products that both persons used, raw materials in these chemical products, and commercially available chemical standards and the 34 bacteria and fungi known to inhabit human skin to determine the origin of the molecules and assign these molecular features to human, microbial, and environmental component of the human skin.  LCMS/MS was also used to analyze cultured human skin cells and human tissue collected from neck, back, and scalp.

More than 80% if the MS/MS spectra remain uncharacterized.  The authors attribute these to secreted dietary molecules not found in the reference database, modified molecules due to exposure to air, light, or enzymes not observed in culture, beauty products used in the past and not used in the analysis, metabolites from bacteria-human skin interaction not present in cultured cells, and other environmental contributions as yet unknown.

Some specific molecules characterized in the paper are (compounds are grouped according to the similar MS/MS spectra):

·         Phosphatidylcholine and phosphatidylserine were found in the skin swabs, cultured keratinocytes, and two types of fungi.

·         Sphingosine lipid molecular family were matched to human origin (basal, differentiated cultured keratinocytes and human skin tissues) but not to microbial samples.

·         Molecular families of Vitamin D3 as well as glycholic and tauracholic acids were found on human skin samples. The function of these bile acids on the skin is not known.

·         Phytophingosine matches were found on the skin but not in the beauty products or the cultured keratinocytes.

·         The fatty acids oleic and palmitic were detected on skin samples and skin bacteria cultures.

·         Tryptamine matches were found on both skin samples and from cultured staphylococcus.

·         Matches for commonly used plasticizers in clothing and other plastics like o-formylbenzoic acid, food constituents or additives such as sinapinic acid, and oxidized polyethylene were found on human skin.

·         Other compounds found in shampoos and cosmetic formulations highlighted include lauryl ether sulfate, cocoamidopropylbetaine, also known as lauroylamide propylbetaine, sunscreen components such as avobenzone and octocrylene.

·         See color-coded topographical maps showing the different chemicals detected and where they were detected on the skin.

Despite the 3-day moratorium on showering and using chemical skin products imposed on the subjects, the dominant molecular families were matched to hygiene and beauty products. The data demonstrate that the human skin is not just made up of molecules derived from human or bacterial cells. The external environment, such as polymeric materials in plastics, as found in clothing, diet, hygiene, and beauty products, contributes significantly to the skin’s chemical composition. These molecular signatures of behavioral regimens remain visible on the skin and may affect our skin microbial communities; they can now be detected and correlated with the local microbial community.

Microbial detection and identification were done using phylogenetic analysis of bacterial and archeal ribosomal 16S rRNA amplicon sequence.  Some noted results:

·         850 microbial operational taxonomic units identified at the 97% level

·         Findings about the most common microbial taxa observed (from the phyla Actinobacteria, Firmicutes,

·         Proteobacteria, Cyanobacteria, and Bacteroidetes) conform to findings from the Human Microbiome Project.

Test results for each subject did not find any correlation between molecular diversity and bacterial diversity suggesting that most of the molecules found are not from the microbial population.  This agrees with their findings that most of the molecules found by LC-MS were associated with beauty and hygiene products.

The researchers also conducted a search of a spatial correlation between molecular and bacterial distribution. Some noted specially colocalized molecular families and microbial populations were:

·         The distribution of propionibacterium correlated with the distribution of 491 molecular features, about 73% have retention times (300 - 500 seconds consistent with hydrophobic lipids) matching that of lipid families.  Interestingly, these molecules were not detected in natural products of cultured propionibacteria.

·         Components of acyl glycerols found in human cell membranes (oleic acid, palmitic acid, monoolein, monopalmitin) were found in large amounts in head, face, hands, chest, and back.

o   Both of these observations, according to the authors, “highlight molecular interrelations among the microbiota, human skin, and environment and reveal molecular microenvironments on the epidermis”.  To further investigate this correlation, the researchers analyzed the metabolic products of cultured propionibacterium acnes and found hydrolysis products such as oleic acid and even an oxidized form of oleic acid with similar molecular mass to that detected on the skin.  These results strongly support the “hypothesis that skin microbiota, especially Propionibacterium, not only contribute molecules to the chemical composition of the SC but also alter the chemical environment on which they live. It is anticipated that not just human skin cell molecules but also molecules produced by other microbes and from environmental origin, including diet, are altered as well.”

·         Microbial populations in the groin area were found to be co-localized with human neutrophil peptides (associated with inflammations).

·         1800 unique molecular features were found in the female groin area co-localized with a group of microbes, heme and lysophosphatidylcholine (associated with inflammation) are examples.

“As more skin chemical maps become available in the future, they will help to gain insight into the diversity of chemistries of the skin surface and their relationship to the colocalization of microbial communities, especially how the chemistry changes over time upon environmental changes or changes of skin health such as influence of infectious agents, medications, environmental exposure, dietary, or even changes in climate. These observations demonstrate the exciting potential for human molecular topographical maps to discover relationships between these markers and specific bacterial communities.”