Review

The human skin microbiome

  • Nature Reviews Microbiology volume 16, pages 143155 (2018)
  • doi:10.1038/nrmicro.2017.157
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Abstract

Functioning as the exterior interface of the human body with the environment, skin acts as a physical barrier to prevent the invasion of foreign pathogens while providing a home to the commensal microbiota. The harsh physical landscape of skin, particularly the desiccated, nutrient-poor, acidic environment, also contributes to the adversity that pathogens face when colonizing human skin. Despite this, the skin is colonized by a diverse microbiota. In this Review, we describe amplicon and shotgun metagenomic DNA sequencing studies that have been used to assess the taxonomic diversity of microorganisms that are associated with skin from the kingdom to the strain level. We discuss recent insights into skin microbial communities, including their composition in health and disease, the dynamics between species and interactions with the immune system, with a focus on Propionibacterium acnes, Staphylococcus epidermidis and Staphylococcus aureus.

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Acknowledgements

This work was supported by the Division of Intramural Research of the National Human Genome Research Institute and the National Institute of Allergy and Infectious Diseases.

Author information

Affiliations

  1. Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

    • Allyson L. Byrd
    •  & Julia A. Segre
  2. Department of Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.

    • Allyson L. Byrd
  3. Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

    • Allyson L. Byrd
    •  & Yasmine Belkaid
  4. Department of Cancer Immunology, Genentech, South San Francisco, California 94080, USA.

    • Allyson L. Byrd
  5. National Institute of Allergy and Infectious Diseases Microbiome Program, Department of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

    • Yasmine Belkaid

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Contributions

A.L.B., Y.B. and J.A.S. contributed to researching data for article. A.L.B., Y.B. and J.A.S. substantially contributed to the discussion of content. A.L.B. and J.A.S. wrote the article. A.L.B., Y.B. and J.A.S. reviewed and edited the manuscript before submission.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Julia A. Segre.

Glossary

Microbiota

An aggregate of microorganisms, including bacteria, archaea, protists, fungi and viruses.

Microbiome

The composition of all microbial genes in a community.

Amplicons

Segments of DNA or RNA that are targeted with primers and amplified in PCR.

Amplicon sequencing

Querying microbial constituents of a community by targeted amplification and sequencing of a conserved marker gene.

Reference genomes

Sequenced and assembled genomic content of a species with genes oriented as they appear on the chromosome.

Shotgun metagenomics sequencing

Unrestricted sequencing of all genomic material present in a clinical or an environmental sample.

Virome

The composition of all viral genes in a community.

Colonization resistance

A mechanism where commensal microorganisms prevent the colonization of harmful microorganisms.

Prebiotic

A substance, such as carbohydrate or fibre, that promotes the growth of beneficial bacteria.

Probiotic

Live microorganisms that are administered or consumed to confer a health benefit on the host.

Sebum

A mixture of lipids produced by sebaceous glands to lubricate and protect the skin.

Stratum corneum

The outermost layer of the epidermis composed of dead, mature skin cell keratinocytes.

Anoxic

A lack or absence of oxygen.

Sebaceous gland

An exocrine gland in the skin, usually attached to hair follicles, that secretes sebum.

Auxotrophic

An organism that is unable to synthesize a particular compound required for its growth.

Mycobiome

The composition of all fungal genes in a community.

Bacteriocin

An antimicrobial peptide produced by bacteria to inhibit or kill closely related or non-related bacteria.

Dysbiosis

A microbial community that is altered or impaired compared with normal.