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Microbiome. 2018 Jan 30;6(1):20. doi: 10.1186/s40168-018-0404-9.

Commensal microbiota modulate gene expression in the skin.

Author information

1
Department of Dermatology, University of Pennsylvania Perelman School of Medicine, 421 Curie Blvd, 1015 BRB II/III, Philadelphia, PA, 19104, USA.
2
Department of Dermatology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
3
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
4
Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, 10021, USA.
5
Department of Dermatology, University of Pennsylvania Perelman School of Medicine, 421 Curie Blvd, 1015 BRB II/III, Philadelphia, PA, 19104, USA. egrice@pennmedicine.upenn.edu.

Abstract

BACKGROUND:

The skin harbors complex communities of resident microorganisms, yet little is known of their physiological roles and the molecular mechanisms that mediate cutaneous host-microbe interactions. Here, we profiled skin transcriptomes of mice reared in the presence and absence of microbiota to elucidate the range of pathways and functions modulated in the skin by the microbiota.

RESULTS:

A total of 2820 genes were differentially regulated in response to microbial colonization and were enriched in gene ontology (GO) terms related to the host-immune response and epidermal differentiation. Innate immune response genes and genes involved in cytokine activity were generally upregulated in response to microbiota and included genes encoding toll-like receptors, antimicrobial peptides, the complement cascade, and genes involved in IL-1 family cytokine signaling and homing of T cells. Our results also reveal a role for the microbiota in modulating epidermal differentiation and development, with differential expression of genes in the epidermal differentiation complex (EDC). Genes with correlated co-expression patterns were enriched in binding sites for the transcription factors Klf4, AP-1, and SP-1, all implicated as regulators of epidermal differentiation. Finally, we identified transcriptional signatures of microbial regulation common to both the skin and the gastrointestinal tract.

CONCLUSIONS:

With this foundational approach, we establish a critical resource for understanding the genome-wide implications of microbially mediated gene expression in the skin and emphasize prospective ways in which the microbiome contributes to skin health and disease.

KEYWORDS:

Cutaneous transcriptome; Germ-free mice; Host-microbe interactions; RNA sequencing; Skin microbiome

PMID:
29378633
PMCID:
PMC5789709
DOI:
10.1186/s40168-018-0404-9
[Indexed for MEDLINE]
Free PMC Article

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