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Microbiome dynamics of human epidermis following skin barrier disruption

Patrick LJM Zeeuwen12, Jos Boekhorst134, Ellen H van den Bogaard12, Heleen D de Koning12, Peter MC van de Kerkhof2, Delphine M Saulnier4, Iris I van Swam4, Sacha AFT van Hijum134, Michiel Kleerebezem45, Joost Schalkwijk12* and Harro M Timmerman4*

Author Affiliations

1 Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen Medical Centre, PO BOX 9101, 6500 HB Nijmegen, The Netherlands

2 Nijmegen Institute for Infection, Inflammation and Immunity (N4i), Radboud University Nijmegen Medical Centre, PO BOX 9101, 6500 HB Nijmegen, The Netherlands

3 Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen Medical Centre, PO BOX 9101, 6500 HB Nijmegen, The Netherlands

4 NIZO Food Research B.V., Kernhemseweg 2, 6718 ZB, Ede, The Netherlands

5 Wageningen University, Host-Microbe Interactomics Group, De Elst 1, 6708 WD, Wageningen, The Netherlands

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Genome Biology 2012, 13:R101  doi:10.1186/gb-2012-13-11-r101

Published: 15 November 2012



Recent advances in sequencing technologies have enabled metagenomic analyses of many human body sites. Several studies have catalogued the composition of bacterial communities of the surface of human skin, mostly under static conditions in healthy volunteers. Skin injury will disturb the cutaneous homeostasis of the host tissue and its commensal microbiota, but the dynamics of this process have not been studied before. Here we analyzed the microbiota of the surface layer and the deeper layers of the stratum corneum of normal skin, and we investigated the dynamics of recolonization of skin microbiota following skin barrier disruption by tape stripping as a model of superficial injury.


We observed gender differences in microbiota composition and showed that bacteria are not uniformly distributed in the stratum corneum. Phylogenetic distance analysis was employed to follow microbiota development during recolonization of injured skin. Surprisingly, the developing neo-microbiome at day 14 was more similar to that of the deeper stratum corneum layers than to the initial surface microbiome. In addition, we also observed variation in the host response towards superficial injury as assessed by the induction of antimicrobial protein expression in epidermal keratinocytes.


We suggest that the microbiome of the deeper layers, rather than that of the superficial skin layer, may be regarded as the host indigenous microbiome. Characterization of the skin microbiome under dynamic conditions, and the ensuing response of the microbial community and host tissue, will shed further light on the complex interaction between resident bacteria and epidermis.